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Molecular nature of RAPD markers from Haemophilus influenzae Rd genome.
Mori, E; Liň, P; Daly, S; Damiani, G; Perito, B; Fani, R
Despite the widespread application of the random amplified polymorphic DNA (RAPD) technique, there is no experimental evidence of the molecular mechanism of random amplification starting from a complex template. To investigate this mechanism, we cloned and sequenced 23 selected RAPD bands amplified from Haemophilus influenzae Rd genomic DNA using eight decamer primers different in GC content and/or nucleotide sequence. As the whole genome sequence of H. influenzae Rd has been reported, the exact nucleotide sequence of each primer-template annealing site was identified. Results showed that, on an average, a homology of eight base pairs was involved in priming events and that the number of nonhomologous base pairings declined exponentially from the 5' end of the primer to its 3' end. The interaction between the primer and the template DNA was stabilized by the formation of secondary structures, and a perfect match of the 3' terminal region of the primer was not necessary for successful amplification. The complexity of the annealing process suggested that, in the studied reaction conditions, many primer-template annealing sites were extended in the first cycles and that differences in the efficiency of priming and replication processes led to amplification of RAPD fragments. Moreover, the distribution of the amplified regions on the H. influenzae chromosome was analyzed. PMID:10209764
Random Amplified Polymorphic DNA (RAPD) Markers
Fevzi BARDAKCI
Due to advances in molecular biology techniques, large numbers of highly informative DNA markers have been developed for the identification of genetic polymorphism. In the last decade, the random amplified polymorphic DNA (RAPD) technique based on the polymerase chain reaction (PCR) has been one of the most commonly used molecular techniques to develop DNA markers. RAPD markers are amplification products
Comprehensive genetic discrimination of Leonurus cardiaca populations by AFLP, ISSR, RAPD and IRAP molecular markers.
Khadivi-Khub, Abdollah; Soorni, Aboozar
Leonurus cardiaca is well known for its medicinal importance. In this investigation, genotypic characterization of this species from six eco-geographical regions of Iran was evaluated by four molecular techniques (AFLP, RAPD, ISSR and IRAP). A total of 899 polymorphic fragments were detected by used molecular markers (AFLP = 356, RAPD = 325, ISSR = 113 and IRAP = 105) with an overall average polymorphism of 81.24%. Genetic variation calculated using Shannon's Information index (I) and Nei's gene diversity index (H) showed high genetic diversity in studied germplasm. Also, analysis of molecular variance showed high genetic variation among (55%) and within populations (45%). UPGMA dendrogram constructed from combined data of molecular markers distinguished studied populations in accordance with the results obtained by each marker which all individuals were clearly differentiated into two major clusters. The correlation coefficients were statistically significant for all marker systems with the highest correlation between similarity matrixes of RAPD and ISSR markers (r = 0.82). The present results have an important implication for L. cardiaca germplasm characterization, improvement, and conservation. Furthermore, the characterized individuals exhibited a great deal of molecular variation and they seem to have a rich gene pool for breeding programs. PMID:24562682
Identification of sex chromosome molecular markers using RAPDs and fluorescent in situ hybridization in rainbow trout
P. Iturra; J. F. Medrano; M. Bagley; N. Lam; N. Vergara; J. C. Marin
The goal of this work is to identify molecular markers associated with the sex chromosomes in rainbow trout to study the mode\\u000a of sex determination mechanisms in this species. Using the RAPD assay and bulked segregant analysis, two markers were identified\\u000a that generated polymorphic bands amplifying preferentially in males of the Mount Lassen and Scottish strains of rainbow trout.\\u000a Chromosomal
Patterns of inheritance with RAPD molecular markers reveal novel types of polymorphism in the honey bee
Greg J. Hunt; Robert E. Page
The polymerase chain reaction (PCR) was used to generate random amplified polymorphic DNA (RAPD) from honey bee DNA samples in order to follow the patterns of inheritance of RAPD markers in a haplodiploid insect. The genomic DNA samples from two parental bees, a haploid drone and a diploid queen, were screened for polymorphism with 68 different tennucleotide primers of random
Molecular profiling for genetic variability in Capsicum species based on ISSR and RAPD markers.
Thul, Sanjog T; Darokar, Mahendra P; Shasany, Ajit K; Khanuja, Suman P S
The taxonomic identity of Capsicum species is found to be difficult as it displays variations at morpho-chemical characters. Twenty-two accessions of six Capsicum species, namely, C. annuum, C. baccatum, C. chinense, C. eximium, C. frutescens, and C. luteum were investigated for phenotypic diversity based on flower color and for genetic differences by molecular makers. The genetic cluster analyses of 27 RAPD and eight ISSR primers, respectively, revealed genetic similarities in the ranges of 23-88% and 11-96%. Principal component analysis of the pooled RAPD and ISSR data further supports the genetic similarity and groupings. Different species showed variations in relation to corolla shade of flower. C. annuum accessions formed a single cluster in the molecular analysis as maintaining their flower characteristic. C. chinense accession shared flower features with the accessions of C. frutescens and were found to be closer at genotypic level. C. luteum was found to be rather closer to C. baccatum complex, both phenotypically and genetically. The only accession of C. eximium presenting purple flowers falls apart from the groupings. The floral characteristics and the molecular markers are found to be useful toward the delineation of the species specificity in Capsicum collection and identification of genetic stock. PMID:21861246
A genetic map of Asparagus officinalis based on integrated RFLP, RAPD and AFLP molecular markers
A. Spada; E. Caporali; G. Marziani; P. Portaluppi; F. M. Restivo; F. Tassi; A. Falavigna
An integrated genetic map of the dioecious species Asparagus officinalis L. has been constructed on the basis of RFLP, RAPD, AFLP and isoenzyme markers. The segregation analysis of the polymorphic\\u000a markers was carried out on the progeny of five different crosses between male and female doubled-haploid clones generated\\u000a by anther culture. A total of 274 markers have been organized to
Molecular markers (RAPD) associated with growth, yield and origin of the silkworm, Bombyx mori L. in India.
Chatterjee, S N; Pradeep, A R
To identify the molecular markers associated with growth and yield parameters in silkworm, Bombyx mori, RAPD profiles generated with seven UBC primers for fourteen silkworm stocks, originated from China, Japan, India and Russia, were statistically analyzed. Stepwise Multiple Regression Analysis establishes significant association of 45 markers with larval span, growth indices and four cocoon yield parameters relevant for silk production and t-test attest significance of the association of 89.5(1500 bp) and 54.13(300 bp), respectively with longer larval duration and high cocoon weight. The validity of this selection of markers was further supported with Discriminant Function Analysis (DFA) done on the basis of Mahalanobis D2 statistics. The two indices of yield/growth were also tested with DFA, which helped in identifying a few markers and thereby opened scope of using such marker (e.g. 91.11(900 bp)) for incorporating molecular markers in the breeding program for crop improvement in silkworm. PMID:14964827
Molecular identification of sex in Actinidia deliciosa var. deliciosa by RAPD markers
Poonam Shirkot; D. R. Sharma; T. Mohapatra
Actinidia deliciosa var. deliciosa a dioecious plant species has become very popular for commercial cultivation in the low and mid-Himalayan regions of India. But dioecy represents an important constraint in kiwifruit breeding programmes and also requires identification of male and female genotypes before planting an orchard. The PCR-based RAPD technique can be used to detail the genetic control of dioecy
RAPD markers linked to the Vf gene for scab resistance in apple
S. Tartarini
Scab (Venturia inaequalis) is one of the most harmful diseases of apple, significantly affecting world apple production. The identification and early selection of resistant genotypes by molecular markers would greatly improve breeding strategies. Bulked segregant analysis was chosen for the identification of RAPD markers linked to the Vf scab resistant gene. Five different RAPD markers, derived from the wild species
Análisis de dos poblaciones de gallinas criollas (Gallus domesticus) utilizando RAPDs como marcadores moleculares An analysis of two native poultry populations (Gallus domesticus) using RAPD's as molecular markers
Irma Morelia Soto Huipe; Guadalupe Zavala Páramoa; Horacio Cano Camacho; Joel E. López Meza
México has a great variety of native poultry but knowledge about its diversity is minimal. In this study, twenty individuals belonging to two populations of native hens (Gallus domesticus) were analyzed. They were chosen by egg production, through polymorphism identification generated by DNA random amplification (RAPD's). Amplification generated products show different sizes between 0.2 to 1.1 kb. Polymorphism was detected
Identification of apple cultivars using RAPD markers
B. Koller; A. Lehmann; J. M. McDermott; C. Gessler
Eleven apple cultivars were differentiated using randomly amplified polymorphic DNA (RAPD) markers obtained by the polymerase chain reaction (PCR). The variability of the technique and of the origin of the DNA extract was analyzed. A set of bands consistent in their presence or absence was chosen to create a differentiating band pattern. A key is proposed by which one can
Elucidating genetic diversity among sour orange rootstocks: a comparative study of the efficiency of RAPD and SSR markers.
Lamine, Myriam; Mliki, Ahmed
In order to compare the effectiveness of two molecular marker systems, a set of six RAPD and nine SSR markers were used to study the genetic diversity in a population of 46 sour orange accessions, a common rootstock used in almost all citrus orchards in Tunisia. Genetic diversity parameters [average and effective number of alleles, percentage of polymorphism, polymorphic information content (PIC), effective marker index (EMI), and marker index (MI) parameters] for RAPD, SSR, and RAPD?+?SSR were determined in order to assess the efficiency of the two marker systems. The results revealed that these parameters were significantly higher when using RAPD markers. Similarly, cluster analysis using the results of RAPD was practically the same as that obtained when combining data from the two marker systems (RAPD?+?SSR) demonstrating the efficiency of RAPD in discriminating between sour orange accessions. Therefore, the use of SSR markers, known to be more efficient and discriminatory, does not bring significant supplementary information in this work. Indeed, results would have been obtained using only the RAPD markers. Accordingly, this work highlights the efficiency and advantages of RAPD, as an easy and efficient technique, in studying citrus rootstock's genetic diversity, and establishing genetic relationships among citrus accessions. PMID:25586488
A genetic linkage map of crested wheatgrass based on AFLP and RAPD markers.
Yu, Xiaoxia; Li, Xiaolei; Ma, Yanhong; Yu, Zhuo; Li, Zaozhe
Using a population of 105 interspecific F(2) hybrids derived from a cross between Agropyron mongolicum Keng and Agropyron cristatum (L.) Gaertn. 'Fairway' as a mapping population, a genetic linkage map of crested wheatgrass was constructed based on AFLP and RAPD molecular markers. A total of 175 markers, including 152 AFLP and 23 RAPD markers, were ordered in seven linkage groups. The map distance was 416 cM, with a mean distance of 2.47 cM between markers. The number of markers ranged from 13 to 46 in each linkage group and the length of groups ranged from 18 to 104 cM. The research found that 30 out of 175 molecular markers showed segregation distortion, accounting for 17% of all markers. This is the first genetic linkage map of crested wheatgrass. This map will facilitate gene localization, cloning, and molecular marker-assisted selection in the future. PMID:22462407
Use of AFLP and RAPD molecular genetic markers and cytogenetic analysis to explore relationships among taxa of the Patagonian Bromus setifolius complex
Bromus setifolius var. pictus (Hook) Skottsb., B. setifolius var. setifolius Presl. and B.setifolius var. brevifolius Ness are three native Patagonian taxa in the section Pnigma Dumort of the genus Bromus L. AFLP and RAPD analysis, in conjunction with genetic distance measurements and statistical techniques, revealed variation within this group and indicated that B. setifolius var. brevifolius was closely related to B. setifolius var. pictus, with both taxa being more distantly related to B. setifolius var. setifolius. Cytogenetic analysis confirmed the chromosomal number of B. setifolius var. pictus (2n = 70) and B. setifolius var. setifolius (2n = 28) and showed for the first time that B. setifolius var. brevifolius had 2n = 70. The combination of molecular genetic and cytogenetic evidence supported a species status for two of the three taxa and suggested hypotheses for the evolutionary origin of these complex taxa. Species status was also indicated for B. setifolius var. setifolius. Based on these findings, we suggest that B. setifolius var. pictus be referred to as B. pictus Hook var. pictus, and B. setifolius var brevifolius as B. pictus Hook var brevifolius. The correlation between AFLP diversity and variation in ecological parameters suggested that this marker system could be used to assess breeding progress and to monitor the domestication of Patagonian Bromus species for agronomic use. PMID:21637686
A method to measure genetic distance between allogamous populations of alfalfa (Medicago sativa) using RAPD molecular markers.
Ghérardi, M; Mangin, B; Goffinet, B; Bonnet, D; Huguet, T
Alfalfa (Medicago sativa L.) is a forage legume of world-wide importance whose both allogamous and autotetraploid nature maximizes the genetic diversity within natural and cultivated populations. This genetic diversity makes difficult the discrimination between two related populations. We analyzed this genetic diversity by screening DNA from individual plants of eight cultivated and natural populations of M. sativa and M. ?falcata using the RAPD method. A high level of genetic variation was found within and between populations. Using five primers, 64 intense bands were scored as present or absent across all populations. Most of the loci were revealed to be highly polymorphic whereas very few population-specific polymorphisms were identified. From these observations, we adopted a method based on the Roger's genetic distance between populations using the observed frequency of bands to discriminate populations pairwise. Except for one case, the between-population distances were all significantly different from zero. We have also determined the minimal number of bands and individuals required to test for the significance of between-population distances. PMID:24710879
Molecular Markers for Identification of Stellantchasmus falcatus and a Phylogenic Study using the HAT-RAPD Method
Wongsawad, Pheravut
Stellantchasmus falcatus is a minute intestinal fluke in the family Heterophyidae. Metacercariae, the infective stage, were reported in a marine fish, mullet Liza subviridis, and a fresh water fish, Dermogenus pusillus, in Thailand. Adults were found in chicks, rats, cats, and humans. Morphological studies were done for comparing Stellantchasmus sp. worms found in 2 different fish hosts; their shapes and organ arrangements were very similar except for the prepharynx length. Therefore, the present study aimed to compare their DNA fingerprints using the HAT-RAPD method for both types of Stellantchasmus and several other related species. Ten arbitrarily selected primers (OPA-04, OPA-09, OPN-02, OPN-03, OPN-09, OPN-12, OPP-11, OPR-15, OPX-13, and OPAD-01) were used. It was found that OPA-09, OPN-03, and OPAD-01 were able to generate S. falcatus specific fragments in mullets which consisted of 200, 760, and 280 bp, respectively. In addition, the results of morphologic, DNA fingerprinting, and phylogenetic analyses strongly suggest that the fresh water and marine specimens of Stellantchamus may be different species. PMID:21234232
RAPD markers linked to the Vf gene for scab resistance in apple.
Tartarini, S
Scab (Venturia inaequalis) is one of the most harmful diseases of apple, significantly affecting world apple production. The identification and early selection of resistant genotypes by molecular markers would greatly improve breeding strategies. Bulked segregant analysis was chosen for the identification of RAPD markers linked to the Vf scab resistant gene. Five different RAPD markers, derived from the wild species Malus floribunda. 821, were identified, and their genetic distance from Vf gene was estimated. The markers OPAM192200 and OPAL07580 were found to be very closely linked to the Vf gene. This result was indirectly confirmed by the analysis of resistant genotypes collected from various breeding programmes. Except for cv 'Murray', which carries the Vm gene, all these resistant genotypes showed the markers OPAM192200 and OPAL07580. PMID:24166544
Diversity among populations of switchgrass based on RAPD markers
Gunter, L.E.; Tuskan, G.A.; Wullschleger, S.D. [Oak Ridge National Lab., TN (United States)
Information on the amount of genetic diversity in switchgrass (Panicum virgatum L.) is necessary to enhance the effectiveness of breeding programs and germplasm conservation efforts. This study characterized and assessed genetic diversity by means of RAPD markers among 14 populations representing upland and lowland switchgrass ecotypes. Forty-five of 128 primers produced polymorphic markers among sets of genomic DNA pooled from individual genotypes of each population. Five primers were selected to amplify a total of 91 polymorphic loci among genotypes. The RAPD markers were scored for presence or absence of bands to generate distance matrices for cluster analysis. Overall similarity was 65% among population compared to 81% within populations. Blackwell and Caddo were the most similar populations (78%) based on RAPD markers, whereas Alamo and Forestburg were the most divergent (53%). Cluster analysis clearly segregated populations into two main groups (putatively based on ecotype) and united individual genotypes within a population into discrete groups within the larger clusters. Although the relationship between ploidy level and ecotype remained unclear, RAPD profiles can be used to identify switchgrass populations and may be useful in predicting relationship between experimental germplasm sources and released populations. 50 refs., 2 figs., 2 tabs.
Identification of broccoli and cauliflower cultivars with RAPD markers
Jinguo Hu; Carlos F. Quiros
RAPD (Random Amplified Polymorphic DNA) markers generated by 4 arbitrary 10-mer primers, discriminated 14 broccoli and 12 cauliflower cultivars (Brassica oleracea L.) by banding profiles. The size of the amplified DNA fragments ranged from 300 to 2600 base pairs. Twenty-eight percent of the markers were fixed in both broccoli and cauliflower, whereas 12.5% were specific to either crop. The rest
Assessment of natural and induced genetic variation in Alstroemeria using random amplified polymorphic DNA (RAPD) markers
E. Anastassopoulos; M. Keil
We have used random amplified polymorphic DNA (RAPD) markers to study genetic variation in Alstroemeria. The first objective was to examine the discriminatory power of RAPD markers in different genotypes of Alstroemeria obtained by traditional breeding. All genotypes examined, including commercial Alstroemeria varieties, could be distinguished on the basis of their RAPD profiles. Progeny plants could be distinguished from their
Molecular analysis of silver crucian carp ( Carassius auratus gibelio Bloch) clones by SCAR markers
Li Zhou; Yang Wang; Jian-Fang Gui
Random amplified polymorphic DNA (RAPD) molecular markers specific for one, two or three clones have been identified from five gynogenetic clones of silver crucian carp (Carassius auratus gibelio Bloch) using RAPD markers developed earlier. In this study, three RAPD markers (RA1-PA, RA2-EF and RA4-D) produced by Opj-1, and two RAPD DNA fragments (RA3-PAD and RA5-D) produced by Opj-7, were selected
RAPD markers linked to microspore embryogenic ability in Brassica crops
Feng-lan Zhang; Satoru Aoki; Yoshihito Takahata
In order to identify the markers linked to microspore embryogenic ability in Brassica crops, RAPD segregation analyses were performed in a microspore-derived (MD) population and a F2 population derived from F1between 'Ho Mei' (high responsive parent in microspore embryogenesis) and '269' (low responsive parent) in Chinese cabbage,\\u000a and between 'Lisandra' (high responsive parent) and 'Kamikita' (low responsive parent) in oil
Identification of RAPD markers linked to sex determination in guggal [ Commiphora wightii (Arnott.)] Bhandari
Sanghamitra Samantaray; K. A. Geetha; K. P. Hidayath; Satyabrata Maiti
Decamer RAPD primers were tested on dioeceious and hermaphrodite plants of Commiphora wightii to identify sex-specific molecular markers. Sixty different random decamer primers were screened out of which only three\\u000a primers were found to be associated with sex expression. A ~1,280-bp fragment from the primer OPN06 was found to be present\\u000a in all the female individuals. Another primer OPN 16
Genetic relationships among ten endod types as revealed by a combination of morphological, RAPD and AFLP markers.
Semagn, Kassa
The genetic relationships among ten types of endod (Phytolacca dodecandra) cultivated by the Institute of Pathobiology of the Addis Ababa University to combat the disease bilharzia in Ethiopia were studied using morphology and molecular markers. A total of 18 morphological characters, 194 amplified fragment length polymorphism (AFLP) and 42 random amplified polymorphic DNA (RAPD) markers were used to determine genetic proximity between types. Genetic distance and cluster analysis of the AFLP data revealed the lack of genetic difference between E47 and E48 but relatively wider genetic difference among the other endod types. Cluster and principal component analyses performed on the AFLP and RAPD markers demonstrated the presence of distinct separation of E56 but not that of E44 from the others. The AFLP and RAPD data, thcrefore, did not support the hypothesis that the superiority of E44 in agronomic traits and molluscicidal potency is linked to its distinct genetic difference from the other endod types. Matrices correspondence tests demonstrated the presence of greater correspondence between AFLP and RAPD data (r = 0.842) but not between the morphology and that of AFLP and RAPD. This indicates the correspondence more between the two DNA markers systems than either of them with morphological traits. The cophenetic correlation coefficients also revealed poor fit for morphology (r = 0.716), good fit for RAPD (r = 0.872) and very good fit for AFLP (r = 0.975), reflecting the hyper-variability and higher resolving power of AFLP. PMID:12627842
Template mixing: a method of enhancing detection and interpretation of codominant RAPD markers
T. M. Davis; H. Yu; K. M. Haigis; P. J. McGowan
Ten codominant RAPD markers, ranging in size from about 300 to about 1350 bp, were identified in mapping populations of chickpea (Cicer arietinum L.) and diploid strawberry (Fragaria vesca L.). A distinguishing feature of all ten markers, and perhaps of codominant RAPD markers in general, was the presence in heterozygous individuals of a non-parental, heteroduplex band migrating more slowly than
Identification of random amplified polymorphic DNA (RAPD) marker for differentiating male from female and sporophytic thalli of Gracilaria changii (Rhodophyta)
M. C. Sim; P. E. Lim; S. Y. Gan; S. M. Phang
There have been limited reports on molecular sex markers for macroalgae. We report the use of random amplified polymorphic\\u000a DNA analysis (RAPD) to identify molecular sex markers for Gracilaria changii (Xia et Abbott) Abbott, Zhang et Xia. Two DNA extraction methods were used: a modified CTAB and phenol-chloroform combination\\u000a method and the DNeasy Plant Mini Kit. The CTAB and phenol-chloroform
Linkage map of the honey bee, Apis mellifera, based on RAPD markers
Greg J. Hunt; Robert E. Page
A linkage map was constructed for the honey bee based on the segregation of 365 random amplified polymorphic DNA (RAPD) markers in haploid male progeny of a single female bee. The X locus for sex determination and genes for black body color and malate dehydrogenase were mapped to separate linkage groups. RAPD markers were very efficient for mapping, with an
Genomic mapping in Pinus pinaster (maritime pine) using RAPD and protein markers
C Plomion; N Bahrman; C-E Durel; D M O'Malley
A detailed genomic map was constructed for one F1 individual of maritime pine, using randomly amplified polymorphic DNA (RAPD) and protein markers scored on megagametophytes of germinated seeds. Proteins allowed the localization of exclusively coding DNA in the large genome of this Pinus species, mapped with RAPD markers that essentially fall within repetitive (i.e. mostly noncoding) DNA. Dot blots experiments
Technology Transfer Automated Retrieval System (TEKTRAN)
A linkage map for European hazelnut (Corylus avellana L.) was constructed using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers and the 2-way pseudotestcross approach. RAPD markers in testcross configuration segregating 1:1, were used to construct maps for each paren...
Molecular characterization and RAPD analysis of Juniperus species from Iran.
Kasaian, J; Behravan, J; Hassany, M; Emami, S A; Shahriari, F; Khayyat, M H
The genus Juniperus L. (Cupressaceae), an aromatic evergreen plant, consists of up to 68 species around the world. We classified five species of Juniperus found in Iran using molecular markers to provide a means for molecular identification of Iranian species. Plants were collected (three samples of each species) from two different provinces of Iran (Golestan and East Azarbayejan). The DNA was extracted from the leaves using a Qiagen Dneasy Plant Mini Kit. Amplification was performed using 18 ten-mer RAPD primers. Genetic distances were estimated based on 187 RAPD bands to construct a dendrogram by means of unweighted pair group method of arithmetic means. It was found that J. communis and J. oblonga were differentiated from the other species. Genetic distance values ranged from 0.19 (J. communis and J. oblonga) to 0.68 (J. communis and J. excelsa). Juniperus foetidissima was found to be most similar to J. sabina. Juniperus excelsa subspecies excelsa and J. excelsa subspecies polycarpos formed a distinct group. PMID:21710457
Characterization of four B-chromosome-specific RAPDs and the development of SCAR markers on the maize B-chromosome.
Kao, Kuo-Wei; Lin, Chien-Yu; Peng, Shu-Fen; Cheng, Ya-Ming
Understanding the molecular organization of the maize B-chromosome is hindered by its high homology with A-chromosomes. Recently, various approaches have been employed to overcome this hindrance, and several B-chromosome-specific sequences have been identified. Here, we cloned and characterized four previously published B-chromosome-specific RAPD fragments in detail. The results of sequence analysis, Southern hybridization and fluorescence in situ hybridization revealed that the four RAPD fragments are repetitive and present on both the B- and A-chromosomes, which supports an A-chromosome origin of the B-chromosome. We further developed four sequence-characterized amplified region (SCAR) markers derived from the four B-chromosome-specific RAPDs. These markers amplified PCR products exclusively in plants with B-chromosomes and were further mapped to definite distal heterochromatic regions of the B-chromosome by 15 B-A translocations. Furthermore, reverse transcriptase-PCR revealed that two of the four B-chromosome-specific RAPD fragments are transcriptionally active. These results demonstrate the feasibility of using B-chromosome-specific RAPD sequences to generate SCAR markers specific to the B-chromosome and might apply to other sequences of the maize B-chromosome. PMID:25258187
Genetic similarity among male bees of Euglossa truncata Rebęlo & Moure (Hymenoptera: Apidae) revealed by RAPD markers.
Suzuki, Karen M; Almeida, Fernanda S; Sodré, Leda M K; Pascual, Amália N T; Sofia, Silvia H
The genetic RAPD (random amplified polymorphic DNA) markers have been used successfully in taxonomical studies of several groups of organisms. In the present study these molecular markers were used to analyze the genetic similarity among eighteen males of Euglossa truncata Rebęlo & Moure exhibiting variations in two morphological characters (colour of the antennal scape and metaepisternal hairs) which are frequently used to identify this species of euglossine bee. The twelve primers used in the RAPD analysis amplified 127 loci, of which 40 (31.5%) were polymorphic, showing some variation among the individuals. The coefficients of genetic similarity among the individuals ranged from 0.79 to 0.95, indicating a rather high genetic similarity among the 18 male bees studied. No RAPD band was specific to any morphological character analyzed. The results indicate that all bees analyzed belong to the same species. The high genetic similarity among the eighteen euglossine males studied indicates that the variations observed in the morphological characters are not in disagreement with the identification of this species of Euglossina and these characters can vary among males of E. truncata. PMID:17061795
Genetic diversity of wild and cultivated genotypes of pigeonpea through RAPD and SSR markers.
Walunjkar, Babasaheb C; Parihar, Akarsh; Singh, Nirbhay Kumar; Parmar, L D
Eight wild and four cultivated pigeonpea genotypes were subjected to RAPD and microsatellite analysis, with 40 primers each. Out of these, eight RAPD and five SSR primers were found polymorphic. RAPD primers showed 100% polymorphism and produced a total of 517 DNA fragments, whereas SSR primers produced 67 fragments and they too showed 100% polymorphism. The RAPD markers revealed highest similarity co-efficient of 0.93 (GT-100 and ICPL-87), whereas the highest similarity co-efficient obtained with SSR markers was 1.00 (GTH-1 and GT-100). Average PIC value obtained with RAPD and SSR were 0.90 and 0.18, respectively. The arithmetic mean heterozygosity and marker index were 0.90 and 22.47 respectively with RAPD marker, whereas the corresponding values for SSR markers were 0.18 and 33.66. Moreover; the four wild genotypes (Cajanus scarabaeoides, Rhyncosia rufescence, Cajanus cajanifolius and Rhyncosia canna) and the four cultivars (GTH-1, GT-100, ICPL-87 and GT-1) grouped distinctly in the same subgroups of the dendrograms obtained with both RAPD and SSR analysis. Therefore, the findings of SSR supplement and validate the results obtained with RAPD analysis. PMID:25895271
Analysis of genetic heterogeneity among five gynogenetic clones of silver crucian carp, Carassius auratus gibelio Bloch, based on detection of RAPD molecular markers
L. Zhou; Y. Wang; J. F. Gui
The gynogenetic silver crucian carp, Carassius auratus gibelio, is a unique model system for studying evolutionary genetics and selective breeding, owing to its specific genetic background and reproductive modes. Five gynogenetic clones were analyzed by the random amplified polymorphic DNA (RAPD) technique, using 30 10-nucleotide-long primers. Twenty-six primers produced well-amplified DNA fragments with reproducible banding patterns, and 24 primers were
RAPD markers reveal polymorphism among some Iranian pomegranate ( Punica granatum L.) genotypes
A. Sarkhosh; Z. Zamani; R. Fatahi; A. Ebadi
In this study RAPD markers were used to determine the diversity level among 24 Iranian pomegranate genotypes. One hundred decamer random primers were used for PCR reactions, among which 16 showed reliable polymorphic patterns. These primers produced 178 bands, of which 102 were polymorphic. Cluster analysis of the genotypes was performed based on data from polymorphic RAPD bands, using Jaccard's
Identification of Anoectochilus formosanus and Anoectochilus koshunensis species with RAPD markers.
Cheng, K T; Fu, L C; Wang, C S; Hsu, F L; Tsay, H S
RAPD (random amplified polymorphic DNA) markers were developed to distinguish Anoectochilus formosanus from Anoectochilus koshunensis and their putative hybrids. Morphological differentiation of these two species beyond the flowering period is difficult. RAPD markers provide a rapid and easy tool for identification of the two Anoectochilus species. In the study, forty arbitrary decamer primers were screened, and nineteen species-specific RAPD markers generated from polymerase chain reactions (PCR) with eight random primers were obtained. Nine were specific to A. formosanus and ten to A. koshunensis. Two primers, OPC-08 and OPL-07, produced two markers, one specific to A. formosanus and the other specific to A. koshunensis, which simultaneously appeared in the hybrids pattern. The RAPD markers can be applied both to identification of A. formosanus and A. koshunensis species and to assessment of the extent fo hybridization in hybrids between them. This information facilitates the breeding program process. PMID:17253217
Genetic structure and inter-generic relationship of closed colony of laboratory rodents based on RAPD markers.
Kumar, Mahadeo; Kumar, Sharad
Molecular genetic analysis was performed using random amplified polymorphic DNA (RAPD) on three commonly used laboratory bred rodent genera viz. mouse (Mus musculus), rat (Rattus norvegicus) and guinea pig (Cavia porcellus) as sampled from the breeding colony maintained at the Animal Facility, CSIR-Indian Institute of Toxicology Research, Lucknow. In this study, 60 samples, 20 from each genus, were analyzed for evaluation of genetic structure of rodent stocks based on polymorphic bands using RAPD markers. Thirty five random primers were assessed for RAPD analysis. Out of 35, only 20 primers generated a total of 56.88% polymorphic bands among mice, rats and guinea pigs. The results revealed significantly variant and distinct fingerprint patterns specific to each of the genus. Within-genera analysis, the highest (89.0%) amount of genetic homogeneity was observed in mice samples and the least (79.3%) were observed in guinea pig samples. The amount of genetic homogeneity was observed very high within all genera. The average genetic diversity index observed was low (0.045) for mice and high (0.094) for guinea pigs. The inter-generic distances were maximum (0.8775) between mice and guinea pigs; and the minimum (0.5143) between rats and mice. The study proved that the RAPD markers are useful as genetic markers for assessment of genetic structure as well as inter-generic variability assessments. PMID:25074272
A first linkage map of pecan cultivars based on RAPD and AFLP markers
Sudheer R. Beedanagari; Sue K. Dove; Bruce W. Wood; Patrick J. Conner
We report here the first genetic linkage maps of pecan [Carya illinoinensis (Wangenh.) K. Koch], using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers. Independent maps were constructed for the cultivars 'Pawnee' and 'Elliot' using the double pseudo-testcross mapping strategy and 120 F1 seedlings from a full-sib family. A total of 477 markers, including 217 RAPD,
Genetic diversity of Palestine landraces of faba bean (Vicia faba) based on RAPD markers.
Basheer-Salimia, R; Shtaya, M; Awad, M; Abdallah, J; Hamdan, Y
Until now, neither phenotypic nor molecular approaches have been used to characterize the landraces of Palestine faba beans (Vicia faba). We used PCR-based RAPD markers to determine the genetic diversity and relatedness among 26 Palestinian faba bean landraces (traditional farmers' varieties) from 8 localities in the West Bank, Palestine. In tests with 37 primers, 14 generated no polymorphic bands, 12 exhibited weak and unclear products, and 11 primers produced good amplification products with high intensity and pattern stability. Ninety-four DNA fragments (loci) were detected, with an average of 8.54 loci per primer and size ranging from 160 to 1370 bp. A minimum of 4 and a maximum of 14 DNA fragments were obtained using (OPA-05 and OPA-09) and (BC-261) primers, respectively. The maximum percentage of polymorphic markers was 71.4 (BC-298) and the minimum was 50.0 (OPA-05, -09, -16). The 11 primers exhibited relatively high collective resolving power (Rp) values of 26.316, and varied from 0.154 for the OPA-09 primer to 5.236 for the BC-261, with an overall mean of 2.392. The primers BC-261, -322, and -298 were found to be the most useful RAPD primers to assess the genetic diversity of Palestinian faba beans, as they revealed relatively high Rp rates (5.236, 3.618, and 3.150, respectively). Based on the Jaccard coefficient, the genetic distance ranged from 0.358 to 0.069, with a mean of 0.213. We conclude that the RAPD technique is useful for determining genetic diversity and for developing suitable fingerprints for faba bean landraces grown in Palestine. PMID:24065673
Identification of RAPD and SCAR markers associated with yield traits in the Indian tropical tasar silkworm Antheraea mylitta drury
Dutta, Suhrid R.; Kar, Prasanta K.; Srivastava, Ashok K.; Sinha, Manoj K.; Shankar, Jai; Ghosh, Ananta K.
The tropical tasar silkworm, Antheraea mylitta, is a semi-domesticated vanya silk-producing insect of high economic importance. To date, no molecular marker associated with cocoon and shell weights has been identified in this species. In this report, we identified a randomly amplified polymorphic DNA (RAPD) marker and examined its inheritance, and also developed a stable diagnostic sequence-characterized amplified region (SCAR) marker. Silkworms were divided into groups with high (HCSW) and low (LCSW) cocoon and shell weights, and the F2 progeny of a cross between these two groups were obtained. DNA from these silkworms was screened by PCR using 34 random primers and the resulting RAPD fragments were used for cluster analysis and discriminant function analysis (DFA). The clustering pattern in a UPGMA-based dendogram and DFA clearly distinguished the HCSW and LCSW groups. Multiple regression analysis identified five markers associated with cocoon and shell weights. The marker OPW16905 bp showed the most significant association with cocoon and shell weights, and its inheritance was confirmed in F2 progeny. Cloning and sequencing of this 905 bp fragment showed 88% identity between its 134 nucleotides and the Bmc-1/Yamato-like retroposon of A. mylitta. This marker was further converted into a diagnostic SCAR marker (SCOPW 16826 bp). The SCAR marker developed here may be useful in identifying the right parental stock of tasar silk-worms for high cocoon and shell weights in breeding programs designed to enhance the productivity of tasar silk. PMID:23271934
RAPD and ISSR markers indicate high genetic variation within Lobathallia radiosa in Turkey
Ertu?rul Yüzba??o?lu; Mehmet Gökhan Hal?c?; Muhammer Karabacak; Ahmet Aksoy
Randomly amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) methods were used for investigating genetic\\u000a variation within L. radiosa and for delimiting species within the genus Lobothallia. Ten RAPD and 11 ISSR primers produced a total of 261 and 260 reproducible bands, respectively, and all of which were polymorphic\\u000a for the two markers, suggesting high genetic variability within
A genetic linkage map for hazelnut (Corylus avellana L.) based on RAPD and SSR markers.
Mehlenbacher, Shawn A; Brown, Rebecca N; Nouhra, Eduardo R; Gökirmak, Tufan; Bassil, Nahla V; Kubisiak, Thomas L
A linkage map for European hazelnut (Corylus avellana L.) was constructed using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers and the 2-way pseudotestcross approach. A full-sib population of 144 seedlings from the cross OSU 252.146 x OSU 414.062 was used. RAPD markers in testcross configuration, segregating 1:1, were used to construct separate maps for each parent. Fifty additional RAPD loci were assigned to linkage groups as accessory markers whose exact location could not be determined. Markers in intercross configuration, segregating 3:1, were used to pair groups in one parent with their homologues in the other. Eleven groups were identified for each parent, corresponding to the haploid chromosome number of hazelnut (n = x = 11). Thirty of the 31 SSR loci were able to be assigned to a linkage group. The maternal map included 249 RAPD and 20 SSR markers and spanned a distance of 661 cM. The paternal map included 271 RAPD and 28 SSR markers and spanned a distance of 812 cM. The maps are quite dense, with an average of 2.6 cM between adjacent markers. The S-locus, which controls pollen-stigma incompatibility, was placed on chromosome 5S where 6 markers linked within a distance of 10 cM were identified. A locus for resistance to eastern filbert blight, caused by Anisogramma anomala, was placed on chromosome 6R for which two additional markers tightly linked to the dominant allele were identified and sequenced. These maps will serve as a starting point for future studies of the hazelnut genome, including map-based cloning of important genes. The inclusion of SSR loci on the map will make it useful in other populations. PMID:16498462
Discrimination among three species of medicinal Scutellaria plants using RAPD markers.
Hosokawa, K; Minami, M; Kawahara, K; Nakamura, I; Shibata, T
An analysis of random amplified polymorphic DNA (RAPD) was performed using nine accessions of three species of medicinal plants in the genus Scutellaria (S. galericulata, S. lateriflora and S. baicalensis; known collectively as skullcap) in an effort to distinguish between members of these three species. Dried aerial parts of the two species S. galericulata and S. lateriflora are difficult to distinguish morphologically. Ten arbitrary primers produced 92 fragments, and eight of the primers yielded 23 species-specific fragments among the three species. Six fragments were specific for S. galericulata, seven for S. lateriflora and ten for S. baicalensis. When primers A02 and A06 were used in the polymerase chain reaction, RAPD fragments that were specific for each of the three species were generated simultaneously. Primer A02 produced five species-specific fragments: one was specific for S. galericulata; two for S. lateriflora; and two for S. baicalensis. Primer A06 produced three species-specific fragments: one for S. galericulata; one for S. lateriflora; and one for S. baicalensis. The RAPD markers that were generated with these two primers should rapidly identify members of the three species of Scutellaria. The consistency of the identifications made with these species-specific RAPD markers was demonstrated by the observation that each respective marker was generated from three accessions of each species, all with different origins. Furthermore, cluster analysis using the 92 RAPD fragments produced a dendrogram of genetic relatedness that was in good agreement with the taxonomic designations of the three species. Thus, the RAPD markers should be useful for the future identification of members of the three species of medicinal Scutellaria plants. PMID:10821055
Molecular markers linked to the fin gene controlling determinate growth habit in common bean
Astrid Pańeda; Cristina Rodríguez-Suárez; Ana Campa; Juan José Ferreira; Ramón Giraldez
Bulked segregant analysis (BSA) was used to identify molecular markers linked to determinate growth habit (fin gene) in a F2 population derived from the cross Andecha (FinFin) × BRB130 (finfin). Fourteen RAPD markers and one microsatellite (BMd45-AIA) were linked to the fin gene when tested on the entire population. The SCAR, SI19b, designed from the RAPD marker OI19385 (linked to the fin
Technology Transfer Automated Retrieval System (TEKTRAN)
We report here the first genetic linkage maps of pecan [Carya illinoinensis (Wandenh.) K. Koch], using random amplified polymorphis DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers. Independent maps were constructed for the cultivars 'Pawnee' and 'Elliot' using the double pseudo...
Identification of RAPD marker associated with brown rust resistance in sugarcane
Technology Transfer Automated Retrieval System (TEKTRAN)
Susceptibility to brown rust caused by Puccinia melanocephala is a major reason for the withdrawal of sugarcane cultivars from production. An efficient way to control the disease is to breed cultivars with durable resistance. Our aim was to identify random amplified polymorphic DNA (RAPD) markers ...
Utility of RAPD Markers in Evaluating the Status of the Hawaiian Tree Fern Cibotium Dheleniae1
Carpenter, Kent E.
Utility of RAPD Markers in Evaluating the Status of the Hawaiian Tree Fern Cibotium Dheleniae1 intermediacy, sporadic occurrence, and their irregular and abortive spores (Palmer 1998). Several of these puta). Of these, our study focuses on the putative hybrid individuals among species of Cibotium tree ferns
Identification of a RAPD marker linked to sex determination in Pistacia vera using bulked segregant analysis
J. I. Hormaza; L. Dollo; V. S. Polito
The Random Amplified Polymorphic DNA (RAPD) technique was used to amplify DNA segments, with the objective of finding markers linked to sex determination in the dioecious species, Pistacia vera. Progenies from two female parents pollinated by a common male parent were studied. Two bulks of DNA were made in each cross, one from males and one from females, by pooling
Analysis of Genetic Diversity in Rough Bluegrass Determined by RAPD Markers
Shanmugam Rajasekar; Shui-hang Fei; Nick E. Christians
Information on genetic variation in rough bluegrass (Poa trivialis L.), a cool-season grass that is grown for sports fields and lawns, is needed. The objective of this study was to assess genetic variation in 27 accessions of rough bluegrass obtained from the National Plant Germplasm System (NPGS) by random amplified polymorphic DNA (RAPD) markers. Fifteen of the 80 primers screened
Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers
W. Qian; S. Ge; D.-Y. Hong
Genetic variation within and between five populations of Oryza granulata from two regions of China was investigated using RAPD (random amplified polymorphic DNA) and ISSR (inter-simple sequence\\u000a repeat amplification) markers. Twenty RAPD primers used in this study amplified 199 reproducible bands with 61 (30.65%) polymorphic;\\u000a and 12 ISSR primers amplified 113 bands with 52 (46.02%) polymorphic. Both RAPD and ISSR
Fingerprinting of alfalfa meiotic mutants using RAPD markers
G. Barcaccia; S. Tavoletti; M. Pezzotti; M. Falcinelli; F. Veronesi
Polymerase chain reaction (PCR), with single ten-base-long nucleotide primers, was used to amplify random regions of genomic DNA from eleven diploid meiotic mutants (2n egg, 2n pollen and jumbo pollen producers) of the Medicago sativa-coerulea-falcata complex. Electrophoretic patterns of the resulting random amplified polymorphic DNA (RAPD) fragments were evaluated to develop a graphical representation of amplification products from which conserved
Genetic variation analysis in the genus Lathyrus using RAPD markers
N. Chtourou-Ghorbel; B. Lauga; N. Ben Brahim; D. Combes; M. Marrakchi
RAPD analysis was applied to five species belonging to the genusLathyrus (Fabaceae): L.sativus, L.cicera, L.ochrus, L.sylvestris and L.latifolius. All the species under study belong to thesection Lathyrus except L.ochrus which is in section Clymenum.Nine populations representing these species were used and ten random10-mer primers were sampled. A total of 129 amplification products,ranging in size from 0.3 to 3 Kb, were
A male and hermaphrodite specific RAPD marker for papaya ( Carica papaya L.)
N. Urasaki; M. Tokumoto; K. Tarora; Y. Ban; T. Kayano; H. Tanaka; H. Oku; I. Chinen; R. Terauchi
The random amplified polymorphic DNA (RAPD) technique was used to determine the sex of a dioecious species, Carica papaya L., with three sex types, male, female and hermaphrodite. A 450 bp marker fragment, named PSDM(Papaya Sex Determination Marker),\\u000a exists in all male and hermaphrodite plants but not in the female plants so far analyzed. The DNA sequence of PSDM exhibited
Identification of RAPD and SCAR markers associated with yield traits in the Indian tropical tasar silkworm Antheraea mylitta drury.
Dutta, Suhrid R; Kar, Prasanta K; Srivastava, Ashok K; Sinha, Manoj K; Shankar, Jai; Ghosh, Ananta K
The tropical tasar silkworm, Antheraea mylitta, is a semi-domesticated vanya silk-producing insect of high economic importance. To date, no molecular marker associated with cocoon and shell weights has been identified in this species. In this report, we identified a randomly amplified polymorphic DNA (RAPD) marker and examined its inheritance, and also developed a stable diagnostic sequence-characterized amplified region (SCAR) marker. Silkworms were divided into groups with high (HCSW) and low (LCSW) cocoon and shell weights, and the F(2) progeny of a cross between these two groups were obtained. DNA from these silkworms was screened by PCR using 34 random primers and the resulting RAPD fragments were used for cluster analysis and discriminant function analysis (DFA). The clustering pattern in a UPGMA-based dendogram and DFA clearly distinguished the HCSW and LCSW groups. Multiple regression analysis identified five markers associated with cocoon and shell weights. The marker OPW16(905 bp) showed the most significant association with cocoon and shell weights, and its inheritance was confirmed in F(2) progeny. Cloning and sequencing of this 905 bp fragment showed 88% identity between its 134 nucleotides and the Bmc-1/Yamato-like retroposon of A. mylitta. This marker was further converted into a diagnostic SCAR marker (SCOPW 16(826 bp)). The SCAR marker developed here may be useful in identifying the right parental stock of tasar silk-worms for high cocoon and shell weights in breeding programs designed to enhance the productivity of tasar silk. PMID:23271934
Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes
Nagl, Nevena; Taski-Ajdukovic, Ksenija; Barac, Goran; Baburski, Aleksandar; Seccareccia, Ivana; Milic, Dragan; Katic, Slobodan
Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon's information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm. PMID:21954370
Molecular markers for sex determination in papaya ( Carica papaya L.)
J. C. Deputy; R. Ming; H. Ma; Z. Liu; M. M. M. Fitch; M. Wang; R. Manshardt; J. I. Stiles
We have developed molecular markers tightly linked to Sex1, the gene that determines plant sex in papaya (Carica papaya L.). Three RAPD products have been cloned and a portion of their DNA sequenced. Based on these sequences SCAR primers were synthesized. SCAR T12 and SCAR W11 produce products in hermaphrodite and male plants and only rarely in females. SCAR T1
A novel strategy for identification of 47 pomegranate (Punica granatum) cultivars using RAPD markers.
Zhang, Y P; Tan, H H; Cao, S Y; Wang, X C; Yang, G; Fang, J G
DNA marker can be used for precise plant cultivar identification. However, DNA markers have often not been used effectively for the identification of plant cultivars due to a lack of an effective analysis strategy. We used a novel strategy for effective identification of plant individuals based on a new way of recording DNA fingerprints of the genotyped plants; a cultivar identification diagram can be manually generated and used as key reference information for quick identification of plant and/or seed samples. Forty-seven pomegranate varieties popularly cultivated in various provinces of China were subjected to RAPD marker analysis. Using the cultivar identification diagram strategy, they were clearly separated by the fingerprints of 11 RAPD primers. The utility and accuracy of the cultivar identification diagram analysis results were confirmed by the identification of three randomly chosen groups of cultivars among the 47 varieties. PMID:22782622
Determination of genetic relationships among shape Phaseolus vulgaris populations in a conical cross from RAPD marker analyses
Yonghe Bai; T. E. Michaels; K. P. Pauls
Random-amplified polymorphic DNA (RAPD) markers were used to determine genetic relationships among Phaseolus vulgaris breeding populations. Genetic distances were calculated from the distribution of 317 RAPD markers among 8 parents, 10 individuals from 8 cycle-one populations, 10 individuals from 6 cycle-two populations and 10 individuals from 2 cycle-three populations of a conical cross. Genetic distances between populations and parents were
Genome-specific repetitive DNA and RAPD markers for genome identification in Elymus and Hordelymus.
Svitashev, S; Bryngelsson, T; Li, X; Wang, R R
We have developed RFLP and RAPD markers specific for the genomes involved in the evolution of Elymus species, i.e., the St, Y, H, P, and W genomes. Two P genome specific repetitive DNA sequences, pAgc1 (350 bp) and pAgc30 (458 bp), and three W genome specific sequences, pAuv3 (221 bp), pAuv7 (200 bp), and pAuv13 (207 bp), were isolated from the genomes of Agropyron cristatum and Australopyrum velutinum, respectively. Attempts to find Y genome specific sequences were not successful. Primary-structure analysis demonstrated that pAgc1 (P genome) and pAgc30 (P genome) share 81% similarity over a 227-bp stretch. The three W genome specific sequences were also highly homologous. Sequence comparison analysis revealed no homology to sequences in the EMBL-GenBank databases. Three to four genome-specific RAPD markers were found for each of the five genomes. Genome-specific bands were cloned and demonstrated to be mainly low-copy sequences present in various Triticeae species. The RFLP and RAPD markers obtained, together with the previously described H and St genome specific clones pHch2 and pP1Taq2.5 and the Ns genome specific RAPD markers were used to investigate the genomic composition of a few Elymus species and Hordelymus europaeus, whose genome formulas were unknown. Our results demonstrate that only three of eight Elymus species examined (the tetraploid species Elymus grandis and the hexaploid species Elymus caesifolius and Elymus borianus) really belong to Elymus. PMID:9549065
Identification of genetically diverse genotypes for photoperiod insensitivity in soybean using RAPD markers
R. K. Singh; V. S. Bhatia; Sanjeev Yadav; Rashmi Athale; N. Lakshmi; K. N. Guruprasad; G. S. Chauhan
Most of the Indian soybean varieties were found to be highly sensitive to photoperiod, which limits their cultivation in only\\u000a localized area. Identification of genetically diverse source of photoperiod insensitive would help to broaden the genetic\\u000a base for this trait. Present study was undertaken with RAPD markers for genetic diversity estimation in 44 accessions of soybean\\u000a differing in response to
Analysis of phylogenetic relationships in the genus Solanum (Solanaceae) as revealed by RAPD markers
P. Poczai; J. Taller; I. Szabó
Phylogenetic relationships and genetic variation were examined in the genus Solanum based on the random amplified polymorphic DNA (RAPD) technique. Genetic distances were estimated for 42 accessions from five\\u000a subgenera [Archaesolanum, Minon (Syn. Brevantherum), Leptostemonum, Potatoe, and Solanum]. This investigation provided new information and reinforced some suggestions from previous phylogenetic studies. Analysis\\u000a with random markers from the total genome clearly
A new citrus linkage map based on SRAP, SSR, ISSR, POGP, RGA and RAPD markers
Osman Gulsen; Aydin Uzun; Ihsan Canan; Ubeyit Seday; Ercan Canihos
Sequence-related amplified polymorphism (SRAP), simple sequence repeats (SSR), inter-simple sequence repeat (ISSR), peroxidase\\u000a gene polymorphism (POGP), resistant gene analog (RGA), randomly amplified polymorphic DNA (RAPD), and a morphological marker,\\u000a Alternaria brown spot resistance gene of citrus named as Cabsr caused by (Alternaria alternata f. sp. Citri) were used to establish genetic linkage map of citrus using a population of 164
Screening for resistance to cucurbit yellow stunting disorder virus, gummy stem blight, and monosporascus root rot and detection of RAPD markers associated with QLT for soluble solids, sugars, and vitamin C in melon (Cucumis melo l.)
Sinclair, Jonathan Walker
random amplified polymorphic DNA (RAPD) markers associated with quantitative trait loci (QTL) for each trait. Out of 500 primers, fifteen RAPD markers were found to be significantly associated with fruit quality QTL. These markers could be useful in a...
In Silico RAPD Priming Sites in Expressed Sequences and iSCAR Markers for Oil Palm
Premkrishnan, Balakrishnan Vasanthakumari; Arunachalam, Vadivel
RAPD is a simple dominant marker system widely used in biology. Effectiveness of RAPD can be improved by selecting and redesigning primers whose priming sites occur in target sequence(s) of gene or organism at optimum distance. We developed software that uses sequences of random decamer primers and nucleotide sequence(s) as two input files. It locates the priming sites in input sequences and generates output files listing frequency and distance between priming sites. When the priming sites of a single primer occur more than once in a sequence with a distance of 200 to 2000?bp, the software also designs pairs of iSCAR primers. An input of 387 RAPD primers and 42,432 expressed sequences of oil palm are used as test. Wet-lab PCR results from a publication that used the same set of primers were compared with software output on priming sites. In the test sequences of oil palm covering 1.4% of genome, we found that at least 60% the primers chosen using software are sure of giving PCR amplification. We designed 641 iSCAR primers suitable for amplification of oil palm DNA. The software successfully predicted 92% (67 out of 73) of published polymorphic RAPD primers in oil palm. PMID:22474414
Identification and confirmation of molecular markers and orange flesh color associated with major QTL for high beta-carotene content in muskmelon
Napier, Alexandra Bamberger
-carotene content, flesh color, and flesh color intensity. Bulk segregent analysis was used with RAPD markers to identify molecular markers associated with high beta-carotene content. Flesh color and flesh color intensity both had significant relationships with beta...
Generation and Characterization of SCARs by Cloning and Sequencing of RAPD Products: A Strategy for Species-specific Marker Development in Bamboo
• Background and Aims The aim of this study was to develop species-specific molecular markers for Bambusa balcooa and B. tulda to allow for their proper identification, in order to avoid unintentional adulteration that affects the quality and quantity of paper pulp production. • Methods Two putative, species-specific RAPD markers, Bb836 for B. balcooa and Bt609 for B. tulda were generated using a PCR-based RAPD technique. Species-specificity of these two markers was confirmed through Southern hybridization in which RAPD gels were blotted and hybridized with radiolabelled cloned RAPD markers. Southern hybridization analyses were also performed to validate homology of the co-migrating Bb836 and Bt609 marker bands amplified from 16 different populations of B. balcooa and B. tulda, respectively. Sequence-characterized amplified region (SCAR) markers were developed from Bb836 and Bt609 sequences, using 20-mer oligonucleotide primers designed from both the flanking ends of the respective RAPD primers. • Key Results As anticipated, Bb836 hybridized with an amplified band from B. balcooa and Bt609 hybridized only with an amplified product from B. tulda; the two markers did not hybridize with the amplified products of any of the other 14 bamboo species studied. The two pairs of SCAR primers amplified the target sequences only in the respective species. The species-specific SCAR fragments were named as 'Balco836' for B. balcooa and 'Tuldo609' for B. tulda. The species-specific 'Balco836' was amplified from the genomic DNA of 80 individuals of 16 populations of B. balcooa studied. Similarly, the presence of 'Tuldo609' was noted in all the 80 individuals representing 16 populations of B. tulda assessed. These SCAR fragments contained no obvious repetitive sequence beyond the primers. • Conclusion These two molecular markers are potentially useful for regulatory agencies to establish sovereign rights of the germplasms of B. balcooa and B. tulda. In addition, this is the first report of species-specific SCAR marker development in bamboo. PMID:15731116
A first linkage map of pecan cultivars based on RAPD and AFLP markers.
Beedanagari, Sudheer R; Dove, Sue K; Wood, Bruce W; Conner, Patrick J
We report here the first genetic linkage maps of pecan [Carya illinoinensis (Wangenh.) K. Koch], using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers. Independent maps were constructed for the cultivars 'Pawnee' and 'Elliot' using the double pseudo-testcross mapping strategy and 120 F1 seedlings from a full-sib family. A total of 477 markers, including 217 RAPD, 258 AFLP, and two morphological markers were used in linkage analysis. The 'Pawnee' linkage map has 218 markers, comprising 176 testcross and 42 intercross markers placed in 16 major and 13 minor (doublets and triplets) linkage groups. The 'Pawnee' linkage map covered 2,227 cM with an average map distance of 12.7 cM between adjacent markers. The 'Elliot' linkage map has 174 markers comprising 150 testcross and 22 intercross markers placed in 17 major and nine minor linkage groups. The 'Elliot' map covered 1,698 cM with an average map distance of 11.2 cM between adjacent markers. Segregation ratios for dichogamy type and stigma color were not significantly different from 1:1, suggesting that both traits are controlled by single loci with protogyny and green stigmas dominant to protandry and red stigmas. These loci were tightly linked (1.9 cM) and were placed in 'Elliot' linkage group 16. These linkage maps are an important first step towards the detection of genes controlling horticulturally important traits such as nut size, nut maturity date, kernel quality, and disease resistance. PMID:15782296
Evaluation of the extent of genetic variation in mahoganies (Meliaceae) using RAPD markers.
Chalmers, K J; Newton, A C; Waugh, R; Wilson, J; Powell, W
Despite the economic importance of mahoganies (Meliaceae) little is known of the pattern of genetic variation within this family of tropical trees. We describe the application of a polymerase chain reaction (PCR)-based polymorphic DNA assay procedure random amplified polymorphic DNAs (RAPDs) to assess the extent of genetic variation between eight mahogany species from four genera. Pronounced genetic differentiation was found between the species and genera. There was a clear separation of Cedrela odorata from the other species, with 95% of the variable amplification products differing, whereas Lovoa trichilioides, Khaya spp. and Swietenia spp. were more closely grouped. These results are consistent with the current taxonomic viewpoint. A number of markers were found to be diagnostic for particular species, which could be of value in determining the status of putative hybrids. The application of RAPDs to the study of genetic variation in mahoganies is discussed in the context of developing genetic conservation and improvement strategies for these species. PMID:24177901
Identification of RAPD markers linked to the gene PM?1 for resistance to powdery mildew in wheat
X. Y. Hu; H. W. Ohm; I. Dweikat
Powdery mildew caused by Blumeria graminis DC. f. sp. tritici?m. Marchal is an important disease of wheat (Triticum aestivum L. em Thell). We report here the identification of three random amplified polymorphic DNA (RAPD) markers closely linked to\\u000a a gene for resistance to B. graminis in wheat. RAPD-PCR (polymerase chain reaction) analysis was conducted using bulked segregant analysis of closely
Assessment of genetic fidelity of micropropagated plants of Simmondsia chinensis (Link) Schneider using RAPD and ISSR markers
Sunil Kumar; Manisha Mangal; A. K. Dhawan; Narender Singh
RAPD (random amplified polymorphic DNA) and ISSR (inter simple sequence repeat) markers were screened to test the genetic\\u000a integrity of jojoba (Simmondsia chinensis) plants multiplied through axillary bud multiplication from nodal segments. The in vitro raised plantlets were maintained\\u000a for up to 12 in vitro subcultures. During the study a total of 48 (32 RAPD and 16 ISSR) primers were
Specific genetic markers for wheat, spelt, and four wild relatives: comparison of isozymes, RAPDs, and wheat microsatellites.
Guadagnuolo, R; Bianchi, D S; Felber, F
Three types of markers-isozymes, RAPDs (random amplified polymorphic DNAs), and wheat microsatellites- were tested on wheat, spelt, and four wild wheat relatives (Aegilops cylindrica, Elymus caninus, Hordeum marinum, and Agropyron junceum). The aim was to evaluate their capability to provide specific markers for differentiation of the cultivated and wild species. The markers were set up for subsequent detection of hybrids and introgression of wheat DNA into wild relatives. All markers allowed differentiation of the cultivated from the wild species. Wheat microsatellites were not amplified in all the wild relatives, whereas RAPDs and isozymes exhibited polymorphism for all species. The dendrograms obtained with RAPD and isozyme data separated Swiss wheat cultivars from those collected in Austria and England, while no difference was found between Swiss spelt and wheat. RAPD data provided a weak discrimination between English and Austrian E. caninus. The microsatellite-based dendrogram discriminated populations of Ae. cylindrica, but no clear separation of H. marinum from E. caninus was revealed. The similarity matrices based on the three different sets of data were strongly correlated. The highest value was recorded between the matrices based on RAPDs and isozymes (Mantel's test, r = 0.93). Correlations between the similarity matrix based on microsatellites and matrices based on RAPDs and isozymes were lower: 0.74 and 0.68, respectively. While microsatellites are very useful for comparisons of closely related accessions, they are less suitable for studies involving less-related taxa. Isozymes provide interesting markers for species differentiation, but their use seems less appropriate for studies of within-species genetic variation. RAPDs can produce a large set of markers, which can be used for the evaluation of both between- and within-species genetic variation, more rapidly and easily than isozymes and microsatellites. PMID:11550895
Linkage map of the honey bee, Apis mellifera, based on RAPD markers
Hunt, G.J.; Page, R.E. Jr. [Univ. of California, Davis, CA (United States)
A linkage map was constructed for the honey bee based on the segregation of 365 random amplified polymorphic DNA (RAPD) markers in haploid male progeny of a single female bee. The X locus for sex determination and genes for black body color and malate dehydrogenase were mapped to separate linkage groups. RAPD markers were very efficient for mapping, with an average of about 2.8 loci mapped for each 10-nucleotide primer that was used in polymerase chain reactions. The mean interval size between markers on the map was 9.1 cM. The map covered 3110 cM of linked markers on 26 linkage groups. We estimate the total genome size to be {approximately}3450 cM. The size of the map indicated a very high recombination rate for the honey bee. The relationship of physical to genetic distance was estimated at 52 kb/cM, suggesting that map-based cloning of genes will be feasible for this species. 71 refs., 6 figs., 1 tab.
Genetic Diversity and Taxonomic Implication of Cordyceps sinensis as Revealed by RAPD Markers
Yongjiu Chen; Ya-Ping Zhang; Yuexiong Yang; Darong Yang
Random amplified polymorphic DNA (RAPD) markersare used to investigate genetic variation andevolutionary relationships of 29 samples of Cordycepssinensis from different geographical populations on theQinghai–Tibet plateau. Out of 137 RAPDbands scored, 100 are polymorphic. A correlation isrevealed between geographical distance and geneticdistance. The molecular phylogenetic tree suggests thatthe 29 samples are divided into three notableclusters, corresponding to the geographical populations,i.e., the
A genetic linkage map of lentil (Lens sp.) based on RAPD and AFLP markers using recombinant inbred lines
I. Eujayl; M. Baum; W. Powell; W. Erskine; E. Pehu
A genetic linkage map of Lens sp. was constructed with 177 markers (89 RAPD, 79 AFLP, six RFLP and three morphological markers) using 86 recombinant inbred\\u000a lines (F6:8) obtained from a partially interspecific cross. The map covered 1073?cM of the lentil genome with an average distance of\\u000a 6.0?cM between adjacent markers. Previously mapped RFLP markers were used as anchor probes.
Genetic diversity in Tunisian Crataegus azarolus L. var. aronia L. populations assessed using RAPD markers
Chayma Rajeb; Chokri Messaoud; Hnia Chograni; Afef Bejaoui; Abdennacer Boulila; Mohamed Nejib Rejeb; Mohamed Boussaid
– \\u000a \\u000a • The genetic diversity of nine wild Tunisian Crataegus azarolus var. aronia L. populations from different bioclimates was assessed using RAPD markers.\\u000a \\u000a \\u000a \\u000a \\u000a – \\u000a \\u000a • Eight selected primers generated a total of 105 bands, 81 of which were polymorphic. Shannon's index (H?) ranged from 0.222 to 0.278 according to a population with an average of 0.245. The genetic variation within
Molecular identification and the features of genetic diversity in interspecific hybrids of Amur sturgeon ( Acipenser schrenckii × A. baerii, A. baerii × A. schrenckii, A. schrenckii × A. ruthenus , and A. ruthenus × A. schrenckii ) based on variability of multilocus RAPD markers
K. V. Rozhkovan; G. N. Chelomina; E. I. Rachek
The method of polymerase chain reaction with random primers (RAPD PCR) was used to identify the progeny of the crosses between\\u000a three sturgeon species, Amur sturgeon (Acipenser schrenckii Brandt, 1869), Siberian sturgeon (A. baerii Brandt, 1869), and sterlet (A. ruthenus Linnaeus, 1758). Using ten primers, genetic variation in 70 yearlings, produced in seven individual crosses: Acipenser schrenckii × A. schrenckii,
Novel male-specific molecular markers (MADC5, MADC6) in hemp
Ottó Törjék; Nándor Bucherna; Erzsébet Kiss; Hajnalka Homoki; Zsuzsanna Finta-Korpelová; Iván Bócsa; István Nagy; László E. Heszky
Decamer RAPD primers were tested on dioecious and monoecious hemp cultivars to identify sex-specific molecular markers. Two\\u000a primers (OPD05 and UBC354) generated specific bands in male plants. These two DNA fragments were isolated, cloned and sequenced.\\u000a Both markers proved to be unique, since no sequence with significant homology to OPD05961 and UBC354151 markers were found in databases. These markers were
Megagametophyte-derived linkage maps of white spruce ( Picea glauca ) based on RAPD, SCAR and ESTP markers
I. Gosselin; Y. Zhou; J. Bousquet; N. Isabel
We have constructed linkage maps for two parents of white spruce [Picea glauca (Moench) Voss]. Haploid megagametophytes from 92 and 96 seeds of parents M2 and 80132, respectively, were analysed with RAPD, SCAR and ESTP markers. Fragments segregating in a 1:1 Mendelian ratio were classified and mapped using MAPMAKER, GMENDEL and JOINMAP. For M2, the analysis with JOINMAP resulted in
A RAPD-derived STS marker is linked to a bacterial wilt ( Burkholderia caryophylli ) resistance gene in carnation
Takashi Onozaki; Natsu Tanikawa; Mitsuyasu Taneya; Kiyofumi Kudo; Takuya Funayama; Hiroshi Ikeda; Michio Shibata
Bacterial wilt caused by Burkholderia caryophylli is one of the most important and damaging diseases of carnations (Dianthus caryophyllus) in Japan. We aimed to identify random amplified polymorphic DNA (RAPD) markers associated with the genes controlling bacterial wilt resistance in a resistance-segregating population of 134 progeny plants derived from a cross between 'Carnation Nou No. 1' (a carnation breeding line
Detection and genetic distance of resistant populations of Pseudosuccinea columella (Mollusca: Lymnaeidae) to Fasciola hepatica (Trematoda: Digenea) using RAPD markers
Aymé Fernandez Calienes; Jorge Fraga; Jean-Pierre Pointier; Mary Yong; Jorge Sanchez; Christine Coustau; Alfredo Gutiérrez; André Théron
Twelve natural populations of Pseudosuccinea columella snails, sampled in the western and central regions of Cuba, were analyzed using the RAPD-PCR technique to screen for resistance to Fasciola hepatica. Ten OPA primers previously shown to produce marker bands for resistance and susceptibility were tested. A new population of P. columella (El Azufre, Pinar del R??o) exhibited the amplification patterns of
Identification of genetically diverse genotypes for photoperiod insensitivity in soybean using RAPD markers.
Singh, R K; Bhatia, V S; Yadav, Sanjeev; Athale, Rashmi; Lakshmi, N; Guruprasad, K N; Chauhan, G S
Most of the Indian soybean varieties were found to be highly sensitive to photoperiod, which limits their cultivation in only localized area. Identification of genetically diverse source of photoperiod insensitive would help to broaden the genetic base for this trait. Present study was undertaken with RAPD markers for genetic diversity estimation in 44 accessions of soybean differing in response to photoperiod sensitivity. The selected twenty-five RAPD primers produced a total of 199 amplicons, which generated 89.9 % polymorphism. The number of amplification products ranged from 2 to 13 for different primers. The polymorphism information content ranged from 0.0 for monomorphic loci to 0.5 with an average of 0.289. Genetic diversity between pairs of genotypes was 37.7% with a range of 3.9 to 71.6%. UPGMA cluster analysis placed all the accessions of soybean into four major clusters. No discernable geographical patterns were observed in clustering however; the smaller groups corresponded well with pedigree. Mantel's test (r = 0.915) indicates very good fit for clustering pattern. Two genotypes, MACS 330 and 111/2/1939 made a very divergent group from other accessions of soybean and highly photoperiod insensitive that may be potential source for broadening the genetic base of soybean for this trait. PMID:23572904
Gene flow from wheat (Triticum aestivum L.) to jointed goatgrass (Aegilops cylindrica Host.), as revealed by RAPD and microsatellite markers
R. Guadagnuolo; D. Savova-Bianchi; F. Felber
In order to estimate the potential of gene flow between wheat (Triticum ?stivum L.) and jointed goatgrass (Aegilops cylindrica Host.), we carried out mixed pollinations in experimental and natural conditions. A set of species-specific RAPD (random\\u000a amplified polymorphic DNA) and microsatellite markers were used to detect the presence of parental markers in the progeny\\u000a of the plants used in these
Genetic stability of micropropagated almond plantlets, as assessed by RAPD and ISSR markers
M. Martins; D. Sarmento; M. M. Oliveira
Almond shoots produced by axillary branching from clone VII derived from a seedling of cultivar Boa Casta were evaluated for somaclonal variation using randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) analysis. To verify genetic stability we compared RAPD and ISSR patterns of plantlets obtained after 4 and 6 years of in vitro multiplication. A total of 64 RAPD
Detection and genetic distance of resistant populations of Pseudosuccinea columella (Mollusca: Lymnaeidae) to Fasciola hepatica (Trematoda: Digenea) using RAPD markers.
Calienes, Aymé Fernandez; Fraga, Jorge; Pointier, Jean-Pierre; Yong, Mary; Sanchez, Jorge; Coustau, Christine; Gutiérrez, Alfredo; Théron, André
Twelve natural populations of Pseudosuccinea columella snails, sampled in the western and central regions of Cuba, were analyzed using the RAPD-PCR technique to screen for resistance to Fasciola hepatica. Ten OPA primers previously shown to produce marker bands for resistance and susceptibility were tested. A new population of P. columella (El Azufre, Pinar del Río) exhibited the amplification patterns of resistant snails, and its resistant status was confirmed after experimental exposure to miracidia. No genetic variability was detected across or within the susceptible isolates. Similarly, the novel resistant isolate displayed an RAPD profile identical to the profile of two other isolates previously identified as resistant to F. hepatica. However, clear differences in RAPD banding patterns and genetic distance were observed between resistant and susceptible isolates. PMID:15301979
A molecular marker-based linkage map of diploid bananas ( Musa acuminata )
S. Fauré; J. L. Noyer; J. P. Horry; F. Bakry; C. Lanaud; D. Go?zalez de León
A partial molecular linkage map of the Musa acuminata diploid genome is presented. This map is based on 58 RFLP, four isozyme and 28 RAPD markers segregating in an F2 population of 92 individuals. A total of 90 loci was detected, 77 of which were placed on 15 linkage groups while 13 segregated independently. Segregation distortions were shown by 36%
Identification and localization of molecular markers linked to the Lr 9 leaf rust resistance gene of wheat
G. Schachermayr; H. Siedler; M. D. Gale; H. Winzeler; M. Winzeler; B. Keller
Near-isogenic lines (NILs) for the leaf rust resistance gene Lr9 were screened for polymorphisms at the molecular level. RAPD (random amplified polymorphic DNA) primers as well as RFLP (restriction fragment length polymorphism) markers were used. Out of 395 RAPD primers tested, three showed polymorphisms between NILs, i.e., an additional band was found in resistant lines. One of these polymorphic bands
Molecular characterization of Desmodium species--an important ingredient of 'Dashmoola' by RAPD analysis.
Irshad, Saba; Singh, Jyotsna; Kakkar, Poonam; Mehrotra, Shanta
Identification of medicinal plants by their molecular signature is a fast growing tool. The identification of Desmodium gangeticum (L.) DC. (Shalparni, a constituent of Ayurvedic formulation "Dashmoolarishtha") was carried out using genomic approach. Authentic samples of D. gangeticum(L.) DC., D. velutinum (Willd.) DC. and D. triflorum (L.) DC. were analyzed and compared to commercial samples of various origin. Within twenty primers used, eleven gave 223 RAPD fragments. RAPD profiles of three species showed very low similarity index (0.21-0.39), whereas market samples showed high similarity of 0.82-0.89 with authenticated D. gangeticum. PMID:19100816
Random amplified polymorphic DNA (RAPDs) markers for genetic analysis in micropropagated plants of Robinia pseudoacacia L
K. Kanwar; K. Bindiya
Four years' old micropropagated plants regenerated by enhanced axillary branching from shoot buds of a single genotype of\\u000a Robinia pseudoacacia were characterized by RAPDs. Random amplified polymorphic DNA analysis was carried outusing 19 random 10-mer DNA primers\\u000a and 286 RAPD bands were examined which showed 30% polymorphism. Similarity indices ranged from 0.86 to 0.96 among different\\u000a plants based on RAPD
Molecular characterization of shiitake medicinal mushroom, Lentinus edodes strains (higher Basidiomycetes) using RAPD and ITS sequencing.
Sharma, Shivani; Khanna, Pardeep Kumar; Kapoor, Shammi
The molecular phylogeny in seven strains of Lentinus edodes was studied based on RAPD and their internal transcribed spacers (ITS) regions. The strains were analyzed by RAPD with 20 arbitrary primers. Fifteen primers were found efficient for the amplification of the genomic DNA. The size of the polymorphic bands were in the range of 100-1000 bp. However, the size of ITS1-2 and ITS1-4 regions varied among the strains from 278 to 575 bp and from 410 to 616 bp, respectively. The higher alignment score of the ITS 1-2 region indicated more variability in the ITS 1-4 region. Thus, on the basis of RAPD-PCR and ITS sequencing it was found that strains LeC and LeI showed a high degree of divergence from all other strains. PMID:24941038
Random amplified polymorphic DNA (RAPD) markers reveal genetic homogeneity in the endangered Himalayan species Meconopsis paniculata and M. simplicifolia
Irshad M. Sulaiman; Seyed E. Hasnain
Random amplified polymorphic DNA (RAPD) marker-based analysis was carried out to study the extent of genetic polymorphism between populations of the two endangered Himalayan poppy species, Meconopsis paniculata and M. Simplicifolia. Of the 90 primers tested, 38 revealed marked inter-species genetic polymorphism between individuals of the two species from geographically isolated populations. However, intra-species genetic homogeneity was also evident with
Identification of RAPD markers linked to a Phytophthora fragariae resistance gene (Rpf1) in the cultivated strawberry
K. M. Haymes; B. Henken; T. M. Davis; W. E. van de Weg
Bulked segregant analysis (BSA) was used to identify seven random amplified polymorphic DNA (RAPD) markers linked to the\\u000a Rpf?1 gene. Rpf?1 confers resistance to Phytophthora fragariae var. fragariae, the causal agent of red stele root rot in Fragaria spp. The bulked DNAs represented subsets of a F1 population obtained from the cross Md683×Senga Sengana which consisted of 60 plants and
Analysis of genetic diversity through AFLP, SAMPL, ISSR and RAPD markers in Tribulus terrestris , a medicinal herb
Maryam Sarwat; S. Das; P. S. Srivastava
Tribulus terrestris is well known for its medicinal importance in curing urino-genital disorders. Amplified fragment length polymorphism (AFLP),\\u000a selective amplification of microsatellite polymorphic loci (SAMPL), inter-simple sequence repeat (ISSR) and randomly amplified\\u000a polymorphic DNA (RAPD) markers were used for the first time for the detection of genetic polymorphism in this medicinal herb\\u000a from samples collected from various geographical regions of
Genetic mapping of RAPD markers linked to the densonucleosis refractoriness gene, nsd-1, in the silkworm, Bombyx mori.
Abe, H; Harada, T; Kanehara, M; Shimada, T; Ohbayashi, F; Oshiki, T
In the silkworm, Bombyx mori, nonsusceptibility to B. mori densonucleosis virus type-1 (BmDNV-1) is controlled by a recessive gene, nsd-1 (nonsusceptibility to DNV-1), located on the twenty-first chromosome. We investigated genetic linkage between five random amplified polymorphic DNA (RAPD) markers and the +nsd-1 gene. Initially, we constructed the CSD-1 strain (nsd-1/+) which is congenic to strain C137 (nsd-1/nsd-1) for the twenty-first chromosome, starting with a female of C137 and a male of strain J137 (+nsd-1/+nsd-1). For the crossing over experiment, a female of C137 was crossed with a male (nsd-1/+) of CSD-1. Segregation analysis showed that the most closely linked RAPD marker mapped 3.0 cM distant from +nsd-1. A more specific marker for +nsd-1 was made by converting this RAPD band into a sequence characterized amplified region (SCAR) using a series of newly designed primer pairs based on its DNA sequence. PMID:9880921
Genetic differentiation induced by selection in an inbred population of the silkworm Bombyx mori, revealed by RAPD and ISSR marker systems.
Pradeep, Appukuttan R; Chatterjee, Shankar N; Nair, Chirakkara V
Artificial selection has been widely utilized in breeding programmes concerning the commercially important silk-producing insect Bombyx mori. Selection increases the frequency of homozygotes and makes homozygous effects stronger. Molecular variation induced by selection in the inbred population of B. mori strain Nistari, was assessed in terms of genic differentiation by using a polymorphic profile generated by RAPD and ISSR marker systems. Artificial selection for longer larval duration (LLD) for 4 generations resulted in a significant prolongation of larval duration (F = 89.28; P = 5.14 x 10(-7)). The lines selected for shorter larval duration (SLD) were not significantly different from the control group. RAPD and ISSR primers generated polymorphic profiles when amplified with genomic DNA of individuals of LLD and SLD lines. Distinct markers specific to LLD individuals were observed from the 3rd generation and indicated selection-induced differentiation of allelic variants for longer larval duration. Both SLD and LLD were characterized by high gene diversity (h approximately equal to 0.197) and total heterozygosity (Ht > or =0.26), low homogeneity (chi-square test, p < 0.005) as well as a large coefficient of gene differentiation (Gst > or =0.42) but low gene flow (Nm < or =0.42). Genetic distance was the highest (0.824) between 3rd generations of SLD and LLD. High heterozygosity and prolonged larval duration substituted for shorter larval duration (the traditional trait of fitness) in the Nistari LLD larvae. PMID:16110186
The use of RAPD markers to distinguish among juniper and cedar cultivars
Hsiang, Tom
. and Juniperus scopulorum Sarg. (Cupressaceae) were subjected to random amplified polymorphic DNA (RAPD) analysis Huang Abstract: Two species of Chamaecyparis and six cultivars each of Juniperus chinensis L Juni- perus scopulorum Sarg. (Cupressaceae) respectivement, ŕ l'analyse RAPD, ŕ l'aide de sept amorces
Microevolutionary Patterns and Molecular Markers: The Genetics of Geographic Variation in Ascaris suum
Nadler, S. A.
Molecular markers have been used only rarely to characterize the population genetic structure of nematodes. Published studies have suggested that different taxa may show distinct genetic architectures. Isoenzyme and RAPD markers have been used to investigate geographic variation of Ascaris suum at the level of infrapopulations (nematodes within individual hosts), within localities, and among geographic regions. Independent estimates of genetic differentiation among population samples based on isoenzyme and RAPD data showed similar patterns and substantial correlation. Heterozygote deficiencies within infrapopulations and large values for inbreeding coefficients among infrapopulations suggested that the composition of these populations was not consistent with a model of random recruitment from a large panmictic pool of life-cycle stages. Both isoenzyme and RAPD markers revealed moderate levels of genetic differentiation among samples representing infrapopulations and localities. Of total gene diversity, 9.4% (isoenzyme) and 9.2% (RAPD) was partitioned among infrapopulations. Geographic localities accounted for 7.8% (isoenzyme) and 6.2% (RAPD) of total diversity. Only infrapopulations from the same farm had low levels of differentiation. PMID:19277145
Identification of specific molecular markers linked to the rust resistance gene M4 in flax
T. Y. Bo; J. J. Ma; J. X. Chen; T. Y. Miao; W. X. Zhai
To identify molecular markers linked to the flax rust-resistance gene M4, RAPD analysis of NM4 (a near-isogenic line containing the M4 gene) and the recurrent parent Bison was performed using 540 decamer primers. The primer OPA18 amplified a specific fragment,\\u000a OPA18432, in the NM4 line. The OPA18432 marker was found to be closely linked to the M4 gene, with a
Evaluation of genetic diversity among Chinese Pleurotus eryngii cultivars by combined RAPD/ISSR marker.
Wang, Shouxian; Yin, Yonggang; Liu, Yu; Xu, Feng
Pleurotus eryngii (DC. Ex. Fr.) Quél is a rare precious edible fungus which belongs to the family Pleurotaceae. This mushroom has highly nutritional, pharmaceutical, economic and ecological values. In the present study, combined randomly amplified polymorphic DNA (RAPD)/inter-simple sequence repeat (ISSR) was used to assess the genetic diversity of P. eryngii strains cultivated in China. For the RAPD and ISSR analyses, 404 and 392 polymorphic bands were obtained from 32 P. eryngii strains using 28 and 24 selected primers, respectively. A combined RAPD/ISSR dendrogram grouped the 32 strains into five clades with coefficient of 0.770. The comparison of RAPD and ISSR was also elucidated in the present study. The results of our study obtained by combined RAPD/ISSR analysis contributed to a better understanding of the genetic relationships among the P. eryngii strains and provide orientation for the strain improvement of P. eryngii species. PMID:22760248
Genetics of resistance to ascochyta blight (Ascochyta lentis) of lentil and the identification of closely linked RAPD markers
R. Ford; E. C. K. Pang; P. W. J. Taylor
Foliar resistance to Ascochyta lentis is controlled at a single major locus by a dominant gene (AbR\\u000a \\u000a \\u000a \\u000a 1\\u000a \\u000a ) in the lentil accession ILL5588 (cv 'Northfield'). Flanking RAPD markers that are closely linked to the resistance locus\\u000a in coupling phase were identified by bulked segregant analysis. Out of 261 decanucleotide primers screened 7 produced a polymorphic\\u000a marker that segregated with
Evaluation of genetically modified sugarcane lines carrying Cry 1AC gene using molecular marker techniques.
Ismail, Roba M
Five genetically modified insect resistant sugarcane lines harboring the Bt Cry 1AC gene to produce insecticidal proteins were compared with non-transgenic control by using three types of molecular marker techniques namely, RAPD, ISSR and AFLP. These techniques were applied on transgenic and non-transgenic plants to investigate the genetic variations, which may appear in sugarcane clones. This variation might demonstrate the genomic changes associated with the transformation process, which could change important molecular basis of various biological phenomena. Genetic variations were screened using 22 different RAPD primers, 10 ISSR primers and 13 AFLP primer combinations. Analysis of RAPD and ISSR banding patterns gave no exclusive evidence for genetic variations. Meanwhile, the percentage of polymorphic bands was 0.45% in each of RAPD and ISSR, while the polymorphism generated by AFLP analysis was 1.8%. The maximum percentage of polymorphic bands was 1.4%, 1.1% and 5.5% in RAPD, ISSR and AFLP, respectively. These results demonstrate that most transgenic lines showed genomic homogeneity and verified minor genomic changes. Dendrograms revealing the relationships among the transgenic and control plants were developed from the data of each of the three marker types. PMID:23549345
Identification and validation of molecular markers linked to the leaf rust resistance gene Lr19 in wheat.
Gupta, Sudhir Kumar; Charpe, Ashwini; Prabhu, Kumble Vinod; Haque, Qazi Mohammad Rizwanul
A leaf rust resistance gene Lr19 on the chromosome 7DL of wheat derived from Agropyron elongatum was tagged with random amplified polymorphic DNA (RAPD) and microsatellite markers. The F(2) population of 340 plants derived from a cross between the leaf rust resistant near-isogenic line (NIL) of Thatcher (Tc + Lr19) and leaf rust susceptible line Agra Local that segregated for dominant monogenic leaf rust resistance was utilized for generating the mapping population. The molecular markers were mapped in the F(2) derived F(3) homozygous population of 140 seedlings. Sixteen RAPD markers were identified as linked to the alien gene Lr19 among which eight were in a coupling phase linkage. Twelve RAPD markers co-segregated with Lr19 locus. Nine microsatellite markers located on the long arm of chromosome 7D were also mapped as linked to the gene Lr19, including 7 markers which co-segregated with Lr19 locus, thus generating a saturated region carrying 25 molecular markers linked to the gene Lr19 within 10.2 +/- 0.062 cM on either side of the locus. Two RAPD markers S265(512) and S253(737) which flanked the locus Lr19 were converted to sequence characterized amplified region markers SCS265(512) and SCS253(736), respectively. The marker SCS265(512) was linked with Lr19 in a coupling phase and the marker SCS253(736) was linked in a repulsion phase, which when used together mimicked one co-dominant marker capable of distinguishing the heterozygous resistant seedlings from the homozygous resistant. The molecular markers were validated on NILs mostly in Thatcher background isogenic for 44 different Lr genes belonging to both native and alien origin. The validation for polymorphism in common leaf rust susceptible cultivars also confirmed the utility of these tightly linked markers to the gene Lr19 in marker-assisted selection. PMID:16896713
Identification of a RAPD marker linked to sex determination in the basket willow (Salix viminalis L.)
C. Alstrom-Rapaport; M. Lascoux; Y. C. Wang; G. Roberts; G. A. Tuskan
In many dioecious plants, gender influences economic value, breeding schemes, and\\/or opportunities for commercial use of genetically transformed materials. The objective of this study was to identify molecular markers linked to sex determina- tion loci in the dioecious plant Salix viminalis L. A 4 3 4 factorial mating design was used to identify sex ratios in full-sibling progeny, to generate
Genetic diversity of bitter gourd ( Momordica charantia L.) genotypes revealed by RAPD markers and agronomic traits
S. S. Dey; A. K. Singh; D. Chandel; T. K. Behera
Bitter gourd or bitter melon (Momordica charantia L.) is considered as minor cucurbitaceous vegetable in spite of having considerable nutritional and medicinal properties. Although some reports on genetic diversity based on morphological characterization are available, no work has been conducted to estimate genetic diversity using molecular markers in this crop. In the present study, 38 genotypes of M. charantia including
Conservation genetics of endangered Brasenia schreberi based on RAPD and AFLP markers
Changkyun Kim; Hye Ryun Na; Hong-Keun Choi
Brasenia schreberi J.F. Gmelin is a declared endangered species found in the lakes and ponds of South Korea. For planning its conservation strategy,\\u000a we examined the genetic diversity within and among six populations, using randomly amplified polymorphic DNA (RAPD) and amplified\\u000a fragment length polymorphism (AFLP). Polymorphisms were more frequently detected per loci with AFLP (69.3%) than RAPD (36.8%).\\u000a High genetic
The use of RAPD markers to distinguish among juniper and cedar cultivars
Tom Hsiang; Junbin Huang
Abstract: Two species of Chamaecyparis,and six cultivars each of Juniperus chinensis L. and Juniperus scopulorum Sarg. (Cupressaceae) were,subjected to random,amplified polymorphic,DNA (RAPD) analysis using seven primers. Un- weighted,pair group method,with averages (UPGMA) and principal component,analyses of genetic distances between cultivars showed,that 42 polymorphic,RAPD bands could distinguish among,all cultivars and properly group them,by species and genera. Where the origin of a
High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers
Medhi, K.; Sarmah, D.K.; Deka, M.; Bhau, B.S.
The genetic diversity in Zanthoxylum species viz. Zanthoxylum nitidum, Zanthoxylum oxyphyllum and Zanthoxylum rhesta collected from the Upper Brahmaputra Valley Zone of Assam (NE India) was amplified using 13 random amplified polymorphic DNA (RAPD) markers and 9 inter-simple sequence repeat (ISSR) markers. RAPD markers were able to detect 81.82% polymorphism whereas ISSR detected 98.02% polymorphism. The genetic similarities were analyzed from the dendrogram constructed by RAPD and ISSR fingerprinting methods which divided the 3 species of Zanthoxylum into 3 clear different clusters. The principle component analysis (PCA) was carried out to confirm the clustering pattern of RAPD and ISSR analysis. Analysis of molecular variance (AMOVA) revealed the presence of significant variability between different Zanthoxylum species and within the species by both RAPD and ISSR markers. Z. nitidum was found to be sharing a high degree of variation with the other two Zanthoxylum species under study. The Nei's gene diversity (h), Shannon's information index (I), observed number of alleles (na) and effective number of alleles (ne) were also found to be higher in ISSR markers (0.3526, 0.5230, 1.9802 and 1.6145) than in RAPD markers (0.3144, 0.4610, 1.8182 and 1.5571). The values for total genotype diversity for among population (HT), within population diversity (Hs) and gene flow (Nm) were more in ISSR (0.3491, 0.2644 and 1.5610) than RAPD (0.3128, 0.2264 and 1.3087) but the mean coefficient of gene differentiation (GST) was more in RAPD (0.2764) than ISSR (0.2426). A comparison of this two finger printing methods was done by calculating MR, EMI and MI. The correlation coefficient between data matrices of RAPD and ISSR based on Mantel test was found to be significant (r = 0.65612). PMID:25606454
Random amplified polymorphic DNA (RAPD) markers for genetic analysis in Allium
Susan E. Wilkie; Peter G. Isaac; Robert J. Slater
RAPD analysis was applied to onion (Allium cepa) and otherAllium species in order to assess the degree of polymorphism within the genus and to investigate if this approach was suitable for genetic studies of onion. Seven cultivars ofA. cepa, including shallot, and single cultivars of Japanese bunching onion (A. fistulosum), chive (A. schoenoprasum), leek (A. ampeloprasum), and a wild relative
Genetic diversity of Central Asian and north Caucasian Aegilops species as revealed by RAPD markers
Kazutoshi Okuno; Kaoru Ebana; Bayarsukh Noov; Hisashi Yoshida
RAPD analysis of 112 accessions of Aegilops tauschii Coss. (genome DD), Ae. cylindrica Host (CCDD), Ae. crassa Boiss. (DDMM), Ae. biuncialis Vis. (UUMM) and Ae. triuncialis L. (UUCC) collected in the Central Asia and north Caucasia was conducted. Aegilops accessions were divided into two major groups, corresponding to the D genome species and the U genome species. These groups were
Sequence comparison of two codominant RAPD markers in Brassica nigra: deletions, substitutions and microsatellites
C. F. Quiros; M. J. Truco; J. Hu
Two RAPD fragments segregating codominantly were investigated in a F2 population of Brassica nigra. Southern hybridization of these DNA fragments to genomic B. nigra DNA digested with several endonucleases revealed similar restriction profiles. Sequencing of the two fragments disclosed 93% homology. The differences were due mainly to an internal 41 nucleotide deletion in one of the fragments. Minor deletions of
Genetic variation detected with RAPD markers among upland and lowland rice cultivars ( Oryza sativa L.)
L.-X. Yu; H. T. Nguyen
Genetic variation of nine upland and four lowland rice cultivars (Oryza sativa L.) was investigated at the DNA level using the randomly amplified polymorphic DNA (RAPD) method via the polymerase chain reaction (PCR). Forty-two random primers were used to amplify DNA segments and 260 PCR products were obtained. The results of agarosegel electrophoretic analysis of these PCR products indicated that
Identification of RAPD markers linked to a fertility restorer gene for the Ogura radish cytoplasmic male sterility of rapeseed ( Brassica napus L.)
R. Delourme; A. Bouchereau; N. Hubert; M. Renard; B. S. Landry
Bulked segregant analysis was employed to identify random amplified polymorphic DNA (RAPD) markers linked to the restorer gene (Rfo) used in theOgura radish cytoplasmic male sterility of rapeseed. A total of 138 arbitrary 10-mer oligonucleotide primers were screened on the DNA of three pairs of bulks, each bulk corresponding to homozygous restored and male sterile plants of three segregating populations.
Genetic variation analysis of the genus Passiflora L. using RAPD markers
Diego Fajardo; Fernando Angel; Mikkel Grum; Joe Tohme; Mario Lobo; William M. Roca; Inés Sanchez
Genetic analysis based on Random Amplified Polymorphic DNA (RAPD) was carried out on 52 accessions representing 14 species\\u000a of the genus Passiflora L. using 50 random 10-mer primers. A dendrogram constructed using the Dice similarity coefficient\\u000a and the UPGMA algorithm based on 626 reproducible polymorphic products ranging in size from 2.8 to 0.3 Kb revealed high levels\\u000a of variation within
Micropropagation and validation of genetic and biochemical fidelity amongst regenerants of Cassia angustifolia Vahl employing RAPD marker and HPLC.
Chetri, Siva K; Sardar, Pratima Rani; Agrawal, Veena
In vitro protocol has been established for clonal propagation of Cassia angustifolia Vahl which is an important source of anticancerous bioactive compounds, sennoside A and B. Nodal explants excised from field raised elite plant (showing optimum level of sennoside A and B) of C. angustifolia when reared on Murashige and Skoog's medium augmented with different cytokinins, viz. N(6)-benzyladenine (BA), N(6)-(2-isopentenyl) adenine (2iP) and 6-furfuryl aminopurine (Kn) differentiated multiple shoots in their axils. Of the three cytokinins, BA at 5 ?M proved optimum for differentiating multiple shoots in 95 % cultures with an average of 9.14 shoots per explant within 8 weeks of culture. Nearly, 95 % of the excised in vitro shoots rooted on half strength MS medium supplemented with 10 ?M indole-3-butyric acid (IBA). The phenotypically similar micropropagated plants were evaluated for their genetic fidelity employing random amplified polymorphic DNA (RAPD) markers. Eleven individuals, randomly chosen amongst a population of 120 regenerants were compared with the donor plant. A total of 36 scorable bands, ranging in size from 100 to 1,000 bp were generated amongst them by the RAPD primers. All banding profiles from micropropagated plants were monomorphic and similar to those of mother plant proving their true to the type nature. Besides, high performance liquid chromatography evaluation of the sennoside A and B content amongst leaves of the mature regenerants and the elite mother plant too revealed consistency in their content. PMID:25320475
Molecular marker-based characterization in candidate plus trees of Pongamia pinnata, a potential biodiesel legume
Kesari, Vigya; Madurai Sathyanarayana, Vinod; Parida, Ajay; Rangan, Latha
Background and aims Pongamia pinnata, a legume tree, has many traditional uses and is a potential biodiesel plant. Despite its importance and the availability of appropriate molecular genetic tools, the full potential of Pongamia is yet to be realized. The objective of this study was to assess genetic diversity among 10 systematically characterized candidate plus trees (CPTs) of P. pinnata from North Guwahati. Methodology The application and informativeness of polymerase chain reaction-based molecular markers [random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP)] to assess the genetic variability and relatedness among 10 CPTs of P. pinnata were investigated. Principal results Polymorphism rates of 10.48, 10.08 and 100 % were achieved using 18 RAPD, 12 ISSR and 4 AFLP primer combinations, respectively. Polymorphic information content (PIC) varied in the range 0.33–0.49, 0.18–0.49 and 0.26–0.34 for RAPD, ISSR and AFLP markers, respectively, whereas the corresponding average marker index (MI) values for the above markers were 7.48, 6.69 and 30.75. Based on Nei's gene diversity and Shannon's information index, inter-population diversity (hsp) was highest when compared with intra-population diversity (hpop) and the gene flow (Nm) ranged from a moderate value of 0.607 to a high value of 6.287 for the three DNA markers. Clustering of individuals was not similar when RAPD- and ISSR-derived dendrogram analyses were compared with that of AFLP. The Mantel test cophenetic correlation coefficient was higher for AFLP (r = 0.98) than for ISSR (r = 0.73) and RAPD (r = 0.84). Molecular markers discriminated the individuals efficiently and generated a high similarity in dendrogram topologies derived using unweighted pair-group arithmetic average, although some differences were observed. The three-dimensional scaling by principal coordinate analysis supported the result of clustering. Conclusions Comparing the results obtained with the three DNA markers, AFLP indicated higher efficiency for estimating the levels of genetic diversity and proved to be reliable for fingerprinting, mapping and diversity studies in Pongamia in view of their suitability for energy production purposes. PMID:22476075
Technology Transfer Automated Retrieval System (TEKTRAN)
Advances in genomic analysis and application of marker-assisted selection to oat genetic improvement is currently limited by a lack of genomic information and molecular genetic tools, particularly user-friendly molecular markers adapted to high-throughput technology. Identification of such markers i...
Identification of RAPD markers linked to the Uvf-1 gene conferring hypersensitive resistance against rust (Uromyces viciae-fabae) in Vicia faba L.
Avila, C M; Sillero, J C; Rubiales, D; Moreno, M T; Torres, A M
Bulk segregant analysis was used to identify random amplified polymorphic DNA (RAPD) markers linked to a gene determining hypersensitive resistance in Vicia faba line 2N52 against race 1 of the rust fungus Uromyces viciae-fabae. The monogenic nature of the resistance was determined by analyzing the F(2) population from a cross between resistant line 2N52 and susceptible line VF-176, and further confirmed in the F(2:3)-derived families. Linkage of the RAPD markers was confirmed by screening 55 F(2) plants segregating for resistance. Three RAPD markers (OPD13(736), OPL18(1032) and OPI20(900)) were mapped in coupling phase to the resistance gene for race 1 ( Uvf-1). No recombinants between OPI20(900) and Uvf-1 were detected. Two additional markers (OPP02(1172) and OPR07(930)) were linked to the gene in repulsion phase at a distance of 9.9 and 11.5 cM, respectively. The application of marker-assisted selection to develop new faba bean varieties with rust resistance genes is discussed. PMID:12698251
Identification of RAPD markers linked to digestive amylase genes using near isogenic lines of the silkworm, Bombyx mori.
Ashwath, S K; Sreekumar, S; Toms, J T; Dandin, S B; Kamble, C K
Digestive amylase has been identified as a useful marker for breeding in the silkwrom, Bombyx mori L (Lepidoptera: Bombycidae), due to its wide genetic divergence, its role in better digestibility and robustness. The low yielding indigenous B. mori breeds of tropics like India are characterized by high activity amylase genes controlled by Amy d(iv) or d(v) alleles, while the high yielding breeds of temperate origin are endowed with 'null' type (Amy d(n)) with low activity. For improving the digestibility and survival of temperate breeds of Japanese origin, Near Isogenic Lines (NILs) were developed introgressing the Amy d(iv) and d(v) alleles from the Donor Parents (DPs) into the genetic background of the Recurrent Parents (RPs) with 'null' type of amylase, which showed significant improvement in viability of the NILs. With the objective to know whether the amylase gene itself may confer higher survival by improving digestibility or some other closely linked genes flanking the amylase locus is responsible for better viability of the NILs, RAPD profiles among six B. mori breeds comprising of the DPs, RPs, and NILs developed through introgression of Amy d(iv) or d(v) alleles were analysed using 27 sets of RAPD primers. Out of the 27 primers, six (OPA01, OPA06, OPA09, OPA15, OPAH03, and OPAH05) showed RAPD products linked to the amylase genes of the DPs introgressed in the NILs, which were absent in their respective RPs. Three amplicons of 1584 bp, 1904 bp, and 1232 bp were specific to Amy d(iv) allele and one amplified product of 1776 bp was found to be linked with the Amy d(v) allele. Interestingly, two PCR products of 2628 and 1375 bp were associated with both Amy d(iv) and d(v) alleles. The results are discussed in light of further characterization of these amplified products leading to identification of DNA sequences that may be responsible for better digestibility and higher survival in B. mori. PMID:20673069
Species-diagnostic markers in Larix spp. based on RAPDs and nuclear, cpDNA, and mtDNA gene sequences, and their phylogenetic implications
Marie-Claude Gros-Louis; Jean Bousquet; Luc E. Pâques; Nathalie Isabel
Genetic markers from the nuclear, chloroplast, and mitochondrial genomes were developed to distinguish unambiguously among\\u000a four larch species [Larix laricina (Du Roi) K. Koch, Larix decidua (Mill.), Larix kaempferi (Lamb.) Sarg., and Larix sibirica (Ledeb.)] used in intensive forestry in eastern North America. Nine random amplified polymorphic DNA (RAPD) fragments had\\u000a good diagnostic value, and 3 out of 12 nuclear
Random amplified polymorphic DNA (RAPD) markers for genetic analysis inAllium.
Wilkie, S E; Isaac, P G; Slater, R J
RAPD analysis was applied to onion (Allium cepa) and otherAllium species in order to assess the degree of polymorphism within the genus and to investigate if this approach was suitable for genetic studies of onion. Seven cultivars ofA. cepa, including shallot, and single cultivars of Japanese bunching onion (A. fistulosum), chive (A. schoenoprasum), leek (A. ampeloprasum), and a wild relative of onion (A. roylei), were evaluated for variability using a set of 20 random 10-mer primers. Seven out of the twenty primers revealed scorable polymorphisms between cultivars ofA. cepa and these will be further evaluated for use in genetic mapping. Wide variations in banding profiles between species were observed with nearly every primer tested. These were assessed for use in systematic studies within the genus. Ninety-one band positions were scored (+/-) for all the cultivars studied. Genetic distances between each of the cultivars were calculated and cluster analysis was used to generate a dendrogram showing phylogenetic relationships between them. The resulting analysis was in broad agreement with previous classifications of the species studied, confirming the validity of the method. However, amongst the species studied, it placedA. roylei as the closest relative ofA. cepa, questioning the current classification of the former species in the section Rhizideum. PMID:24193598
Molecular markers based identification of diversity for drought tolerance in bread wheat varieties and synthetic hexaploids.
Shah, Zahid Hussain; Munir, Muhammad; Kazi, Abdul Mujeeb; Mujtaba, Tahir; Ahmed, Zaheer
The complexity of the wheat genome has delayed the development and application of molecular markers to this species and wheat now lies behind barley, maize and rice in marker development. However, improvements in marker detection systems and in the techniques used to identify markers linked to useful traits has allowed considerable advances to be made in recent years. To evaluate the genetic diversity 53 genotypes of Richard's selection, were studied at National Agriculture Reseach Center (NARC) Islamabad. The present study found that RAPD analysis is a valuable diagnostic tool. Different sets of RAPD primers were used to study the polymorphism at molecular level. Highest number of amplifications was shown by primer OpG-2 in Richard's material. Coefficient of similarity as well as genetic distances among these three sets of materials was calculated by using Unweighted Pair Group of Arithamatic Means (UPGMA) function (Nei and Li, 1979). The SHs derived genotypes of Richard's selection were highly polymorphic with a polymorphism percentage of 69.70 as compared to NUYT (rainfed) and elite Pakistani bread wheat varieties with a polymorphism of 44.44% and 61.11% respectively. Cluster analysis was done in which grouping of genotypes was done on the basis of genetic distances. Cluster analysis revealed that genotypes of Richard's genotypes are showing high level of among cultivar variation as compared to NUYT (Rainfed) and elite Pakistani drought tolerant bread wheat varieties. These genotypes were also phenotypically evaluated. PMID:19430030
A synteny map of the horse genome comprised of 240 microsatellite and RAPD markers
Y. L. Shiue; L. A. Bickel; A. R. Caetano; R. S. Clark; M. L. Eggleston; R. Michelmore; E. Bailey; G. Guerin; S. Godard; J. R. Mickelson; S. J. Valberg; J. D. Murray; A. T. Bowling
Summary To generate a domestic horse genome map we integrated synteny information for markers screened on a somatic cell hybrid (SCH) panel with published information for markers physi- cally assigned to chromosomes. The mouse- horse SCH panel was established by fusing pSV2neo transformed primary horse fibroblasts to either RAG or LMTk-mouse cells, followed by G418 antibiotic selection. For each of
The concordance of terpenoid, ISSR and RAPD markers, and ITS sequence data sets among genotypes: an example from Juniperus
Robert P. Adams; Andrea E. Schwarzbach; R. Naresh Pandey
Twelve individual genotypes selected from Juniperus populations, varieties and species were analyzed using ITS sequences, RAPDs, ISSRs, and leaf volatile terpenoids. These four data sets, all analyzed in the same manner, illustrated that these data sets can be used at different organizational levels: specific, inter-specific and intraspecific. Similarity matrices for the ITS, RAPD, and ISSR data sets were highly correlated
Identification of molecular markers linked to the Agropyron elongatum -derived leaf rust resistance gene Lr24 in wheat
G. M. Schachermayr; M. M. Messmer; C. Feuillet; H. Winzeler; M. Winzeler; B. Keller
The objective of this study was to identify molecular markers linked to the wheat leaf rust resistance gene Lr24 derived from Agropyron elongatum (3DL\\/3Ag translocation). Two near isogenic lines (NILs), 'Arina' and Lr24\\/7* "Arina", were screened for polymorphism at the DNA level with 115 RFLP probes. Twenty-one of these probes map to the homoeologous group 3. In addition, 360 RAPD
A Pseudoautosomal Random Amplified Polymorphic DNA Marker for the Sex Chromosomes of Silene dioica
Veronica S. Di Stilio; Richard V. Kesseli; David L. Mulcahy
The segregation pattern of an 810-bp random amplified polymorphic DNA (RAPD) band in the F1 and backcross generations of a Silene dioica (L.) Clairv. family provides evidence that this molecular marker is located in the pseudoautosomal region (PAR) of the X and Y chromosomes. The marker was found through a combination of bulked segregant analysis (BSA) and RAPD techniques. Recombination
Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories
C. J. Jones; K. J. Edwards; S. Castaglione; M. O. Winfield; F. Sala; C. van de Wiel; G. M. M. Bredemeijer; B. Vosman; M. Matthes; A. Daly; R. Brettschneider; P. Bettini; M. Buiatti; E. Maestri; A. Malcevschi; N. Marmiroli; R. Aert; G. Volckaert; J. Rueda; R. Linacero; A. Vazquez; A. Karp
A number of PCR-based techniques can be used to detect polymorphisms in plants. For their wide-scale usage in germplasm characterisation and breeding it is important that these marker technologies can be exchanged between laboratories, which in turn requires that they can be standardised to yield reproducible results, so that direct collation and comparison of the data are possible. This article
[RAPD analysis of Aspergilli and its application in brewing industry].
Pan, Li; Wang, Bin; Guo, Yong
Phylogenetic analysis of sixteen Aspergilli was done by RAPD technology, using Aspergillus oryzae AS3.951, Aspergillus flavus GIM3.18 and Aspergillus sojae AS3.495 as controls. First, genome DNA of the sixteen test strains were prepared by improved extraction method, and their quality was verified by electrophoresis and spectrophotometry. They displayed an identical band (approximately 20 kb) in agarose gel electrophoresis, which conformed to the fact that these strains all belong to Aspergillus. OD260/OD280 of the prepared DNA ranged from 1.80 to 1.90, illustrating that they were good enough to be used as templates in the following RAPD-PCR experiment. Then, three appropriate primers (Primerl, Primer2, Primer5) for RAPD-PCR were screened from nine random primers, and repetitive experiments demonstrated that the RAPD-PCR polymorphic patterns of the sixteen test strains based on these three primers were stable. There were usually 8-14 bands in their RADP-PCR patterns, where the number of the main bands was 4-9 and the secondary bands were abundant. There were totally 181 bands in their RAPD-PCR patterns, where the percentage of polymorphic bands reached to 40.9% (74 bands). The similarity coefficient between the strains was calculated based on their RAPD-PCR patterns, ranging from 8.0% to 96.6%. All these data suggests that the genetic polymorphism of the strains is abundant and they have evident genetic differentiation. The phylogenetic tree of the sixteen test strains was reconstructed according to their RAPD-PCR patterns with Primer1, Primer2 and Primer5. It basically corresponded to traditional morphological taxonomy, demonstrating that the application of RAPD molecular marker in the phylogenetic analysis of these Aspergilli is feasible. Besides, the aflatoxin-producing strains (GIM3.17, CICC2219, CICC2357, CICC2390, CICC2402, CICC2404) could be easily discriminated by RAPD molecular marker, whereas it is difficult to distinguish them by conventional morphological taxonomy. Consequently, RAPD molecular marker provides a novel clue to discriminating aflatoxin-producing strains in brewing industry. PMID:17672321
Technology Transfer Automated Retrieval System (TEKTRAN)
Molecular markers are useful to improve germplasm collection management and for identifying genes for future enhancement and breeding. Safflower (Carthamus tinctorius L.) accessions from the U.S. germplasm collection were characterized using AFLP (Amplified Length Polymorphisms) markers. After DNA e...
Characterizing Safflower Germplasm with AFLP Molecular Markers
Technology Transfer Automated Retrieval System (TEKTRAN)
Characterization of safflower (Carthamus tinctorius L.) germplasm with molecular markers is needed to enhance germplasm management and utilization. Amplified Fragment Length Polymorphism (AFLP) analysis was completed in safflower using two selective primer pairs resulting in 102 unambiguous polymor...
Source apportionment based on organic molecular markers provides a promising approach for meeting the Detroit Exposure and Aerosol Research Study (DEARS) objective of comparing source contributions between community air monitoring stations and various neighborhoods. Source appor...
Identification of a locus characteristic of male individuals of buffalo grass [Buchloe dactyloides (Nutt.) Engelm.] by using an RAPD marker.
Li, Y X; Wang, X G; Yang, C H; Cong, L L; Wu, F F; Xue, J G; Han, Y H
Buffalo grass [Buchloe dactyloides (Nutt.) Engelm.] plants can be either male, female, or hermaphrodite (monoecious). As there is no morphological difference in the early vegetative growth of these three classes of plants, it is worthwhile to use molecular biological methods to attempt to identify the sex of a plant at this early growth period. In this study, we identified 23 plants that had a stable sex for over at least 3 years. Of these, 9 were male plants, 10 were female plants, and 4 were hermaphrodites. Screening of 300 RAPD primers identified a primer, namely S211 (5'-ttccccgcga-3'), which is capable of identifying male plants. The specific fragment was cloned, sequenced, and submitted to the GenBank database (accession No. JN982469). When used to identify the sex of 188 plants during their first growing season, the S211 primer correctly identified 85.8% of all male plants. Our results showed that the S211 primer can identify the male, and in doing so, it facilitates buffalo grass breeding work. PMID:24089096
Varijabilnost germplazme lucerne (Medicago spp.) procijenjena RAPD markerima
Marijana TUCAK
The aim of the study was to analyse the level of genetic variability and germplasm diversity of 17 alfalfa (Medicago spp.) cultivars\\/populations with different geographic origin by RAPD markers. 93 polymorphic markers were found across 340 individual plants by six primers. Genetic distance within germplasm varied from 0.28 to 0.42. Variability within cultivars and populations estimated by analysis of molecular
Molecular markers linked to the apple scab resistance gene Vbj derived from Malus baccata jackii.
Gygax, M; Gianfranceschi, L; Liebhard, R; Kellerhals, M; Gessler, C; Patocchi, A
Breeding for scab-resistant apple cultivars by pyramiding several resistance genes in the same genetic background is a promising way to control apple scab caused by the fungus Venturia inaequalis. To achieve this goal, DNA markers linked to the genes of interest are required in order to select seedlings with the desired resistance allele combinations. For several apple scab resistance genes, molecular markers are already available; but until now, none existed for the apple scab resistance gene Vbj originating from the crab apple Malus baccata jackii. Using bulk segregant analysis, three RAPD markers linked to Vbj were first identified. These markers were transformed into more reliable sequence-characterised amplified region (SCAR) markers that proved to be co-dominant. In addition, three SSR markers and one SCAR were identified by comparing homologous linkage groups of existing genetic maps. Discarding plants showing genotype-phenotype incongruence (GPI plants) plants, a linkage map was calculated. Vbj mapped between the markers CH05e03 (SSR) and T6-SCAR, at 0.6 cM from CH05e03 and at 3.9 cM from T6-SCAR. Without the removal of the GPI plants, Vbj was placed 15 cM away from the closest markers. Problems and pitfalls due to GPI plants and the consequences for mapping the resistance gene accurately are discussed. Finally, the usefulness of co-dominant markers for pedigree analysis is also demonstrated. PMID:15365630
SCAR, RAPD and RFLP markers linked to a dominant gene (Are) conferring resistance to anthracnose in common bean
A. F. Adam-Blondon; M. Sévignac; H. Bannerot; M. Dron
Anthracnose, caused by the fungusColletotrichum lindemuthianum, is a severe disease of common bean (Phaseolus vulgaris L.) controlled, in Europe, by a single dominant gene,Are. Four pairs of near-isogenic lines (NILs) were constructed, in which theAre gene was introgressed into different genetic backgrounds. These pairs of NILs were used to search for DNA markers linked to the resistance gene. Nine molecular
Evaluating genetic variation and relationships among two bromegrass species and their hybrid using RAPD and AFLP markers
Yasas S. N. Ferdinandez; Bruce E. Coulman
The two most widely grown bromegrass species in North America are smooth bromegrass (Bromus inermis Leyss.), a hay type grass, and meadow bromegrass (Bromus riparius Rehmann), a pasture type grass. Recently a hybrid bromegrass population between the two species has been produced as a dual-purpose\\u000a hay-pasture grass. Molecular markers have the potential to improve selection procedures to enhance bromegrass breeding.
Screening of tea (Camellia sinensis) for trait-associated molecular markers.
Mphangwe, Nicholas I K; Vorster, Juan; Steyn, J Martin; Nyirenda, Hastings E; Taylor, Nicolette J; Apostolides, Zeno
This study was done to identify random amplified polymorphic DNA (RAPD) markers that may associate with seven important traits in tea. Sixty RAPD primers were first screened using 18 cultivars under each of the 7 traits, followed by confirmatory screening of 20 promising primers with 32 tea cultivars. Six RAPD primers generated a total of nine specific bands that associated with six desired traits: black tea quality and tolerance to drought, high temperature, low temperature, Phomopsis theae, and high yield. These markers would allow early identification of plant material with the desired traits that can be advanced to the next stage of selection and enhance targeted choice of breeding stocks with the desirable traits. The nine RAPD markers identified in this study could improve precision and efficiency in tea breeding and selection and are an important contribution towards the establishment of marker-assisted selection in tea breeding programmes. PMID:23852798
Genetic analysis of Indian mulberry varieties through molecular markers.
Vijayan, K; Awasthi, A K; Srivastava, P P; Saratchandra, B
India is one of the countries where sericulture is being practiced traditionally. Due to the higher economic return and the greater employment potential, attempts are being made to increase the productivity by developing high yielding mulberry varieties. At the present, Mysore local, Bomaypiasbari, Kanva-2, Bilidevalaya, Kajli, S1, BC(2)59, C776, RFS-175, S-36 and Victory-1 are being cultivated extensively in different parts of India for rearing the silkworm Bombyx mori L. Using 17 random amplified polymorphic DNA (RAPD) and 11 inter-simple sequence repeat (ISSR) primers the genetic relationships among these varieties were analyzed. The RAPD and ISSR primers revealed more than 75% polymorphism among the varieties. The genetic similarity estimated from RAPD markers varied from 0.645, between Kajli and Victory-1 to 0.887, between Kanva-2 and Bilidevalaya. Similarly, the genetic similarity estimated from the ISSR markers ranged from 0.600, between Kajli and Victory-1, to 0.873 between Kanva-2 and BC(2)59. The dendrogram constructed from these markers grouped the varieties into three major groups comprising the low yielding, medium yielding and high yielding. The low genetic similarity between the group of varieties originating from the eastern regions with that of the southern region encourages formation of extensive breeding programs between these groups as to transfer the high yield potential of the southern varieties to the low yielding but highly adaptive eastern varieties. PMID:15383066
Genetic variability of the postharvest pathogen Gilbertella persicaria: identification of randomly amplified polymorphic DNA (RAPD) markers correlating with (+) and (-) mating types.
Papp, T; Vastag, M; Michailides, T J; Ferenczy, L; Vágvölgyi, C
Random amplified polymorphic DNA (RAPD) and isoenzyme polymorphisms among 16 isolates of the postharvest pathogen Gilbertella persicaria were examined. Six different 10-bp primers were used to determine the extent of intraspecific genetic variability. Nine composite amplification types were identified. RAPD markers were obtained which correlated with the mating types of the G. persicaria isolates. The variability of the isoenzyme patterns was very low and no correlation was found between the isoenzyme markers and the mating abilities. When 80 single carbon substrates were tested in utilization assays, most of them were utilized uniformly by the 16 G. persicaria strains. However, some compounds elicited differences between the isolates representing the two mating types. Beta-alanine (0.2%) has little effect on the germination of the sporangiospores of the (+) isolates, but inhibited the germination of (-) sporangiospores. Glycerol-1-monoacetate supported the growth of both mating types, but at concentrations higher than 4% this was accompanied with a compact (colonial) growth for plus mating type isolates only. PMID:11827216
We compared genetic diversity estimated from allozymes and from random amplified polymorphic DNA (RAPDs) in a sample of 210 Great Basin bristlecone pines (Pinus longaeva Bailey) from three groves in the White Mountains, California, USA. The White Mountains are the most westerly extension of bristlecone pine and home to the oldest known living trees. We assayed two forks of each
Molecular markers in pediatric neuro-oncology
Ichimura, Koichi; Nishikawa, Ryo; Matsutani, Masao
Pediatric molecular neuro-oncology is a fast developing field. A multitude of molecular profiling studies in recent years has unveiled a number of genetic abnormalities unique to pediatric brain tumors. It has now become clear that brain tumors that arise in children have distinct pathogenesis and biology, compared with their adult counterparts, even for those with indistinguishable histopathology. Some of the molecular features are so specific to a particular type of tumors, such as the presence of the KIAA1549-BRAF fusion gene for pilocytic astrocytomas or SMARCB1 mutations for atypical teratoid/rhabdoid tumors, that they could practically serve as a diagnostic marker on their own. Expression profiling has resolved the existence of 4 molecular subgroups in medulloblastomas, which positively translated into improved prognostication for the patients. The currently available molecular markers, however, do not cover all tumors even within a single tumor entity. The molecular pathogenesis of a large number of pediatric brain tumors is still unaccounted for, and the hierarchy of tumors is likely to be more complex and intricate than currently acknowledged. One of the main tasks of future molecular analyses in pediatric neuro-oncology, including the ongoing genome sequencing efforts, is to elucidate the biological basis of those orphan tumors. The ultimate goal of molecular diagnostics is to accurately predict the clinical and biological behavior of any tumor by means of their molecular characteristics, which is hoped to eventually pave the way for individualized treatment. PMID:23095836
XIAO-HONG WANGAND; Charles H. Trost
Black-billed Magpies (Pica hudsonia) are a relatively sedentary corvid, with greater dispersal of females than males. To genetically confirm that dispersal pattern, 29 reproductively active adults were captured over two years and were scored for primer-spe- cific random amplified polymorphic DNA (RAPD) bands (53 polymorphic bands in 1996 and 104 in 1997). In both years, we captured more previously banded
Genetic variability among elite red clover ( Trifolium pratense L.) parents used in Chile as revealed by RAPD markers
Hugo Campos-de Quiroz; Fernando Ortega-Klose
Red clover (Trifolium pratense L.) is one of the main forage species of temperate regions. Cultivars of red clover are heterogeneous which makes their genetic\\u000a analysis difficult. We applied RAPDs (Random Amplifed Polymorphic DNA) in order to assess the genetic relationship and levels\\u000a of genetic variability existing among a group of 16 elite red clover parents organised in four subsets
Genetic Variation of Salmo trutta L. Populations from the Catchment Areas of the Rega, Parseta and Wieprza Rivers Evaluated by RAPD and SSR Markers.
Achrem, Magdalena; Skuza, Lidia; Kirczuk, Lucyna; Domagala, Józef; Pilecka-Rapacz, Ma?gorzata; Czerniawski, Robert
By using simple sequence repeats (SSR) and random amplification of polymorphic DNA (RAPD) markers, the genetic variability of three Salmo trutta L. populations from three rivers, the Wieprza, the Rega and the Parseta, was determined. The investigated populations showed a high level of genetic variability. Microsatellites showed that observed heterozygosity (Ho) was higher than the expected heterozygosity (He), with most heterozygotes found in the population from the Parseta river and the fewest in the Wieprza population. The F(IS) coefficient in all investigated populations of the sea trout indicate a high excess of heterozygotes. The highest genetic differentiation was observed between the sea trout from the Rega river and those from the Wieprza (0.366). The obtained results based on microsatellite and RAPD analysis showed that the investigated populations formed two groups. The first group consisted of the sea trout populations from the Wieprza and the Parseta rives, while the second group was formed solely by the Rega river population. PMID:26103679
Application of RAPD for molecular characterization of plant species of medicinal value from an arid environment.
Arif, I A; Bakir, M A; Khan, H A; Al Farhan, A H; Al Homaidan, A A; Bahkali, A H; Al Sadoon, M; Shobrak, M
The use of highly discriminatory methods for the identification and characterization of genotypes is essential for plant protection and appropriate use. We utilized the RAPD method for the genetic fingerprinting of 11 plant species of desert origin (seven with known medicinal value). Andrachne telephioides, Zilla spinosa, Caylusea hexagyna, Achillea fragrantissima, Lycium shawii, Moricandia sinaica, Rumex vesicarius, Bassia eriophora, Zygophyllum propinquum subsp migahidii, Withania somnifera, and Sonchus oleraceus were collected from various areas of Saudi Arabia. The five primers used were able to amplify the DNA from all the plant species. The amplified products of the RAPD profiles ranged from 307 to 1772 bp. A total of 164 bands were observed for 11 plant species, using five primers. The number of well-defined and major bands for a single plant species for a single primer ranged from 1 to 10. The highest pair-wise similarities (0.32) were observed between A. fragrantissima and L. shawii, when five primers were combined. The lowest similarities (0) were observed between A. telephioides and Z. spinosa; Z. spinosa and B. eriophora; B. eriophora and Z. propinquum. In conclusion, the RAPD method successfully discriminates among all the plant species, therefore providing an easy and rapid tool for identification, conservation and sustainable use of these plants. PMID:21064026
Molecular mapping and construction of SCAR markers of the strawberry Rpf1 resistance gene to Phytophthora fragariae and their use in breeding programmes
K. M. Haymes; Weg van de W. E; P. Arens; B. Vosman; A. P. M. den Nijs
The commercial strawberry (Fragaria x ananassa) resistance gene Rpfl conferring resistance to various isolates of Phytophthora fragariae, was mapped using 7 RAPD markers. A DNA fragment representing a RAPD marker linked to susceptibility was cloned, sequenced and converted into a sequence characterized amplified region (SCAR) marker. Next, SCAR primers to the resistant allele (SCAR-R) were developed based upon a deletion
Molecular mapping and construction of SCAR markers of the strawberry Rpf 1 resistance gene to Phytophthora fragariae and their use in breeding programs
K. M. Haymes; Weg van de W. E; P. Arens; B. Vosman; Nijs den A. P. M
The commercial strawberry (Fragaria x ananassa) resistance gene Rpfl conferring resistance to various isolates of Phytophthora fragariae, was mapped using 7 RAPD markers. A DNA fragment representing a RAPD marker linked to susceptibility was cloned, sequenced and converted into a sequence characterized amplified region (SCAR) marker. Next, SCAR primers to the resistant allele (SCAR-R) were developed based upon a deletion
Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology1
Robarts, Daniel W. H.; Wolfe, Andrea D.
In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance. PMID:25202637
Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation
Chris Duran; Nikki Appleby; David Edwards; Jacqueline Batley
Molecular genetic markers represent one of the most powerful tools for the analysis of genomes and enable the association of heritable traits with underlying genomic variation. Molecular marker technology has developed rapidly over the last decade and two forms of sequence based marker, Simple Sequence Repeats (SSRs), also known as microsatellites, and Single Nucleotide Polymorphisms (SNPs) now predominate applications in
[Characterization of the genetic diversity of the fish Brycon henni (Characiformes: Characidae) in central Colombia with RAPD markers].
Pineda Santis, Hermes; Arboleda Chacón, Lucy; Echeverry Echavarria, Amparo; Urcuqui Inchima, Silvio; Pareja Molina, Diego; Olivera Angel, Martha; Builes Gómez, Juan
Knowledge on the genetic diversity of wild fish species is essential for conservation and appropriate management of individuals in repopulation programs. In Colombia, Brycon henni has been reported in the Magdalena and Cauca river basins, but the population and range have diminished as a consequence of anthropic activities. In this study, the Random Amplified Polymorphic DNA (RAPD) was used to estimate the actual genetic structure in this species. For the purpose, six sample sites located in the department of Antioquia (Central Chain Mountains of Colombia) were used. Thirty five primers (87.5%), out of forty used, yielded 1 466 reliable and consistent fragments; 417 were considered as unique fragments able to discriminate among the Magdalena (Humarada-1 and Humarada-2) and Cauca (Piedras, La Clara y Guaracfi) river basins samples, suggesting that each is a discrete unit. This diversity suggests that anthropic effects of over fishing, dam building, deforestation and water pollution, have contributed to the isolation of these fish groups on the high mountains. Brycon moorei and Colossoma macropomum, as an interspecific control groups, were placed out of the B. henni general group, confirming their taxonomic classification through morphologic data. The RAPD technique was useful to know the genetic diversity and to discriminate among B. henni populations from different geographic origins, as a basis for an appropriate plan of repopulation, conservation and wildlife management. PMID:19086404
Morphological characterization and molecular fingerprinting of Nostoc strains by multiplex RAPD.
Hillol, Chakdar; Pabbi, Sunil
Morphological parameters studied for the twenty selected Nostoc strains were mostly found to be consistent with the earlier reports. But the shape of akinetes observed in this study was a little deviation from the existing descriptions and heterocyst frequency was also found to be different in different strains in spite of growing in the same nitrogen free media. Multiplex RAPD produced reproducible and completely polymorphic amplification profiles for all the strains including some strain specific unique bands which are intended to be useful for identification of those strains. At least one to a maximum of two unique bands was produced by different dual primer combinations. For ten strains out of twenty, strain specific bands were found to be generated. Cluster analysis revealed a vast heterogeneity among these Nostoc strains and no specific clustering based on geographical origin was found except a few strains. It was also observed that morphological data may not necessarily correspond to the genetic data in most of the cases. CCC92 (Nostoc muscorum) and CCC48 (Nostoc punctiforme) showed a high degree of similarity which was well supported by high bootstrap value. The level of similarity of the strains ranged from 0.15 to 0.94. Cluster analysis based on multiplex RAPD showed a good fit revealing the discriminatory power of this technique. PMID:23610928
Development of a sex-specific molecular marker for Japanese hop Humulus Japonicus Siebold & Zucc
O. S. Aleksandrov; M. G. Divashuk; G. I. Karlov
Japanese hop (Humulus japonicus Siebold & Zucc.) is a dioecious plant and a suitable model for studying the XX\\/XY1Y2 system of sex chromosomes. To develop a sex-specific marker, 12 RAPD and 36 ISSR markers were analyzed on the basis of pools\\u000a of male and female plants identified after flowering. We were the first to identify ISSR marker K-16, which manifested
DNA markers for sex: Molecular evidence for gender dimorphism in dioecious Mercurialis annua L
D. K. Khadka; A. Nejidat; M. Tal; A. Golan-Goldhirsh
Male specific Random Amplified Polymorphic DNA (RAPD) markers, OPB01-1562 and OPC07-303, were identified and sequenced in dioecious Mercurialis annua. Sequence Characterized Amplified Region (SCAR) primers were designed. Several internal segments of OPB01-1562 were amplified as male specific SCAR markers. These markers were PCR amplified from strong, intermediate and weak male subtypes selected according to their resistance to feminization by cytokinin.
Nuclear DNA diversity, population differentiation, and phylogenetic relationships in the California closed-cone pines based on RAPD and allozyme markers
J. Wu; K. V. Krutovskii; S. H. Strauss
We studied nuclear gene diversity and population differentiation using 91-98 randomly amplified polymorphic DNA (RAPD) loci in the California closed-cone pines knobcone (Pinus attenuata Lemm.), bishop (P. muricata D. Don), and Monterey (P. radiata D. Don) pines. A total of 384 trees from 13 populations were analyzed for RAPDs and another sample of 242 trees from 12 of these 13
Direct sequencing of RAPD fragments using 3'-extended oligonucleotide primers and dye terminator cycle-sequencing
Keith R. Mitchelson; Janneke Drenth; Hong Duong; José X. Chaparro
Random amplified polymorphic DNA (RAPD) markers are used widely to develop high resolution genetic maps and for genome fingerprinting. Typically, single oligomers of ~10 nucleotides are used to PCR amplify characteristic RAPD marker fragments. We describe an efficient method for the direct end- sequencing of gel-purified RAPD fragments using one primer from a set of four 3'-terminal extended (A, T,
Technology Transfer Automated Retrieval System (TEKTRAN)
Three types of species-specific DNA markers, namely, PCR, RAPD, and microsatellites, have been recently developed at the USDA-ARS, SRRC, Sugarcane Research Unit, Houma, Louisiana. Of these, the microsatellite markers are the most polymorphic and can produce distinctive fingerprints (or molecular al...
RAPD fingerprinting of blackcurrant ( Ribes nigrum L.) cultivars
P. G. Lanham; R. M. Brennan; C. Hackett; R. J. McNicol
Ribes nigrum germplasm was screened for random amplified polymorphic DNA (RAPD) markers. Fiftyfour markers were identified which generated individual fingerprints for each of 21 cultivars. Genetic variation within R. nigrum germplasm, as detected by RAPDs, demonstrated that the genetic basis for improvement of blackcurrant is narrower than would be expected by the analysis of parentage.
Characterization of Genetic Structure and Genealogies Using RAPD-PCR
Grosberg, Rick
-CHAPTER 4 Characterization of Genetic Structure and Genealogies Using RAPD-PCR Markers: A Random, Genealogical, and Phylogenetic Implications of Dominance and Cryptic Variation: A Preliminary Overview PROBLEMS Protocol Analysis of Repeatability Inheritance of Markers Genealogical Analysis of Banding Patterns
Technology Transfer Automated Retrieval System (TEKTRAN)
The historicity of marker development, map construction, and the utility of marker-assisted selection is presented. Experimental results indicate that the identification of marker-trait associations will continue to be extremely expensive and time consuming, but will likely pay large dividends for ...
Molecular markers for the characterization of Brazilian Cercospora caricis isolates.
Inglis, P W; Teixeira, E A; Ribeiro, D M; Valadares-Inglis, M C; Tigano, M S; Mello, S C
Cercospora caricis is of interest as a potential mycoherbicide for control of purple nutsedge, Cyperus rotundus, which is considered to be the world's worst weed. The genetic variation of a collection of Brazilian Ce. caricis isolated from Cy. rotundus was analyzed by using RAPD, RFLP with a telomeric probe, [TTAGGG]18 and sequencing of the ITS1-5.8S-ITS2 regions of the ribosomal RNA gene. The Brazilian isolates were also compared with a Ce. caricis isolate from Florida, USA and with some other Cercospora species. A cluster of isolates from the Brazilian cerrado region was identified showing high genetic similarity. In contrast, isolates originating in other geographic regions of Brazil were less than 50% and 25% related to the former group according to similarity estimates produced from RAPD and telomeric RFLP analyses respectively. ITS sequence analysis did not support taxonomic division of the Brazilian strains, but did confirm the distant relatedness of these strains to the Ce. caricis isolate from Florida. The data indicate a need for an extensive molecular survey of Cercospora species associated with the Cyperaceae. PMID:11270654
The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...
The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...
Molecular identification of sex in Hippophae rhamnoides L. using isozyme and RAPD markers
Amit Sharma; Gaurav Zinta; Satender Rana; Poonam Shirko
In many dioecious plants, gender affects economic value, breeding schemes and opportunities for commercial harvests. Hippophae rhamnoides L. is a dioecious plant species in which female genotypes are commercially preferred over male genotypes. Its berries have\\u000a rich medicinal, nutritional and pharmaceutical properties because of their large amounts of vitamins, essential oils, proteins,\\u000a fatty acids, free amino acids and flavanoids. Primary
Characterizing Safflower Germplasm with AFLP Molecular Markers
Technology Transfer Automated Retrieval System (TEKTRAN)
Safflower (Carthamus tinctorius L.) accessions from the U.S. germplasm collection were characterized using AFLP (Amplified Length Polymorphisms) markers. Separation and scoring of 392 markers was completed using the Beckman CEQ8000 capillary electrophoresis system. Twelve plants from each of eight...
[Prognostic and predictive molecular markers for urologic cancers].
Hartmann, A; Schlomm, T; Bertz, S; Heinzelmann, J; Hölters, S; Simon, R; Stoehr, R; Junker, K
Molecular prognostic factors and genetic alterations as predictive markers for cancer-specific targeted therapies are used today in the clinic for many malignancies. In recent years, many molecular markers for urogenital cancers have also been identified. However, these markers are not clinically used yet. In prostate cancer, novel next-generation sequencing methods revealed a detailed picture of the molecular changes. There is growing evidence that a combination of classical histopathological and validated molecular markers could lead to a more precise estimation of prognosis, thus, resulting in an increasing number of patients with active surveillance as a possible treatment option. In patients with urothelial carcinoma, histopathological factors but also the proliferation of the tumor, mutations in oncogenes leading to an increasing proliferation rate and changes in genes responsible for invasion and metastasis are important. In addition, gene expression profiles which could distinguish aggressive tumors with high risk of metastasis from nonmetastasizing tumors have been recently identified. In the future, this could potentially allow better selection of patients needing systemic perioperative treatment. In renal cell carcinoma, many molecular markers that are associated with metastasis and survival have been identified. Some of these markers were also validated as independent prognostic markers. Selection of patients with primarily organ-confined tumors and increased risk of metastasis for adjuvant systemic therapy could be clinically relevant in the future. PMID:24700189
Genetic structure and variation in the relict populations of Alsophila spinulosa from southern China based on RAPD markers and cpDNA atpB-rbcL sequence data.
Wang, Ting; Su, Ying-juan; Li, Xue-Yan; Zheng, Bo; Chen, Guo-Pei; Zeng, Qing-Lu
RAPD markers and sequences of chloroplast DNA (cpDNA) atpB-rbcL intergenic spacers were used to characterize the pattern of genetic variation and the phylogenetic relationships of the relict populations of Alsophila spinulosa located in Jian Feng Ling (JFL) and Diao Luo Shan (DLS), Hainan, and Tang Lang Shan (TLS), Ding Hu Shan (DHS), and Da Xi Shan (DXS), Guangdong, of southern China. 28 random primers generated 118 bands, out of which 26 (22.03%) were polymorphic loci, distinguishing 17 different RAPD phenotypes. Percentage of polymorphic loci, Shannon phenotypic diversity and Nei's gene diversity comprehensively indicated that JFL possessed the highest diversity, TLS and DHS in intermediate and DLS or DXS the least; the corresponding values of the population appeared correlated with the population size. Differentiation was detected among populations of A. spinulosa (1-Hpop/Hsp=0.7453, GST=0.7763, and phist=0.8145). AMOVA showed that 47.44% of the variance was partitioned among regions (Hainan and Guangdong), 34.01% attributed among populations within regions, whereas only 18.55% occurring within populations. Low level of intra-specific diversity was maintained in A. spinulosa with Shannon diversity and gene diversity merely 0.0560 and 0.0590, repectively. Sequence length of atpB-rbcL intergenic spacer varied from 724 bp to 730 bp. Base composition was with A+T content between 63.17% and 63.70%. 13 haplotypes of atpB-rbcL noncoding spacers were identified. UPGMA dendrogram of RAPD phenotypes, principal components analysis based on RAPD patterns, minimum spanning network and neighbour-joining (NJ) tree established on atpB-rbcL haplotypes consistently suggested the geographical subdivision of populations of A. spinulosa between Hainan and Guangdong. Breeding system and conservation strategy of A. spinulosa was discussed based on the information of population genetic structure and variation. PMID:15032942
Applicability of inter-simple sequence repeat polymorphisms in wheat for use as DNA markers in comparison to RFLP and RAPD markers
T. Nagaoka; Y. Ogihara
Inter-simple sequence repeat polymorphic DNA (ISSR) was evaluated for its applicability as a genetic marker system in wheat.\\u000a PCR was carried out with primers that annealed to simple sequence repeats. The resultant products were subjected to agarose-gel\\u000a electrophoresis, and the banding patterns were compared among six wheat accessions containing diploid, tetraploid, and hexaploid\\u000a members. Out of 100 examined, 33 primers
Authentication of the medicinal plant Sennaangustifolia by RAPD profiling
Khan, Salim; Mirza, Khanda Jabeen; Al-Qurainy, Fahad; Abdin, Malik Zainul
In this study "RAPD" molecular marker was employed for the identification of Sennaangustifolia, Sennaacutifolia, Sennatora and Sennasophera. Total 32 decamer primers were screened in amplification with genomic DNA extracted from all species, of which 6 primers yielded species-specific reproducible bands. Out of 42 loci detected, the polymorphic, monomorphic and unique loci were 24, 2 and 16, respectively. Based on dendrogram and similarity matrix, 4 species were differentiated from each other and showed more divergence. Thus, this technique may prove and to contribute the identification of these species of Senna having similar morphology sold in the local markets. PMID:23961137
RAPD variation within and among natural populations of outcrossing buffalograss [ Buchloë dactyloides (Nutt.) Engelm.
D. R. Huff; R. Peakall; P. E. Smouse
RAPD markers provide a powerful tool for the investigation of genetic variation in natural and domesticated populations. Recent studies of strain\\/cultivar identification have shown extensive RAPD divergence among, but little variation within, inbred species or cultivars. In contrast, little is known about the pattern and extent of RAPD variation in heterogeneous, outcrossing species. We describe the population genetic variation of
Identification and cloning of molecular markers for UV-B tolerant gene in wild sugarcane (Saccharum spontaneum L.).
Li, Yuan; He, Yongmei; Zu, Yanqun; Zhan, Fangdong
Previously we have selected wild sugarcane (Saccharum spontaneum L.) sterile lines that are tolerant or susceptible to UV-B radiation based on response index (RI) in a field screening test. The RI was established according to plant height, tiller number, leaf index, total biomass and brix under enhanced ultraviolet-B (UV-B, 280-310 nm) radiation. In this experiment, molecular markers linked to the UV-B tolerant and susceptible genes were identified and cloned. RAPD (Randomly amplified polymorphic DNAs) assay using 100 arbitrary primers followed by clustering analysis separated the tolerant and susceptible lines into two groups at the genetic distance of 0.380. The UV-B tolerant and susceptible gene pools were constructed and compared using the Bulked Segregate Analysis (BSA) approach. Of the 100 arbitrary RAPD primers, primer OPR16 produced polymorphic DNA banding patterns from both gene pools. The OPR16-1200 bp DNA fragment was only amplified from the tolerant lines and the OPR16-800 bp from the susceptible ones. These two PCR fragments were cloned onto T-vector. DNA sequence alignment analysis determined that 42% homology existed between the reverse and forward sequences of the OPR16-1200 bp clone, and 36% homology between the forward sequences of the OPR16-800 bp and OPR16-1200 bp clones. The two DNA clones were determined to be linked to the UV-B tolerant and susceptible genes, and they can be used to develop molecular markers for the associated traits. PMID:21925894
Molecular markers linked to white rust resistance in mustard Brassica juncea
K. V. Prabhu; D. J. Somers; G. Rakow; R. K. Gugel
White rust, caused by Albugo candida (Pers.) Kuntze, is an economically important disease of Brassica juncea (L.) Czern. and Coss mustard, particularly in India. The most efficient and cost-effective way of protecting mustard plants\\u000a from white rust disease is through genetic resistance. The objective of this study was to identify RAPD markers for white\\u000a rust resistance in an F1-derived doubled-haploid
Phenotypic and Molecular (RAPD) Differentiation of Four Infraspecific Groups of Cultivated Flax ( Linum usitatissimum L. subsp. usitatissimum )
Axel Diederichsen; Yong-Bi Fu
Based on agro-botanical characterization data, 3101 accessions of cultivated flax (Linum usitatissimum L. subsp. usitatissimum) from the flax collection held by Plant Gene Resources of Canada (PGRC) were grouped into four infraspecific groups according\\u000a to the classification proposed by Kulpa and Danert (1962) . The objective of this study was to investigate phenotypic and\\u000a RAPD variation within and among the
Drosophila hematopoiesis: markers and methods for molecular genetic analysis
Evans, Cory J.; Liu, Ting; Banerjee, Utpal
Analyses of the Drosophila hematopoietic system are becoming more and more prevalent as developmental and functional parallels with vertebrate blood cells become more evident. Investigative work on the fly blood system has, out of necessity, led to the identification of new molecular markers for blood cell types and lineages and to the refinement of useful molecular genetic tools and analytical methods. This review briefly describes the Drosophila hematopoietic system at different developmental stages, summarizes the major useful cell markers and tools for each stage, and provides basic protocols for practical analysis of circulating blood cells and of the lymph gland, the larval hematopoietic organ. PMID:24613936
EST-PCR markers developed for Highbush Blueberry are also useful for genetic fingerprinting and relationship studies in Rabbiteye Blueberry
Technology Transfer Automated Retrieval System (TEKTRAN)
Up until now, randomly amplified polymorphic DNA (RAPD) has been the only type of molecular marker used extensively in rabbiteye blueberry (Vaccinium virgatum). Here we have tested whether a type of sequence-tagged site (STS) marker which utilizes specific ~20-mer primers from Expressed Sequence Tag...
Mosaic down syndrome with a marker: molecular cytogenetic characterization of the marker chromosome.
Dutta, Usha R; Pidugu, Vijaya Kumar; Goud, Venkatesh; Dalal, Ashwin B
Down syndrome is a complex disorder characterized by well defined and distinctive phenotypic features. Approximately 2-3% of all live-born Down individuals are mosaics. Here we report a boy with suspected Down syndrome showing mosaicism for two different cell lines where one cell line is unexpected. The cytogenetic analysis by G-banding revealed a karyotype of 47 XY+21 [20]/46,X+marker [30]. Further, molecular cytogenetic analysis with spectral karyotyping identified the marker as a derivative of Y chromosome. The delineation of Y chromosomal DNA was done by quantitative real-time PCR and aneuploidy detection by quantitative fluorescence PCR. The Y-short tandem repeats typing was performed to estimate the variation in quantity as well as to find out the extent of deletion on Y chromosome using STR markers. Fluorescence in situ hybridization using Y centromeric probe was also performed to confirm the origin of the Y marker. Further fine mapping of the marker was carried out with three bacterial artificial chromosome clones RP11-20H21, RP11-375P13, RP11-71M14, which defined the hypothetical position of the deletion. In our study we defined the extent of deletion of the marker chromosome and also discussed it in relation with mosaicism. This is the first report of mosaic Down syndrome combined with a second de novo mosaic marker derived from the Y chromosome. PMID:22245181
Mapping of the Rf3 nuclear fertility-restoring gene for WA cytoplasmic male sterility in rice using RAPD and RFLP markers
G. Zhang; Y. Lu; T. S. Bharaj; S. S. Virmani; N. Huang
The cytoplasmic male sterility (CMS) of wild-abortive (WA) cytoplasm has been widely used for breeding hybrid rice. Two restorer\\u000a genes for the CMS have been found by traditional genetic analysis. To tag the restorer genes we used a set of near-isogenic\\u000a lines (NILs) of Zhenshan 97 carrying different genotypes for fertility restoration from IR24, to perform RAPD analysis. From\\u000a the
Acceleration of peanut breeding programs by molecular marker assisted selection
Technology Transfer Automated Retrieval System (TEKTRAN)
Peanut breeding has played a significant role in yield increases and disease control. Conventional breeding focuses on field selection and phenotypic analysis and it typically takes 12-15 years before a new cultivar can be released. Molecular markers developed from sequencing data can be of great ...
Tracking different Northern Wheatear populations during migration with molecular markers
Julia Delingat
Stopover decisions of long distance migrating birds, like the Northern Wheatear, Oenanthe oenanthe, depend very much on already covered distances as well as on the ongoing migration route. To test optimality models all available information about the migration route of the in- vestigated individuals is important. Morphometric data and Molecular markers for different breeding populations offer information about the breeding
RESEARCH ARTICLE Uncloaking a cryptic, threatened rail with molecular markers
Beissinger, Steven R.
RESEARCH ARTICLE Uncloaking a cryptic, threatened rail with molecular markers: origins Black Rail lives under dense marsh vegetation, is rarely observed, flies weakly and has a highly disjunct distribution. The largest population of rails is found in 810 large wetlands in San Francisco Bay
A contribution to characterisation of genetic variation in some natural Polish populations of Elymus repens (L.) Gould and Elymus hispidus (Opiz) Melderis (Poaceae) as revealed by RAPD markers.
Szczepaniak, M; Bieniek, W; Boro?, P; Szklarczyk, M; Mizianty, M
To determine the relative importance of clonal growth and sexual reproduction, the Randomly Amplified Polymorphic DNA (RAPD) method was used to study genetic diversity and clonal structure of six populations of Elymus repens and four populations of Elymus hispidus from Poland. These outbreeding species are virtually self-sterile and form widely spreading and long-lived rhizomes. Using 12 primers, a total of 150 unambiguous RAPD fragments were amplified and scored. Results of AMOVA showed no significant genetic distinction between morphologically distinguished varieties of E. repens and E. hispidus. E. repens had slightly higher intra-specific genetic polymorphism than E. hispidus; the percentage of polymorphic bands per population ranged from 38 to 49 and from 19 to 38 respectively. Clonal diversity measured using the Simpson diversity index (D) indicated different contributions of clonal reproduction in particular populations of E. repens (D: 0.20-0.72). Populations of E. hispidus were dominated by one or a few clones, which were generally restricted to a single population (D: 0.00-0.22). RAPD revealed that most genetic diversity resided within populations of the two studied species, suggesting that, despite their clonal character, propagation by seeds contributes considerably to reproduction of E. repens and E. hispidus. PMID:19689785
Predictive markers in bladder cancer: do we have molecular markers ready for clinical use?
Sanguedolce, Francesca; Bufo, Pantaleo; Carrieri, Giuseppe; Cormio, Luigi
Bladder cancer (BC) is a heterogeneous disease. Approximately 75% of patients present with non-muscle-invasive BC (NMIBC), which has a high recurrence rate and a low but unpredictable progression rate. Conversely, patients with muscle-invasive BC (MIBC) are at high risk for progression and cancer-specific mortality, but, again, disease behavior is unpredictable. To date, risk assessment for tumor recurrence and progression is based on clinico-pathological factors only. A risk assessment calculator that is based on several such parameters is available for NMIBC, but it has been reported to have potential flaws. In the last two decades, great effort has been made to evaluate the prognostic and predictive role of several molecular markers in MIBC and, even more so, in NMIBC, where the need for more precise risk stratification is urgently needed. This review addresses current evidence for the role of several molecular markers easily assessable by immunohistochemical techniques in prognosticating/predicting the outcome of NMIBC and MIBC. To date, because of divergent results among the many studies, no molecular marker has yet entered routine clinical practice; however, some of them (e.g., p53, pRb, p21, and survivin) have proved their predictive value in studies that included a homogeneous patient population on standardized treatment, and, therefore, are probably ready for clinical validation on a larger scale. Even more interesting is the possibility of constructing multimarker panels that could be used in routine clinical practice, as all these markers can easily be evaluated by immunohistochemistry on routine surgical pathology specimens. The molecular markers described herein hold promise for becoming widely available and cost-effective tools for reliable risk assessment, which would represent a great advancement in counseling patients, in selecting them for neoadjuvant and adjuvant treatments, and in determining their eligibility for clinical trials. PMID:25036341
Reviewing and Updating the Major Molecular Markers for Stem Cells
Calloni, Raquel; Cordero, Elvira Alicia Aparicio; Henriques, Joăo Antonio Pęgas
Stem cells (SC) are able to self-renew and to differentiate into many types of committed cells, making SCs interesting for cellular therapy. However, the pool of SCs in vivo and in vitro consists of a mix of cells at several stages of differentiation, making it difficult to obtain a homogeneous population of SCs for research. Therefore, it is important to isolate and characterize unambiguous molecular markers that can be applied to SCs. Here, we review classical and new candidate molecular markers that have been established to show a molecular profile for human embryonic stem cells (hESCs), mesenchymal stem cells (MSCs), and hematopoietic stem cells (HSCs). The commonly cited markers for embryonic ESCs are Nanog, Oct-4, Sox-2, Rex-1, Dnmt3b, Lin-28, Tdgf1, FoxD3, Tert, Utf-1, Gal, Cx43, Gdf3, Gtcm1, Terf1, Terf2, Lefty A, and Lefty B. MSCs are primarily identified by the expression of CD13, CD29, CD44, CD49e, CD54, CD71, CD73, CD90, CD105, CD106, CD166, and HLA-ABC and lack CD14, CD31, CD34, CD45, CD62E, CD62L, CD62P, and HLA-DR expression. HSCs are mainly isolated based on the expression of CD34, but the combination of this marker with CD133 and CD90, together with a lack of CD38 and other lineage markers, provides the most homogeneous pool of SCs. Here, we present new and alternative markers for SCs, along with microRNA profiles, for these cells. PMID:23336433
Genomic analysis in maritime pine ( Pinus pinaster ). Comparison of two RAPD maps using selfed and open-pollinated seeds of the same individual
C. Plomion; D. M. O'Malley; C. E. Durel
Two genomic maps were constructed for one individual tree of maritime pine, Pinus pinaster Ait., using a common set of 263 RAPD markers (random amplified polymorphic DNA). The RAPD markers were chosen from a larger number of polymorphic RAPD fragments on the basis of repeatability and inheritance in a three-generation pedigree. The maps were constructed from two independent mapping samples
Simultaneous analysis of five molecular markers provides a well-supported phylogenetic hypothesis for the living
Hopkins, Carl D.
Simultaneous analysis of five molecular markers provides a well-supported phylogenetic hypothesis hypothesis for this group, based on the analysis of more than 4000 characters from five molecular markers parsimony analysis of combined and equally weighted characters from the five molecular markers and Bayesian
Biological (molecular and cellular) markers of toxicity
Shugart, L.R.
The overall objective of this study is to evaluate the use of the small aquarium fish, Japanese Medaka (Oryzias latipes), as a predictor of potential genotoxicity following exposure to carcinogens. This will be accomplished by quantitatively investigating the early molecular events associated with genotoxicity of various tissues of Medaka subsequent to exposure of the organism to several known carcinogens, such as diethylnitrosamine (DEN) and benzo(a)pyrene (BaP). Because of the often long latent period between initial contact with certain chemical and physical agents in our environment and subsequent expression of deleterious health or ecological impact, the development of sensitive methods for detecting and estimating early exposure is needed so that necessary interventions can ensue. A promising biological endpoint for detecting early exposure to damaging chemicals is the interaction of these compounds with cellular macromolecules such as Deoxyribonucleic acids (DNA). This biological endpoint assumes significance because it can be one of the critical early events leading eventually to adverse effects (neoplasia) in the exposed organism.
Molecular Markers for Breast Cancer: Prediction on Tumor Behavior
Banin Hirata, Bruna Karina; Oda, Julie Massayo Maeda; Losi Guembarovski, Roberta; Ariza, Carolina Batista; de Oliveira, Carlos Eduardo Coral; Watanabe, Maria Angelica Ehara
Breast cancer is one of the most common cancers with greater than 1,300,000 cases and 450,000 deaths each year worldwide. The development of breast cancer involves a progression through intermediate stages until the invasive carcinoma and finally into metastatic disease. Given the variability in clinical progression, the identification of markers that could predict the tumor behavior is particularly important in breast cancer. The determination of tumor markers is a useful tool for clinical management in cancer patients, assisting in diagnostic, staging, evaluation of therapeutic response, detection of recurrence and metastasis, and development of new treatment modalities. In this context, this review aims to discuss the main tumor markers in breast carcinogenesis. The most well-established breast molecular markers with prognostic and/or therapeutic value like hormone receptors, HER-2 oncogene, Ki-67, and p53 proteins, and the genes for hereditary breast cancer will be presented. Furthermore, this review shows the new molecular targets in breast cancer: CXCR4, caveolin, miRNA, and FOXP3, as promising candidates for future development of effective and targeted therapies, also with lower toxicity. PMID:24591761
Molecular markers and sentinel organisms for environmental monitoring.
Graczyk, T K; Conn, D B
Molecular methods are useful for both to monitor anthropogenic viral, bacterial, and protozoan enteropathogens, and to track pathogen specific markers in a complex environment in order to reveal sources of these pathogens. Molecular genetic markers for fecal viruses, bacteria, and protozoans hold promise for monitoring environmental pollution and water quality. The demand for microbiologically safe waters grows exponentially due to the global demographic rise of the human population. Economically important shellfish, such as oysters, which are harvested commercially and preferentially consumed raw can be of public health importance if contaminated with human waterborne pathogens. However, feral molluscan shellfish which do not have an apparent economic value serve as indicators in monitoring aquatic environments for pollution with human waterborne pathogens and for sanitary assessment of water quality. Current technology allows for multiplexed species-specific identification, genotyping, enumeration, viability assessment, and source-tracking of human enteropathogens which considerably enhances the pathogen source-tracking efforts. PMID:18814723
Molecular markers for wheat leaf rust resistance gene Lr41
Xiaochun Sun; Guihua Bai; Brett F. Carver
Leaf rust, caused by Puccinia triticina Eriks., is an important foliar disease of common wheat (Triticum aestivum L.) worldwide. Pyramiding several major rust-resistance genes into one adapted cultivar is one strategy for obtaining more\\u000a durable resistance. Molecular markers linked to these genes are essential tools for gene pyramiding. The rust-resistance gene\\u000a Lr41 from T.\\u000a tauschii has been introgressed into chromosome
Potential of marker-assisted selection in hemp genetic improvement
G. Mandolino; A. Carboni
Summary The development and applications of molecular markers to hemp breeding are recent, dating back only to the mid-1990s. The main achievements in this field are reviewed. The analysis of Cannabis germplasm by RAPD, AFLP and microsatellites is discussed, with its consequence for the still debated species concept in Cannabis. DNA-based markers have also been exploited in the field of forensic
Molecular Markers, Natural History, and Conservation of Marine Animals
NSDL National Science Digital Library
Ronald Burton (Scripps Institution of Oceanography, University of California, San Diego; Marine Biology Research Division)
Molecular genetic techniques have found broad utility in modern marine ecology, and applications continue to grow. Databases of DNA sequences now permit nonexperts to identify eggs and larval stages of many marine animals that were previously mysteries. Molecular identifications of field-collected organisms and tissues are used to help assess population connectivity, investigate marine food webs, and identify marketed commodities. Advances in technology already include prototype development of in situ robotic instrumentation for sampling and molecular identification of animal larvae. Studies of population connectivity, once limited to a few gene loci, are slowly giving way to new genomic arrays of markers and high-throughput methodologies for scoring genotypes. Population genetic theory is providing new computational techniques to assess patterns of population structure, estimate effective population sizes, and infer aspects of demographic history. In this article I review a subset of recent work in this growing area of molecular marine ecology.
Are molecular markers useful predictors of adaptive potential?
Mittell, Elizabeth A; Nakagawa, Shinichi; Hadfield, Jarrod D
Estimates of molecular genetic variation are often used as a cheap and simple surrogate for a population's adaptive potential, yet empirical evidence suggests they are unlikely to be a valid proxy. However, this evidence is based on molecular genetic variation poorly predicting estimates of adaptive potential rather than how well it predicts true values. As a consequence, the relationship has been systematically underestimated and the precision with which it could be measured severely overstated. By collating a large database, and using suitable statistical methods, we obtain a 95% upper bound of 0.26 for the proportion of variance in quantitative genetic variation explained by molecular diversity. The relationship is probably too weak to be useful, but this conclusion must be taken as provisional: less noisy estimates of quantitative genetic variation are required. In contrast, and perhaps surprisingly, current sampling strategies appear sufficient for characterising a population's molecular genetic variation at comparable markers. PMID:25989024
Genetic diversity within and among Lepidium draba populations from Eastern Anatolia based on RAPD analysis.
Aksakal, Ozkan; Sunar, Serap; Kaya, Yusuf; Agar, Guleray
Genetic variation and structure of six natural populations of Lepidium draba L. from Eastern Anatolia were assessed using random amplified polymorphic DNA (RAPD) markers. For RAPD analysis, 12 primers generated 218 reproducible bands across the six populations analyzed, of which 73 bands (33.3%) were polymorphic. The mean Nei's gene diversity value for all six populations was 0.1771. Shannon's information index varied with population (0.2278-0.3082), averaging 0.2608. Analysis of molecular variance (AMOVA) showed that genetic diversity was greater within populations (58.66%) than among populations (30.68%). In addition, the variation between groups was 10.33%. The genetic differentiation among populations (G (ST)) was 0.3210, indicating that most genetic diversity occurs within populations. Gene flow (Nm) was low, at only 0.5288. PMID:20496111
A family of LRR sequences in the vicinity of the Co2 locus for anthracnose resistance in Phaseolus vulgaris and its potential use in marker-assisted selection
V. Geffroy; F. Creusot; J. Falquet; M. Sévignac; A.-F. Adam-Blondon; H. Bannerot; P. Gepts; M. Dron
Molecular markers offer new opportunities for breeding for disease resistance. Resistance gene pyramiding in a single cultivar,\\u000a as a strategy for durable resistance, can be facilitated by marker-assisted selection (MAS). A RAPD marker, ROH20450, linked to the Mesoamerican Co-2 anthracnose resistance gene, was previously transformed into a SCAR marker, SCH20. In the present paper we have further characterized\\u000a the relevance
Fasciola hepatica: identification of molecular markers for resistant and susceptible Pseudosuccinea columella snail hosts.
Gutiérrez, Alfredo; Pointier, Jean-Pierre; Fraga, Jorge; Jobet, Edouard; Modat, Sylvain; Pérez, R T; Yong, Mary; Sanchez, J; Loker, Eric S; Théron, André
Protein electrophoresis, RAPD-PCR and nuclear rDNA ITS sequencing were performed to search for genetic differences between Pseudosuccinea columella snails susceptible and resistant to Fasciola hepatica infection. Of the 21 enzymatic loci analyzed in both populations, none of them exhibited neither within- or between-group variation. Such an absence of enzyme polymorphism support the hypothesis of selfing as the "prevalent" mating system for this hermaphroditic species. Conversely, the RAPD profiles displayed clear differences between susceptible and resistant isolates for 17 of the 26 primers tested while no within-group variation was detected. rDNA ITS sequence analysis from snails of each isolates showed only two bases that differed between groups accounting for a 0.17% of variation confirming that susceptible and resistant snails belong to the same species. This is the first time that a genetic variation using RAPD markers is demonstrated between susceptible and resistant lymnaeid snails vis-a-vis of F. hepatica infection in absence of experimental selection. PMID:14990314
Genetic diversity analysis with RAPD linked to sex identification in the sugar cane borer Diatraea saccharalis.
Heideman, C; Munhoz, R E F; Pattaro Júnior, J R; Fernandez, M A
Diatraea saccharalis is an insect that causes considerable losses in the sugar cane crop. Our aim was to contribute to the knowledge of the biology of D. saccharalis, with the report of DNA fragments involved in the differentiation between the male and female of this species using the RAPD sex molecular marker GyakuU-13, which is specific for the W chromosome of Bombyx mori. Another point evaluated in this study was the genetic diversity of a D. saccharalis population maintained by inbreeding in a laboratory culture. The profile of sex-specific fragments was analyzed, and the genetic variability of this population was estimated. An analysis of the molecular markers showed only one fragment, of approximately 700 bp, that could be considered as a female sex marker in D. saccharalis. PMID:21128215
The Promise of Novel Molecular Markers in Bladder Cancer
Miremami, Jahan; Kyprianou, Natasha
Bladder cancer is the fourth most common malignancy in the US and is associated with the highest cost per patient. A high likelihood of recurrence, mandating stringent surveillance protocols, has made the development of urinary markers a focus of intense pursuit with the hope of decreasing the burden this disease places on patients and the healthcare system. To date, routine use of markers is not recommended for screening or diagnosis. Interests include the development of a single urinary marker that can be used in place of or as an adjunct to current screening and surveillance techniques, as well identifying a molecular signature for an individual's disease that can help predict progression, prognosis, and potential therapeutic response. Markers have shown potential value in improving diagnostic accuracy when used as an adjunct to current modalities, risk-stratification of patients that could aid the clinician in determining aggressiveness of surveillance, and allowing for a decrease in invasive surveillance procedures. This review discusses the current understanding of emerging biomarkers, including miRNAs, gene signatures and detection of circulating tumor cells in the blood, and their potential clinical value in bladder cancer diagnosis, as prognostic indicators, and surveillance tools, as well as limitations to their incorporation into medical practice. PMID:25535079
RAPD variation within and among natural populations of outcrossing buffalograss [Buchloë dactyloides (Nutt.) Engelm].
Huff, D R; Peakall, R; Smouse, P E
RAPD markers provide a powerful tool for the investigation of genetic variation in natural and domesticated populations. Recent studies of strain/cultivar identification have shown extensive RAPD divergence among, but little variation within, inbred species or cultivars. In contrast, little is known about the pattern and extent of RAPD variation in heterogeneous, outcrossing species. We describe the population genetic variation of RAPD markers in natural, diploid sources of dioecious buffalograss [Buchloë dactyloides (Nutt.) Engelm.]. Buffalograss is native to the semi-arid regions of the Great Plains of North America, where it is important for rangeland forage, soil conservation, and as turfgrass. Most sources of buffalograss germplasm are polyploid; diploid populations are previously known only from semi-arid Central Mexico. This is the first report of diploids from humid Gulf Coastal Texas. These two diploid sources represent divergent adaptive ecotypes. Seven 10-mer primers produced 98 polymorphic banding sites. Based on the presence/ absence of bands, a genetic distance matrix was calculated. The new Analysis of Molecular Variance (AMOVA) technique was used to apportion the variation among individuals within populations, among populations within adaptive regions, and among regions. There was considerable variation within each of the four populations, and every individual was genetically distinct. Even so, genetic divergence was found among local populations. Within-population variation was larger and among-population variation smaller in Mexico than in Texas. The largest observed genetic differences were those between the two regional ecotypes. These patterns of genetic variation were very different from those reported for inbred species and provide important baseline data for cultivar identification and continuing studies of the evolution of polyploid races in this species. PMID:24193999
A molecular marker of artemisinin-resistant Plasmodium falciparum malaria
NASA Astrophysics Data System (ADS)
Ariey, Frédéric; Witkowski, Benoit; Amaratunga, Chanaki; Beghain, Johann; Langlois, Anne-Claire; Khim, Nimol; Kim, Saorin; Duru, Valentine; Bouchier, Christiane; Ma, Laurence; Lim, Pharath; Leang, Rithea; Duong, Socheat; Sreng, Sokunthea; Suon, Seila; Chuor, Char Meng; Bout, Denis Mey; Ménard, Sandie; Rogers, William O.; Genton, Blaise; Fandeur, Thierry; Miotto, Olivo; Ringwald, Pascal; Le Bras, Jacques; Berry, Antoine; Barale, Jean-Christophe; Fairhurst, Rick M.; Benoit-Vical, Françoise; Mercereau-Puijalon, Odile; Ménard, Didier
Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain (`K13-propeller') with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread.
A molecular marker of artemisinin-resistant Plasmodium falciparum malaria.
Ariey, Frédéric; Witkowski, Benoit; Amaratunga, Chanaki; Beghain, Johann; Langlois, Anne-Claire; Khim, Nimol; Kim, Saorin; Duru, Valentine; Bouchier, Christiane; Ma, Laurence; Lim, Pharath; Leang, Rithea; Duong, Socheat; Sreng, Sokunthea; Suon, Seila; Chuor, Char Meng; Bout, Denis Mey; Ménard, Sandie; Rogers, William O; Genton, Blaise; Fandeur, Thierry; Miotto, Olivo; Ringwald, Pascal; Le Bras, Jacques; Berry, Antoine; Barale, Jean-Christophe; Fairhurst, Rick M; Benoit-Vical, Françoise; Mercereau-Puijalon, Odile; Ménard, Didier
Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain ('K13-propeller') with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread. PMID:24352242
Molecular Markers for the Characterization of Brazilian Cercospora caricis Isolates
Peter W. Inglis; Eliria A. Teixeira; Djanira M. Ribeiro; M. Cléria Valadares-Inglis; Myrian S. Tigano; Sueli C. M. Mello
Cercospora caricis is of interest as a potential mycoherbicide for control of purple nutsedge, Cyperus rotundus, which is considered to be the world's worst weed. The genetic variation of a collection of Brazilian Ce. caricis isolated from Cy. rotundus was analyzed by using RAPD, RFLP with a telomeric probe, [TTAGGG]18 and sequencing of the ITS1-5.8S-ITS2 regions of the ribosomal RNA
Identification and validation of molecular markers linked to the leaf rust resistance gene Lr19 in wheat
Sudhir Kumar Gupta; Ashwini Charpe; Kumble Vinod Prabhu; Qazi Mohammad Rizwanul Haque
A leaf rust resistance gene Lr19 on the chromosome 7DL of wheat derived from Agropyron elongatum was tagged with random amplified polymorphic DNA (RAPD) and microsatellite markers. The F2 population of 340 plants derived from a cross between the leaf rust resistant near-isogenic line (NIL) of Thatcher (Tc + Lr19) and leaf rust susceptible line Agra Local that segregated for dominant monogenic
Identification of microspore-derived plants in anther culture of flax (Linum usitatissimum L.) using molecular markers
Y. Chen; G. Hausner; E. Kenaschuk; D. Procunier; P. Dribnenki; G. Penner
The microspore origin of anther-culture-derived plants of flax was determined using inter-simple sequence repeat (ISSR) and\\u000a randomly amplified polymorphic DNA (RAPD) markers. Polymorphic fragments between the two parents of the F1 donor plants were identified and their segregation patterns in anther-culture-derived plants were used to elucidate the origin\\u000a of those plants and to determine the degree of independence of plants
Genetic variation inferred from RAPD fingerprinting in three species of tilapia
K. R. Dinesh; T. M. Lim; W. K. Chan; V. P. E. Phang
This study used random amplified polymorphic DNA (RAPD) fingerprinting for estimating genetic variation and species differentiation in three species of tilapia. A 16-mer random primer generated RAPD markers ranging from 250 to 2400 base pairs (bp). Genetic similarity estimates obtained by pairwise comparisons based on the method of Nei and Li (1979) indicated high genetic similarity (mean genetic similarity (±
Genetic diversity of two Portuguese populations of the pullet carpet shell Venerupis senegalensis, based on RAPD markers: contribution to a sustainable restocking program
NASA Astrophysics Data System (ADS)
Joaquim, Sandra; Pereira, Jorge; Leităo, Alexandra; Matias, Domitília; Chaves, Raquel; Guedes-Pinto, Henrique; Chícharo, Luís; Gaspar, Miguel
The pullet carpet shell Venerupis senegalensis (= V. pullastra) is a commercially important species in Portugal, Spain, France, and Italy. In Portugal, this species was once abundant in the Ria Formosa (southern Portugal). However, in the early 1980s, its abundance declined dramatically due to overfishing. In order to reverse this negative trend, the genetic sustainable management of the wild stocks of V. senegalensis should be performed by promoting successful restocking actions and the development of an aquaculture commercial production program of this species. In order to find the best broodstock for aquaculture purposes and therefore minimize the deleterious effects of hatchery practices, we analyzed the genetic diversity of the natural population to be restocked (Ria Formosa) but also of another potential genetically close population (Ria de Aveiro) by RAPD. Similar and substantive percentage of polymorphic loci, effective number of alleles, Nei's gene diversity, and Shannon's diversity index was found within both populations. This high genetic variability within populations suggests that they might have a gene pool with sufficient genetic plasticity to support changes in the environmental conditions. Analyses of population genetic structure also revealed a small genetic differentiation between the two populations. The high genetic variability of the natural population to be restocked makes it the preferential broodstock for aquaculture purposes. However, the Ria de Aveiro population could also be a viable alternative, due to its genetic plasticity and the genetic similarity of both populations. The results of this study can be useful to the sustainable management of wild stocks as well as in promoting successful restocking actions based on aquaculture production.
[Cloning and analyzing of the female-specific marker in the dioecious species Asparagus officinalis L].
Lu, Long Dou; Li, Rui Li; Gao, Wu Jun; Deng, Chuan Liang; Wang, Lian Jun
Sex-linked molecular markers are being obtained, which would be essential to be used in the screening of different sex of dioecious plants at the seedling stage. Furthermore, it is important in cloning the gene related to the sex. In this study the random amplified polymorphic DNA (RAPD) technique was employed with the objective to find markers linked to sex determination in Asparagus. A total of 100 primers were tested with the same PCR cycling procedure. A female-associated fragment with a length of about 867bp was generated with S12 primer. The fragment was cloned and sequenced, showing it is abundant in AT and contains 2 shorter open reading frames. In order to convert the RAPD marker into SCAR (sequence characterized amplified regions) marker, 24bp specific primers were constructed and used for PCR amplifying. The female-linked dominant SCAR marker was obtained, which would be efficient to identify the different sex of Asparagus officinalis L. PMID:16944605
New models and molecular markers in evaluation of developmental toxicity
Huuskonen, Hannele [National Product Control Agency for Welfare and Health, Chemicals Department, STTV c/o National Public Health Institute, P.O. Box 95, FIN-70701 Kuopio (Finland)]. E-mail: email@example.com
Mammalian and non-mammalian embryos and embryonic stem cells may be used as models in mechanistic studies and in testing embryotoxicity of compounds. In addition to conventional culture methods, genetic modifications and use of molecular markers offer significant advantages in mechanistic studies as well as in developing new test methods for embryotoxicity. Zebrafish model has been used for a long time and at present several applications are available. It is an easy vertebral non-mammalian model, whose genome is largely known and several genetic modifications are easily constructed to study gene expression or knocked down genes. Fluorescent marker proteins can be used also in zebrafish to indicate gene activation in transgenic models. Chemical genetics approach has been developed using zebrafish model. This is a new approach to screen small molecules that regulate signaling pathways. Embryonic stem cells have been used in mechanistic studies and mouse embryonic stem cell test has been validated to study embryotoxicity in vitro. This method has been improved using quantitative measurements of molecular endpoints by real-time RT-PCR or fluorescent activated cell sorting methods (FACS). Methods facilitating differentiation to several different cell types are available. We have studied preimplantation mouse embryos as a possible model for in vitro testing. In this method, superovulated and in vivo fertilized preimplantation embryos were collected at morula stage and cultured up to blastocysts. The mouse preimplantation culture test was improved by quantitative gene expression measurement using two-step real-time RT-PCR methods. New endpoints improve the tests of in vitro embryotoxicity because subjective assessments are replaced by objective measurements. In addition, automation is possible and less time is needed for analysis. Thus, high throughput screening will come possible to test large numbers of compounds.
Immune Response to Mycobacterium tuberculosis and Identification of Molecular Markers of Disease
Mercedes Gonzalez-Juarrero; Luke C. Kingry; Diane J. Ordway; Marcela Henao-Tamayo; Marisa Harton; Randall J. Basaraba; William H. Hanneman; Ian M. Orme; Richard A. Slayden
The complex molecular events that occur within the host during the establishment of a Mycobacterium tuberculosis infection are poorly defined, thus preventing identification of predictive markers of disease progression and state. To identify such molecular markers during M. tuberculosis infection, global changes in transcriptional response in the host were assessed using mouse whole genome arrays. Bacterial load in the lungs,
Molecular evidence for the hybrid origin of Paulownia Taiwaniana based on RAPD markers and RFLP of chloroplast DNA
W. Y. Wang; R. C. Pai; C. C. Lai; T. P. Lin
Genomic DNA of Paulownia fortunei, P. kawakamii and P. taiwaniana were amplified with 10-base primers of arbitrary sequences using the polymerase chain reaction (PCR). A total of 351 DNA fragments were amplified from 23 primers and of these 265 fragments (75.5%) were polymorphic. Almost all of the PCR-amplified products of P. taiwaniana were shared by either P. fortunei or P.
A novel and efficient strategy for practical identification of tomato (Solanum lycopersicon) varieties using modified RAPD fingerprints.
Korir, N K; Li, X Y; Leng, X P; Wu, Z; Wang, C; Fang, J G
Tomato breeding and variety development have led to the generation of a large number of varieties in many countries worldwide. This has created a growing and urgent need for an improved strategy for genotyping and identification since the traditional methods based on phenotype are growing unreliable. DNA markers could provide distinct benefits in tomato variety identification; however, DNA fingerprint analyses have not made DNA marker data readily usable for identification of varieties in tomato and other crops. A manual cultivar and/or variety identification diagram (MCID) strategy has been developed and has been found to make DNA markers more usable for the identification of genotyped plant individuals. We adopted this strategy, using modified RAPD markers to identify 42 tomato varieties from different geographical origins and seed merchants. All of the varieties were clearly separated and individually identified by reproducible fingerprints of only 6 RAPD primers. The tomato MCID that is generated is usable for the identification of any two or more tomato varieties. In addition, fewer primers can be used to make a distinction between varieties using this approach, since the selected fingerprints from each primer are used after they have been generated. The information in this first version of the tomato MCID can be enriched through identification and incorporation of more varieties and adaptation to other molecular markers in order to provide a more comprehensive tomato variety identification service for the horticultural industry. PMID:23913374
Molecular typing by random amplification of polymorphic DNA (RAPD) and detection of virulence genes of Salmonella enterica subspecies enterica serovar Gallinarum biovar gallinarum.
Jin, Ji-Dong; Lee, Dong-Seok; Shin, Eun-Kyung; Kim, Sun-Joong; Jung, Rose; Hahn, Tae-Wook
Salmonella enterica subspecies enterica serovar Gallinarum biovar Gallinarum is the causative agent of fowl typhoid in chickens, outbreaks of which have devastated poultry populations in Korea since 1992. In order to identify genetic differences among S. Gallinarum isolates, bacteria were examined using the random amplified polymorphic DNA (RAPD) method. Of 13 arbitrary primers screened initially, the primer designated as universal rice primer-6 (URP-6) was selected for subsequent typing assays because it produced a distinctive and reproducible DNA fingerprint for a S. Gallinarum reference strain. URP-6-based RAPD analysis assigned 30 S. Gallinarum isolates into 6 types, with 26 isolates (86.6%) belonging to 2 major RAPD types. The distribution of virulence genes in S. Gallinarum isolates was examined by Southern hybridization. All tested isolates had the invasion gene, invA, the virulence plasmid gene, spvB, and the S. Enteritidis fimbrial gene, sefC. The distribution of virulence genes among S. Gallinarum isolates did not correlate with any specific RAPD type. PMID:17213701
Molecular markers and their use in animal breeding
The use of DNA markers to define the genetic makeup (genotype) and predict the performance of an animal is a powerful aid to animal breeding. One strategy is known as marker-assisted selection (MAS). MAS facilitates the exploitation of existing genetic diversity in breeding populations and can be used to improve a whole range of desirable traits. DNA markers are, by
A pseudoautosomal random amplified polymorphic DNA marker for the sex chromosomes of Silene dioica.
Di Stilio, V S; Kesseli, R V; Mulcahy, D L
The segregation pattern of an 810-bp random amplified polymorphic DNA (RAPD) band in the F1 and backcross generations of a Silene dioica (L.) Clairv. family provides evidence that this molecular marker is located in the pseudoautosomal region (PAR) of the X and Y chromosomes. The marker was found through a combination of bulked segregant analysis (BSA) and RAPD techniques. Recombination rates between this pseudoautosomal marker and the differentiating portion of the Y chromosome are 15% in both generations. Alternative explanations involving nondisjunction or autosomal inheritance are presented and discussed. Chromosome counts provide evidence against the nondisjunction hypothesis, and probability calculations argue against the possibility of autosomal inheritance. This constitutes the first report of a pseudoautosomal DNA marker for plant sex chromosomes. PMID:9691057
A pseudoautosomal random amplified polymorphic DNA marker for the sex chromosomes of Silene dioica.
Di Stilio, V S; Kesseli, R V; Mulcahy, D L
The segregation pattern of an 810-bp random amplified polymorphic DNA (RAPD) band in the F1 and backcross generations of a Silene dioica (L.) Clairv. family provides evidence that this molecular marker is located in the pseudoautosomal region (PAR) of the X and Y chromosomes. The marker was found through a combination of bulked segregant analysis (BSA) and RAPD techniques. Recombination rates between this pseudoautosomal marker and the differentiating portion of the Y chromosome are 15% in both generations. Alternative explanations involving nondisjunction or autosomal inheritance are presented and discussed. Chromosome counts provide evidence against the nondisjunction hypothesis, and probability calculations argue against the possibility of autosomal inheritance. This constitutes the first report of a pseudoautosomal DNA marker for plant sex chromosomes. PMID:9691057
RAPD and ISSR fingerprinting in cultivated chickpea ( Cicer arietinum L.) and its wild progenitor Cicer reticulatum Ladizinsky
L. S. Rao; P. Usha Rani; P. S. Deshmukh; P. A. Kumar; S. K. Panguluri
Detection of genetic relationships between 19 chickpea cultivars and five accessions of its wild progenitor Cicer reticulatum Ladizinsky were investigated by using RAPD and ISSR markers. On an average, six bands per primer were observed in RAPD analysis\\u000a and 11 bands per primer in ISSR analysis. In RAPD, the wild accessions shared 77.8% polymorphic bands with chickpea cultivars,\\u000a whereas they
Genetic divergence among gerbera accessions evaluated by RAPD
Thiago Luiz Da Mata; Monique Inęs Segeren; Aline Segeren Fonseca; Carlos Augusto Colombo
Genetic diversity was evaluated by RAPD markers and morpho-agronomic characters for a total of 42 accessions of Barberton daisy (Gerbera jamesonii) consisting of 29 commercial and 13 wild accessions. A total of 74 polymorphic bands were obtained employing a set of 12 primer pairs. The average genetic similarity coefficient for the 42 accessions, evaluated by Jaccard index was 0.55 ranging
Ancient metalloenzymes as possible markers in molecular archaeology.
Kaup, Y; Weser, U
The successful preparation of an active remnant of Cu,Zn-superoxide dismutase from mummified brain tissue stimulated the isolation of both biochemically and immunologically active alkaline Zn2Mg-phosphatase from antique bone samples of different archaeological sites and age. In particular, specimens from pharaonic Egypt being up to 4000 years of age were used. Gel filtration, ion exchange and affinity chromatographies were employed to optimise the preparation of the ancient enzyme. Compared to the specific activity of alkaline phosphatase from modern autopsy some 50% for a Ptolemaic and 10% for the Old Kingdom enzyme was detectable. The possibility of microbial contamination was checked by employing specific monoclonal antibodies directed against the human bone enzyme. Fortunately, ubiquitously present specified microorganisms on the respective ancient bones did not cross-react with these antibodies while the ancient metalloenzyme reacted with high specificity. Alkaline phosphatase mimicks could be excluded as in the presence of the inhibitors 1,10-phenanthroline and L-homoarginine the enzyme activity was diminished. The presence of ortho-vanadate as a substrate analogon abolished the catalytic function of the enzyme. Likewise, heating to 100 degrees C and replacement of zinc(II) by cadmium(II) resulted in a dramatic loss of activity. In conclusion, alkaline phosphatase appears to be a useful marker enzyme in molecular archaeology. PMID:10830839
Identifying commercially relevant Echinacea species by AFLP molecular markers.
Russi, Luigi; Moretti, Chiaraluce; Raggi, Lorenzo; Albertini, Emidio; Falistocco, Egizia
The rising interest in medicinal plants has brought several species of the genus Echinacea to the attention of many scientists. Echinacea angustifolia, E. pallida, and E. purpurea are the most important for their immunological properties, well known and widely used by the native Americans. The three species are easily distinguishable on the basis of their morphological characteristics, but it would be difficult, if not impossible, to distinguish them in commercial preparations of ground, dry plant parts of E. purpurea (the most valuable species for chemotherapeutic properties) mixed with the other two species. Species-specific molecular markers could be useful to address this issue. In the present work, using fresh material collected from cultivated Echinacea spp., AFLP analysis was used to discriminate the three species and to detect species-specific DNA fragments. By using 14 primer combinations it was possible to detect a total of 994 fragments, of which 565 were polymorphic. Overall, 89 fragments were unique to E. purpurea, 32 to E. angustifolia, and 26 to E. pallida. E+CAC/M+AAT or E+CAC/M+AGC alone provided 13, 9, and 4 or 7, 5, and 5 specific fragments for E. purpurea, E. angustifolia, and E. pallida, respectively. A validation trial to confirm the results was carried out on bulked samples of 23 accessions covering most of the genetic diversity of the three species. The results are discussed in terms of practical applications in the field of popular medicine, detecting frauds, and implications for the genus Echinacea. PMID:19935915
Identification of leaf rust resistance genes in wheat ( Triticum aestivum L.) cultivars using molecular markers
O. Yu. Urbanovich; S. V. Malyshev; T. V. Dolmatovich; N. A. Kartel
A collection of 68 cultivars of common wheat has been screened for leaf rust resistance genes with the use of molecular markers.\\u000a Markers of genes Lr1, Lr9, Lr10, Lr19, Lr20, Lr21, Lr24, and Lr26 have been used. It has been suggested that allele Xgwm295 be used as a marker for identifying the Lr34 gene. The genes originating from Triticum aestivum
Molecular Markers of Lung Cancer in MAYAK Workers
Steven A. Belinsky, PhD
The molecular mechanisms that result in the elevated risk for lung cancer associated with exposure to radiation have not been well characterized. Workers from the MAYAK nuclear enterprise are an ideal cohort in which to study the molecular epidemiology of cancer associated with radiation exposure and to identify the genes targeted for inactivation that in turn affect individual risk for radiation-induced lung cancer. Epidemiology studies of the MAYAK cohort indicate a significantly higher frequency for adenocarcinoma and squamous cell carcinoma (SCC) in workers than in a control population and a strong correlation between these tumor types and plutonium exposure. Two hypotheses will be evaluated through the proposed studies. First, radiation exposure targets specific genes for inactivation by promoter methylation. This hypothesis is supported by our recent studies with the MAYAK population that demonstrated the targeting of the p16 gene for inactivation by promoter methylation in adenocarcinomas from workers (1). Second, genes inactivated in tumors can serve as biomarkers for lung cancer risk in a cancer-free population of workers exposed to plutonium. Support for this hypothesis is based on exciting preliminary results of our nested, case-control study of persons from the Colorado cohort. In that study, a panel of methylation markers for predicting lung cancer risk is being evaluated in sputum samples from incident lung cancer cases and controls. The first hypothesis will be tested by determining the prevalence for promoter hypermethylation of a panel of genes shown to play a critical role in the development of either adenocarcinoma and/or SCC associated with tobacco. Our initial studies on adenocarcinoma in MAYAK workers will be extended to evaluate methylation of the PAX5 {alpha}, PAX5 {beta}, H-cadherin, GATA5, and bone morphogenesis 3B (BMP3B) genes in the original sample set described under Preliminary studies. In addition, studies will be initiated in SCC from workers and controls to identify genes targeted for inactivation by plutonium in this other common histologic form of lung cancer. We will examine methylation of the p16, O{sup 6}-methylguanine-DNA methyl-transferase (MGMT), and death associated protein kinase genes ([DAP-K], evaluated previously in adenocarcinomas) as well as the new genes being assessed in the adenocarcinomas. The second hypothesis will be tested in a cross-sectional study of cancer-free workers exposed to plutonium and an unexposed population. A cohort of 700 cancer-free workers and 700 unexposed persons is being assembled, exposures are being defined, and induced sputum collected at initial entry into the study and approximately 1-year later. Exposed and unexposed persons will be matched by 5-year age intervals and smoking status (current and former). The frequency for methylation of four genes that show the greatest difference in prevalence in tumors from workers and controls will be determined in exfoliated cells within sputum. These studies will extend those in primary tumors to determine whether difference in prevalence for individual or multiple genes are detected in sputum samples from high-risk subjects exposed to plutonium. Follow-up of this cohort offers the opportunity to validate these endpoints and future biomarkers as true markers for lung cancer risk.
Association between molecular markers for beef tenderness and growth traits in Argentinian angus cattle.
Pintos, D; Corva, P M
Molecular markers for beef tenderness are classic examples of the contribution of genome technology to animal breeding through marker-assisted selection (MAS). Markers on the ?-calpain (CAPN1) and calpastatin (CAST) genes have been extensively evaluated for their association with tenderness. However, little is known about their potential effect on other economically important traits. In this work, the association of molecular markers for beef tenderness with growth traits was evaluated in Angus cattle of Argentina. Expected progeny differences were extracted from the 2008 Angus Sire Summary of Argentina. Information corresponding to 268 influential bulls that had been genotyped for two markers in CAPN1 and two markers in CAST was provided by the Argentine Angus Association. Genotype probabilities were assigned, by segregation analysis, to those bulls in the Sire Summary that had no marker information. Expected progeny differences of 1365 sires were regressed on the number of alleles favouring tenderness at each locus. There was a significant effect of markers on expected progeny differences of birth weight, weaning weight (direct), weight at 18 months and rib eye area. In general, there was a negative effect of alleles favouring tenderness on growth traits. These correlated responses should be taken into account when molecular markers are used in selection schemes that aim to improve beef tenderness. PMID:21554351
A review on SNP and other types of molecular markers and their use in animal genetics
Alain Vignal; Denis Milan; Magali SanCristobal; André Eggen
During the last ten years, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in animal genetics studies. Amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high
Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.
Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki
In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561
Organic molecular markers were measured in airborne particulate matter (PM10) from the City of Philadelphia North Broad Street air quality monitoring site to identify the seasonal abundances of key tracer compounds together with their dominant sources. Daily PM10...
The use of molecular markers in apple breeding for disease resistance.
Stankiewicz, Marta; Pitera, Emilian; Gawro?ski, Stanis?aw W
Molecular markers have become a useful tool simplifying and speeding up breeding work. They are also helpful in the genetic analysis of complex agronomic traits. The investigations concern the use of already available SCAR markers for molecular analysis of breeding materials. The markers are the apple powdery mildew resistance gene Pl2, originating from Malus zumi, and the apple scab resistance gene Vf, from M. floribunda 821. The clone U 211 was found to be highly resistant to mildew under field conditions and transmitted a high level of resistance to the majority of its progeny. The presence of the Vf gene conferring resistance to scab was confirmed by molecular analysis. As the molecular markers for the Pl2 gene are not present in the DNA of U 211, it is probable that the clone U 211 is a new source of mildew resistance. PMID:12378248
ZIP4 is a novel molecular marker for glioma
Lin, Yi; Chen, Yong; Wang, Yongzhi; Yang, Jingxuan; Zhu, Vivian F.; Liu, Yulun; Cui, Xiaobo; Chen, Leon; Yan, Wei; Jiang, Tao; Hergenroeder, Georgene W.; Fletcher, Stephen A.; Levine, Jonathan M.; Kim, Dong H.; Tandon, Nitin; Zhu, Jay-Jiguang; Li, Min
Background Dysregulated zinc transport has been observed in many cancers. However, the status of zinc homeostasis and the expression profile of zinc transporters in brain and brain tumors have not been reported. Methods The gene profiles of 14 zinc importers (ZIPs) and 10 zinc exporters (ZnTs) in patients with glioma were studied by investigating the association between the zinc transporters and brain tumor characteristics (tumor grade and overall survival time). Three independent cohorts were analyzed to cross-validate the findings: the Chinese Glioma Genome Atlas (CGCA) cohort (n = 186), the US National Cancer Institute Repository for Molecular Brain Neoplasia Data (REMBRANDT) cohort (n = 335), and The University of Texas (UT) cohort (n = 34). Results The expression of ZIP3, 4, 8, 14, ZnT5, 6, and 7 were increased, and the expression of ZnT10 was decreased in grade IV gliomas, compared with grade II gliomas. Among all 24 zinc transporters, ZIP4 is most significantly associated with tumor grade and overall survival; this finding is consistent across 2 independent cohorts (CGCA and REMBRANDT) and is partially validated by the third cohort (UT). High ZIP4 expression was significantly associated with higher grade of gliomas and shorter overall survival (hazard ratio = 1.61, 95% confidence interval = 1.02–2.53, P = .040 in CGCA cohort; hazard ratio = 1.32, 95% confidence interval = 1.08–1.61, P = .007 in REMBRANDT cohort). Conclusions Dysregulated expression of zinc transporters is involved in the progression of gliomas. Our results suggest that ZIP4 may serve as a potential diagnostic and prognostic marker for gliomas. PMID:23595627
Differential survival of mosquitofish exposed to radionuclides is dependent on RAPD genotype
Theodorakis, C.W. [Oak Ridge Associated Universities, TN (United States); Shugart, L.R. [Oak Ridge National Lab., TN (United States)
In previous studies, it was found that certain RAPD (Randomly Amplified Polymorphic DNA) markers were present at higher frequencies in radionuclide-contaminated mosquitofish (Gambusia affinis) populations than in reference populations. These markers will be referred to as contaminant specific markers. In the present study, fish with and without these markers were collected from non-contaminated populations and exposed in situ to radionuclides by caging them in one of the contaminated sites. Forty fish were exposed for 1--6 weeks, after which the survivors were collected and DNA was extracted for genotypic analysis. In one experiment, the frequencies of contaminant specific markers in the survivors were compared to the frequencies of these markers in the native contaminated and uncontaminated (the source of the caged fish) populations. It was found that the genotypic distributions were more similar to the native contaminated population. In another experiment, samples of caudal fin tissue were collected for DNA extraction before and after placing fish in the cages, in order to compare survival rates of different genotypes. It was found that fish with the contaminant indicative bands had higher percent survival than the other fish. Experiments are underway or are being planned in order to determine the molecular identity of these bands and the ecological significance of altered band frequencies in hopes of developing population-level biomarkers of contaminant exposure and ecological affects.
Fingerprinting and Genetic Stability of Rubus Using Molecular Markers
Technology Transfer Automated Retrieval System (TEKTRAN)
DNA markers were used to identify raspberries and blackberries and to evaluate genetic stability of four cryopreserved Rubus accessions following 12 years of storage in liquid nitrogen. In the first study, 12 genomic Simple Sequence Repeat (SSR) markers and one Expressed Sequence Tag- (EST)-SSR wer...
Molecular Markers of Radiation-related Normal Tissue Toxicity
Okunieff, Paul; Chen, Yuhchyau; Maguire, David J.; Huser, Amy K.
Over the past five decades, those interested in markers of radiation effect have focused primarily on tumor response. More recently, however, the view has broadened to include irradiated normal tissues—markers that predict unusual risk of side-effects, prognosticate during the prodromal and therapeutic phases, diagnose a particular toxicity as radiation-related, and, in the case of bioterror, allow for tissue-specific biodosimetry. Currently, there are few clinically useful radiation-related biomarkers. Notably, levels of some hormones such as thyroid-stimulating hormone (TSH) have been used successfully as markers of dysfunction, indicative of the need for replacement therapy, and for prevention of cancers. The most promising macromolecular markers are cytokines: TGF?, IL-1, IL-6, and TNF? being lead molecules in this class as both markers and targets for therapy. Genomics and proteomics are still in nascent stages and are actively being studied and developed. PMID:18506399
Molecular Markers for Genetic Diversity and Bayoud Disease Resistance in Date Palm
My H. Sedra
\\u000a The date palm (Phoenix dactylifera L) is a monocotyledoneus woody perennial and dioecious plant with a long generation life time. Traditional and modern genetic\\u000a improvement in date palm need long time and considerable funds. The molecular markers can assist the selection and give better\\u000a and efficient research strategies. Several researches cited in this overview paper showed the use molecular markers
Molecular markers for population genetic analyses in the family Psittacidae (Psittaciformes, Aves)
Patrícia J. Faria; Cristina Y. Miyaki
The selection of molecular markers for population studies is an important tool for biodiversity conservation. The fam- ily Psittacidae contains many endangered and vulnerable species and we tested three kinds of molecular markers for their potential use in population studies of five psitacid species: 43 hyacinth macaws (Anodorhynchus hyacinthinus), 42 blue-and-yellow macaws (Ara ararauna), 23 red-and-green macaws (Ara chloroptera), 19
New sequence-tagged site molecular markers for identification of sex in Distichlis spicata.
Eppley, Sarah M; O'Quinn, Robin; Brown, Anna L
Sex-linked molecular markers have become valuable tools for understanding sex ratio evolution and sex-specific physiology in pre-reproductive plants. To develop new accurate methods for sexing Distichlis spicata juveniles and nonflowering individuals, we converted a random amplified polymorphic DNA-polymerase chain reaction marker that co-segregated with the female phenotype into a set of sequence-tagged site markers. We tested the marker pair on known males and females from populations in Oregon and California. A single band was obtained for all female samples but never for males. PMID:21564910
Comparison of RAPD, AFLP, and EF-1? Sequences for the Phylogenetic Analysis of Fusarium oxysporum and Its formae speciales in Korea
Park, Jae-Min; Kim, Gi-Young; Lee, Song-Jin; Kim, Mun-Ok; Huh, Man-Kyu; Lee, Tae-Ho
Although Fursarium oxysporum causes diseases in economically important plant hosts, identification of F. oxysporum formae speciales has been difficult due to confusing phenotypic classification systems. To resolve these complexity, we evaluated genetic relationship of nine formae speciales of F. oxysporum with random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and translation elongation factor-1 alpha (EF-1?) gene. In addition, the correlation between mycotoxin content of fusaric acid and isolates based on molecular marker data was evaluated using the modified Mantel's test. According to these result, these fusaric acid-producing strains could not identify clearly, and independent of geographic locations and host specificities. However, in the identification of F. oxysporum formae speciales, especially, AFLP analysis showed a higher discriminatory power than that of a the RAPD and EF-1? analyses, all three techniques were able to detect genetic variability among F. oxysporum formae speciales in this study. PMID:24039470
Molecular and cytological analyses of Deschampsia cespitosa populations from Northern Ontario (Canada).
Nkongolo, K K; Deck, A; Michael, P
Deschampsia cespitosa is widely dispersed around the globe, particularly in the northern hemisphere. A high tolerance to adverse environmental conditions allows D. cespitosa to colonize and dominate plots of land that are uninhabitable by other plants. The main objective of the present study was to determine the degree of genetic variation and relatedness among D. cespitosa populations from heavy metal contaminated sites and uncontaminated sites in Northern Ontario, using RAPD markers. Genomic DNA samples from individual plants were analyzed using 35 oligonucleotides of random sequence. Twenty-eight of these primers allowed amplification of random polymorphic DNA (RAPD) loci. Overall, 90% of RAPD bands were polymorphic. Analysis of molecular variance revealed that 72% of the variation could be attributed to individual differences within each of the populations. The within- and among-region variations accounted for 14 and 15% of the total molecular variance, respectively. Population-specific RAPD markers were identified. RAPD markers specific to D. cespitosa were isolated, cloned, and characterized. Cytogenetic analysis revealed a high level of aneuploidy in all the populations from Northern Ontario, with chromosome numbers varying from 2n = 18 to 2n = 26. PMID:11681605
Genetic diversity in Indonesian shallot ( Allium cepa var. ascalonicum ) and Allium × wakegi revealed by RAPD markers and origin of A. × wakegi identified by RFLP analyses of amplified chloroplast genes
Noor Sugiharto Arifin; Yukio Ozaki; Hiroshi Okubo
RAPD and PCR-RFLP analyses were conducted to establish the phylogenetic relationships among collected accessions of shallot and Allium × wakegi, and to assess the origin of A. × wakegi. Twenty out of 100 primers were amplified with 112 scorable bands for cluster analysis. Two main cluster groups consisting of one group for shallot and another group for A. × wakegi
The Effects of Water Matrix on Decay of Human Fecal Molecular Markers and Campylobacter spp.
Although molecular source tracking for human fecal contamination is used on a wide range of sample types, little is known about comparative decay of proposed molecular markers under different conditions, or correlation with pathogen decay. Our purpose was to measure correlations ...
Molecular markers from the transcribed/expressed region of the genome in higher plants.
Gupta, P K; Rustgi, S
In recent years, molecular marker technology in higher plants has witnessed a shift from the so-called random DNA markers (RDMs), developed in the past arbitrarily from genomic DNA and cDNA, to the molecular markers representing the transcriptome and the other coding sequences. These markers have been described as gene targeted markers (GTMs). Another specific class of markers includes the so-called functional markers (FMs), which are supposed to have a cause and effect relationship with the traits of interest. In this review, we first describe the development of these markers representing the transcriptome or genes per se; we then discuss the uses of these markers in some detail and finally add a note on the future directions of research and the implications of the wider application of these markers in crop improvement programmes. Using suitable examples, we describe markers of different classes derived from cDNA clones, expressed sequence tags (ESTs), gene sequences and the unique (coding) sequences obtained through methyl filtration or genome normalization (high C(0) t fraction) from gDNA libraries. While we briefly describe RFLPs, SSRs, AFLPs and SNPs developed from the transcriptome (cDNA clones and EST databases), we have discussed in more detail some of the novel markers developed from the transcriptome and specific genes. These novel markers include expressed sequence tag polymorphisms (ESTPs), conserved orthologue set (COS) markers, amplified consensus genetic markers (ACGMs), gene specific tags (GSTs), resistance gene analogues (RGAs) and exon-retrotransposon amplification polymorphism (ERAP). Uses of these markers have been discussed in some detail under the following headings: development of transcript and functional maps, estimations of genetic diversity, marker-assisted selection (MAS), candidate-gene (CG) approach and map-based cloning, genetical genomics and identification of eQTLs, study of genome organization and taxonomic and phylogenetic studies. At the end, we also append a list of websites relevant to further studies on the transcriptome. For want of space, considerable information including voluminous data in the form of 12 tables, and a long list of references cited in these tables, has been placed on the Internet as electronic supplementary material (ESM), which the readers may find useful. PMID:15095058
A Comparison of Three Molecular Markers for the Identification of Populations of Globodera pallida.
Hoolahan, Angelique H; Blok, Vivian C; Gibson, Tracey; Dowton, Mark
Potato cyst nematodes cost the potato industry substantial financial losses annually. Through the use of molecular markers, the distribution and infestation routes of these nematodes can be better elucidated, permitting the development of more effective preventative methods. Here we assess the ability of three molecular markers to resolve multiple representatives of five Globodera pallida populations as monophyletic groups. Molecular markers included a region of the rbp-1 gene (an effector), a non-coding nuclear DNA region (the ITS region), and a novel marker for G. pallida, a ?3.4 kb non-coding mitochondrial DNA (mtDNA) region. Multiple phylogenetic analysis methods were performed on the three DNA regions separately, and on a data set of these three regions combined. The analyses of the combined data set were similar to that of the sole mtDNA marker; resolving more populations as monophyletic groups, relative to that of the ITS region and rbp-1 gene region. This suggests that individual markers may be inadequate for distinguishing populations of G. pallida. The use of this new non-coding mtDNA marker may provide further insights into the historical distribution of G. pallida, as well as enable the development of more sensitive diagnostic methods. PMID:23482966
Applications and Implications of Neutral versus Non-neutral Markers in Molecular Ecology
Kirk, Heather; Freeland, Joanna R.
The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection. PMID:21747718
Genetic Diversity Within and Among Lepidium draba Populations from Eastern Anatolia Based on RAPD Analysis
Ozkan Aksakal; Serap Sunar; Yusuf Kaya; Guleray Agar
Genetic variation and structure of six natural populations of Lepidium draba L. from Eastern Anatolia were assessed using random amplified polymorphic DNA (RAPD) markers. For RAPD analysis, 12 primers\\u000a generated 218 reproducible bands across the six populations analyzed, of which 73 bands (33.3%) were polymorphic. The mean\\u000a Nei's gene diversity value for all six populations was 0.1771. Shannon's information index
Clonal and population RAPD variation of cercariae obtained from Bucephalus polymorphus sporocysts (Trematoda: Bucephalidae)
A. V. Korsunenko; A. V. Tyutin; S. K. Semyenova
Three arbitrary primers produced 114 RAPD markers for 37 cercariae from nine Bucephalus polymorphus sporocysts obtained from three Dreissena polymorpha mollusks, which were collected in two water reservoirs of the Volga basin. Analysis of the RAPD patterns established a unique\\u000a genotype for each cercaria. The topology of an UPGMA dendrogram did not reliably differentiate the cercaria according to the\\u000a corresponding
Technology Transfer Automated Retrieval System (TEKTRAN)
There have been 40 sequence characterized amplified region (SCAR) markers (http://www.usda.prosser.wsu.edu/miklas/Scartable3.pdf) generated across laboratories that are available for indirect selection of 27 qualitatively and 8 quantitatively expressed genes conditioning resistance to bacterial, fun...
A SCAR marker for the sex types determination in Colombian genotypes of Carica papaya
Giovanni Chaves-Bedoya; Víctor Nuńez
Sex type determination in papaya (Carica papaya L.) is very important for crop improvement processes because it accelerates the identification of the fruitful plants. The\\u000a use of molecular technology provides a quick and reliable identification of sex types in plantlets growing in seedbeds. Random\\u000a amplified polymorphic DNA (RAPD) markers were used to determine the sex types of Colombian cultivars of
RAPD typing in microbiology—a technical review
E. G. M. Power
Many biochemical and molecular techniques can be used for distinguishing isolates of a given bacterial species. Traditional typing techniques based on phenotypic characteristics such as serotyping are being increasingly challenged by the use of DNA-based methods. The introduction of the polymerase chain reaction (PCR) has led to typing techniques based on DNA amplification. Randomly amplified polymorphic DNA (RAPD) typing (also
Molecular markers to study competition and diversity of Rhizobium
A. Sessitsch
The research described in this thesis was directed to the development of molecular identification and detection techniques for studying the ecology of Rhizobium, a nitrogen- fixing bacterium of agricultural importance. Competition of inoculant strains with indigenous microbes is a serious problem in agricultural practice and was therefore addressed in this work using the developed tools. Furthermore, various molecular techniques have
DNA markers in molecular diagnostics for hepatocellular carcinoma
Su, Ying-Hsiu; Lin, Selena Y; Song, Wei; Jain, Surbhi
Hepatocellular carcinoma (HCC) is the one of the leading causes of cancer mortality in the world, mainly due to the difficulty of early detection and limited therapeutic options. The implementation of HCC surveillance programs in well-defined, high-risk populations were only able to detect about 40–50% of HCC at curative stages (Barcelona Clinic Liver Cancer stages 0 & 1) due to the low sensitivities of the current screening methods. The advance of sequencing technologies has identified numerous modifications as potential candidate DNA markers for diagnosis/surveillance. Here we aim to provide an overview of the DNA alterations that result in activation of cancer pathways known to potentially drive HCC carcinogenesis and to summarize performance characteristics of each DNA marker in the periphery (blood or urine) for HCC screening. PMID:25098554
Genetic variability of Brazilian isolates of Alternaria alternata detected by AFLP and RAPD techniques
Dini-Andreote, Francisco; Pietrobon, Vivian Cristina; Andreote, Fernando Dini; Romăo, Aline Silva; Spósito, Marcel Bellato; Araújo, Welington Luiz
The Alternaria brown spot (ABS) is a disease caused in tangerine plants and its hybrids by the fungus Alternaria alternata f. sp. citri which has been found in Brazil since 2001. Due to the recent occurrence in Brazilian orchards, the epidemiology and genetic variability of this pathogen is still an issue to be addressed. Here it is presented a survey about the genetic variability of this fungus by the characterization of twenty four pathogenic isolates of A. alternata f. sp. citri from citrus plants and four endophytic isolates from mango (one Alternaria tenuissima and three Alternaria arborescens). The application of two molecular markers Random Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) had revealed the isolates clustering in distinct groups when fingerprintings were analyzed by Principal Components Analysis (PCA). Despite the better assessment of the genetic variability through the AFLP, significant modifications in clusters components were not observed, and only slight shifts in the positioning of isolates LRS 39/3 and 25M were observed in PCA plots. Furthermore, in both analyses, only the isolates from lemon plants revealed to be clustered, differently from the absence of clustering for other hosts or plant tissues. Summarizing, both RAPD and AFLP analyses were both efficient to detect the genetic variability within the population of the pathogenic fungus Alternaria spp., supplying information on the genetic variability of this species as a basis for further studies aiming the disease control. PMID:24031413
Genetic variability of Brazilian isolates of Alternaria alternata detected by AFLP and RAPD techniques.
Dini-Andreote, Francisco; Pietrobon, Vivian Cristina; Andreote, Fernando Dini; Romăo, Aline Silva; Spósito, Marcel Bellato; Araújo, Welington Luiz
The Alternaria brown spot (ABS) is a disease caused in tangerine plants and its hybrids by the fungus Alternaria alternata f. sp. citri which has been found in Brazil since 2001. Due to the recent occurrence in Brazilian orchards, the epidemiology and genetic variability of this pathogen is still an issue to be addressed. Here it is presented a survey about the genetic variability of this fungus by the characterization of twenty four pathogenic isolates of A. alternata f. sp. citri from citrus plants and four endophytic isolates from mango (one Alternaria tenuissima and three Alternaria arborescens). The application of two molecular markers Random Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) had revealed the isolates clustering in distinct groups when fingerprintings were analyzed by Principal Components Analysis (PCA). Despite the better assessment of the genetic variability through the AFLP, significant modifications in clusters components were not observed, and only slight shifts in the positioning of isolates LRS 39/3 and 25M were observed in PCA plots. Furthermore, in both analyses, only the isolates from lemon plants revealed to be clustered, differently from the absence of clustering for other hosts or plant tissues. Summarizing, both RAPD and AFLP analyses were both efficient to detect the genetic variability within the population of the pathogenic fungus Alternaria spp., supplying information on the genetic variability of this species as a basis for further studies aiming the disease control. PMID:24031413
Identification of molecular markers linked to adult plant leaf rust resistance gene Lr48 in wheat and detection of Lr48 in the Thatcher near-isogenic line with gene Lr25
D. Samsampour; B. Maleki Zanjani; J. K. Pallavi; Anupam Singh; A. Charpe; S. K. Gupta; K. V. Prabhu
The recessive adult plant resistance (APR) gene Lr48 in wheat was tagged with flanking random amplified polymorphic DNA (RAPD) markers. Markers S336775 in coupling and S3450 in repulsion with Lr48 were identified in wheat line CSP44. Tests of these markers on available Thatcher near-isogenic lines (NILs) detected the\\u000a likely presence of Lr48 in TcLr25. A test of allelism of APR
Detection of genetic variabiltiy in nonhuman isolates of Fasciola hepatica and Fasciola gigantica by the RAPD-PCR technique.
Ramadan, Nashwa I; Saber, Lobna M
The present study shows the molecular characterization of Fasciola gigantica and F. hepatica isolates collected from cows and sheep, using the random amplified polymorphic DNA fragments-polymerase chain reaction (RAPDs-PCR) technique. Optimal standardization of amplification conditions and thermocyclation were made, using genetic markers. The methodology used compared the genetic pattern between the two species (inter-species) and inside each species (intra-species) between cow and sheep and the amplification fragments were between 135 and 741 base pairs of marker. The results showed genetic variations (polymorphisms) of Fasciola gigantica and F. hepa-tica with amplification fragment based on a 500-400 base pair (bp). Inside each species, there were genetic variations in bovine and ovine and the amplification fragments were between 600 and 400 base pairs (bp). This assay is useful for both individual diagnosis and epidemiological surveys in endemic regions. PMID:15287188
QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum × Gossypium barbadense
Dao-Hua He; Zhong-Xu Lin; Xian-Long Zhang; Yi-Chun Nie; Xiao-Ping Guo; Yan-Xin Zhang; Wu Li
A high-density molecular marker linkage map of cotton based entirely on polymerase chain reaction-based markers is useful\\u000a for a marker-assisted breeding program. Four kinds of markers—simple sequence repeats (SSRs), sequence-related amplified polymorphism\\u000a (SRAP), random amplified polymorphic DNA (RAPD), and retrotransposon-microsatellite amplified polymorphism (REMAP)—were used\\u000a to assay an F2 population from a cross between "Handan208" (Gossypium hirsutum) and "Pima90" (Gossypium barbadense).
Construction of a genetic linkage map in tetraploid species using molecular markers.
Luo, Z W; Hackett, C A; Bradshaw, J E; McNicol, J W; Milbourne, D
This article presents methodology for the construction of a linkage map in an autotetraploid species, using either codominant or dominant molecular markers scored on two parents and their full-sib progeny. The steps of the analysis are as follows: identification of parental genotypes from the parental and offspring phenotypes; testing for independent segregation of markers; partition of markers into linkage groups using cluster analysis; maximum-likelihood estimation of the phase, recombination frequency, and LOD score for all pairs of markers in the same linkage group using the EM algorithm; ordering the markers and estimating distances between them; and reconstructing their linkage phases. The information from different marker configurations about the recombination frequency is examined and found to vary considerably, depending on the number of different alleles, the number of alleles shared by the parents, and the phase of the markers. The methods are applied to a simulated data set and to a small set of SSR and AFLP markers scored in a full-sib population of tetraploid potato. PMID:11238421
Designing a SCAR molecular marker for monitoring Trichoderma cf. harzianum in experimental communities* #
Pérez, Gabriel; Verdejo, Valentina; Gondim-Porto, Clarissa; Orlando, Julieta; Carú, Margarita
Several species of the fungal genus Trichoderma establish biological interactions with various micro- and macro-organisms. Some of these interactions are relevant in ecological terms and in biotechnological applications, such as biocontrol, where Trichoderma could be considered as an invasive species that colonizes a recipient community. The success of this invasion depends on multiple factors, which can be assayed using experimental communities as study models. Therefore, the aim of this work is to develop a species-specific sequence-characterized amplified region (SCAR) marker to monitor the colonization and growth of T. cf. harzianum when it invades experimental communities. For this study, 16 randomly amplified polymorphic DNA (RAPD) primers of 10-mer were used to generate polymorphic patterns, one of which generated a band present only in strains of T. cf. harzianum. This band was cloned, sequenced, and five primers of 20–23 mer were designed. Primer pairs 2F2/2R2 and 2F2/2R3 successfully and specifically amplified fragments of 278 and 448 bp from the T. cf. harzianum BpT10a strain DNA, respectively. Both primer pairs were also tested against the DNA from 14 strains of T. cf. harzianum and several strains of different fungal genera as specificity controls. Only the DNA from the strains of T. cf. harzianum was successfully amplified. Moreover, primer pair 2F2/2R2 was assessed by quantitative real-time polymerase chain reaction (PCR) using fungal DNA mixtures and DNA extracted from fungal experimental communities as templates. T. cf. harzianum was detectable even when as few as 100 copies of the SCAR marker were available or even when its population represented only 0.1% of the whole community. PMID:25367789
Designing a SCAR molecular marker for monitoring Trichoderma cf. harzianum in experimental communities.
Pérez, Gabriel; Verdejo, Valentina; Gondim-Porto, Clarissa; Orlando, Julieta; Carú, Margarita
Several species of the fungal genus Trichoderma establish biological interactions with various micro- and macro-organisms. Some of these interactions are relevant in ecological terms and in biotechnological applications, such as biocontrol, where Trichoderma could be considered as an invasive species that colonizes a recipient community. The success of this invasion depends on multiple factors, which can be assayed using experimental communities as study models. Therefore, the aim of this work is to develop a species-specific sequence-characterized amplified region (SCAR) marker to monitor the colonization and growth of T. cf. harzianum when it invades experimental communities. For this study, 16 randomly amplified polymorphic DNA (RAPD) primers of 10-mer were used to generate polymorphic patterns, one of which generated a band present only in strains of T. cf. harzianum. This band was cloned, sequenced, and five primers of 20-23 mer were designed. Primer pairs 2F2/2R2 and 2F2/2R3 successfully and specifically amplified fragments of 278 and 448 bp from the T. cf. harzianum BpT10a strain DNA, respectively. Both primer pairs were also tested against the DNA from 14 strains of T. cf. harzianum and several strains of different fungal genera as specificity controls. Only the DNA from the strains of T. cf. harzianum was successfully amplified. Moreover, primer pair 2F2/2R2 was assessed by quantitative real-time polymerase chain reaction (PCR) using fungal DNA mixtures and DNA extracted from fungal experimental communities as templates. T. cf. harzianum was detectable even when as few as 100 copies of the SCAR marker were available or even when its population represented only 0.1% of the whole community. PMID:25367789
Relationships among cultivated and wild lentils revealed by RAPD analysis
S. K. Sharma; I. K. Dawson; R. Waugh
RAPD markers were used to distinguish between six different Lens taxa, representing cultivated lentil and its wild relatives. Twenty-four arbitrary sequence 10-mer primers were identified which revealed robust and easily interpretable amplification-product profiles. These generated a total of 88 polymorphic bands in 54 accessions and were used to partition variation within and among Lens taxa. The data showed that, of
Molecular and cellular markers of toxicity in the Japanese Medaka @
Shugart, L.R.; McCarthy, J.F.; D'Surney, S.J.; Greeley, M.S. Jr.; Hull, C.G.
The Japanese Medaka (Oryzias latipes) has been recommended for use as a model organism to detect carcinogenic, teratogenic, cytotoxic, and genotoxic compounds in aquatic systems. Because a long latent period often occurs between initial contact with deleterious chemicals and subsequent expression of the pathology, we are investigating early biologically-relevant responses that can be used as genotoxicity markers of exposure and effect. This project focuses on the development of genotoxic bioassays and experimental protocols for exposing Japanese Medaka to genotoxic compounds. 21 refs., 8 figs, 2 tabs.
Volatility of organic molecular markers used for source apportionment analysis: measurements and implications for atmospheric lifetime.
May, Andrew A; Saleh, Rawad; Hennigan, Christopher J; Donahue, Neil M; Robinson, Allen L
Molecular markers are organic species used to define fingerprints for source apportionment of ambient fine particulate matter. Traditionally, these markers have been assumed to be stable in the atmosphere. This work investigates the gas-particle partitioning of eight organic species used as molecular markers in receptor models for biomass burning (levoglucosan), motor vehicles (5?-cholestane, n-hexacosane, n-triacontane, 1,2-benz[a]anthracene, coronene), and meat cooking (cholesterol, oleic acid). Experiments were conducted using a thermodenuder to measure the evaporation of single component particles. The data were analyzed using the integrated volume method to determine saturation concentrations and enthalpies of vaporization for each compound. The results indicate that appreciable quantities (>10%) of most of these markers exist in the gas phase under typical atmospheric conditions. Therefore, these species should be considered semivolatile. Predictions from a chemical kinetics model indicate that gas-particle partitioning has important effects on the atmospheric lifetime of these species. The atmospheric decay of semivolatile compounds proceeds much more rapidly than nonvolatile compounds because gas-phase oxidation induces evaporation of particle-phase material. Therefore, both gas-particle partitioning and chemical reactions need to be accounted for when semivolatile molecular markers are used for source apportionment studies. PMID:23013599
Evaluation of the random amplified polymorphic DNA (RAPD) assay for the detection of DNA damage and mutations
Franck A Atienzar; Paola Venier; Awadhesh N Jha; Michael H Depledge
The random amplified polymorphic DNA (RAPD) assay and related techniques like the arbitrarily primed polymerase chain reaction (AP-PCR) have been shown to detect genotoxin-induced DNA damage and mutations. The changes occurring in RAPD profiles following genotoxic treatments include variation in band intensity as well as gain or loss of bands. However, the interpretation of the molecular events responsible for differences
Molecular markers of dental pulp tissue during orthodontic tooth movement: a pilot study.
Abdul Wahab, Rohaya Megat; Zainal Ariffin, Shahrul Hisham; Yeen, Wong Woan; Ahmad, Nurul Atikah; Senafi, Sahidan
Three specific orthodontic tooth movement genes, that is, FCRL1, HSPG2, and LAMB2 were detected at upper first premolar (with appliance) dental pulp tissue by using GeneFishing technique as compared to lower first premolar (without appliance). These three differentially expressed genes have the potential as molecular markers during orthodontic tooth movement by looking at molecular changes of pulp tissue. PMID:22629122
[Differentiation of two hemp nettle species (Galeopsis bifida Boenn. and G. tetrahit L.) inferred from morphological characters and DNA markers].
Maslova, E V
Two species of the genus Galeopsis L., G. tetrahit L. and G. bifida (family Lamiaceae), are problematic to distinguish often wrongly recognized, and treated by some taxonomists as a single species. Morphological diagnostical characters of these species are variable and partly overlap. Species independence of G. tetrahit and G. bifida was evaluated and their diagnostic characters verified using ISSR and RAPD markers. A total of 57 ISSR and 28 RAPD fragments were obtained providing distinct subdivision of the accessions examined into two groups. Analysis of molecular data using the neighbor-joining method showed that the accessions studied fell into two clades in the same way as demonstrated by the analysis of 20 morphological characters using single linkage method. The morphological characters were found to be more variable compared to the molecular markers, although the combined of these characters provided differentiation of the species. PMID:18664141
Molecular Characterization of Entomopathogenic Fungi Using Microsatellite Markers.
Technology Transfer Automated Retrieval System (TEKTRAN)
Identification of entomopathogenic fungi isolated from their arthropod hosts or other sources can be cumbersome when certain morphological features are not clear or time consuming when the organism needs to reach a certain growth stage for proper identification. Molecular tools can be handy and offe...
Keratin Classes as Molecular Markers Epithelia: Cell Culture Studies
The keratins are a highly heterogeneous group of proteins that form intermediate filaments in a wide variety of epithelial cells. These proteins can be divided into at least seven major classes according to their molecular weight and their immunological reactivity with monoclonal antibodies. Tissue-distribution studies have revealed a correlation between the expression of specific keratin classes and different morphological features
Use of Molecular Markers for Catfish Production and Product Quality
Technology Transfer Automated Retrieval System (TEKTRAN)
Channel catfish are a diploid species native to North America and the primary product of U.S. aquaculture, and molecular genetic research supports selective breeding of catfish for commercial production. To date, short tandem repeat loci have been used to characterize DNA sequence variation within ...
Molecular imaging of rheumatoid arthritis: emerging markers, tools, and techniques
Early diagnosis and effective monitoring of rheumatoid arthritis (RA) are important for a positive outcome. Instant treatment often results in faster reduction of inflammation and, as a consequence, less structural damage. Anatomical imaging techniques have been in use for a long time, facilitating diagnosis and monitoring of RA. However, mere imaging of anatomical structures provides little information on the processes preceding changes in synovial tissue, cartilage, and bone. Molecular imaging might facilitate more effective diagnosis and monitoring in addition to providing new information on the disease pathogenesis. A limiting factor in the development of new molecular imaging techniques is the availability of suitable probes. Here, we review which cells and molecules can be targeted in the RA joint and discuss the advances that have been made in imaging of arthritis with a focus on such molecular targets as folate receptor, F4/80, macrophage mannose receptor, E-selectin, intercellular adhesion molecule-1, phosphatidylserine, and matrix metalloproteinases. In addition, we discuss a new tool that is being introduced in the field, namely the use of nanobodies as tracers. Finally, we describe additional molecules displaying specific features in joint inflammation and propose these as potential new molecular imaging targets, more specifically receptor activator of nuclear factor ?B and its ligand, chemokine receptors, vascular cell adhesion molecule-1, ?V?3 integrin, P2X7 receptor, suppression of tumorigenicity 2, dendritic cell-specific transmembrane protein, and osteoclast-stimulatory transmembrane protein. PMID:25099015
Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers
Technology Transfer Automated Retrieval System (TEKTRAN)
Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In...
Proceedings of the second international symposium on molecular markers in horticulture Acta Horticulturae
Technology Transfer Automated Retrieval System (TEKTRAN)
The second International Symposium on Molecular Markers in Horticulture was held at the CH2M Hill Alumni Center at Oregon State University (OSU), Corvallis (Oregon, US), from July 29 to August 1st, 2009. This symposium was convened by a scientist at the National Clonal Germplasm Repository (NCGR) of...
Molecular markers to study population structure and dynamics in beneficial insects (predators and parasitoids)
Catherine MacDonald; Hugh Loxdale
For beneficial insects--predators and parasitoids--to be used effectively within pest control scenarios, it is often necessary to have fundamental as well as more applied information about them, including data on population dynamics, host switching and breeding systems. In recent years, such information has been gained by the use of molecular DNA markers. In this article, we briefly discuss the range
POPULATION BIOLOGY/GENETICS Molecular Markers Reveal Infestation Dynamics of the Bed Bug
Vargo, Ed
POPULATION BIOLOGY/GENETICS Molecular Markers Reveal Infestation Dynamics of the Bed Bug (Hemiptera://dx.doi.org/10.1603/ME11256 ABSTRACT The bed bug, Cimex lectularius L. (Hemiptera: Cimicidae), has experienced. Once considered a pest of lower socioeconomic classes, bed bugs are now found extensively across all
Polycyclic aromatic hydrocarbons, black carbon, and molecular markers in soils of Switzerland
Thomas D. Bucheli; Franziska Blum; André Desaules; Örjan Gustafsson
Polycyclic aromatic hydrocarbons (PAH) were analysed in 23 soil samples (0–10 cm layer) from the Swiss soil monitoring network (NABO) together with total organic carbon (TOC) and black carbon (BC) concentration, as well as some PAH source diagnostic ratios and molecular markers. The concentrations of the sum of 16 EPA priority PAHs ranged from 50 to 619 ?g\\/kg dw. Concentrations
Correlation between molecular markers and adaptively significant genetic variation in Bromus tectorum (Poaceae), an inbreedingannual grass
A. P. Ramakrishnan; SUSAN E. MEYER; JENNIFER WATERS; MIKEL R. STEVENS; CRAIG E. COLEMAN; DANIEL J. FAIRBANKS
Single sequence repeat (SSR) and amplified fragment length polymorphic (AFLP) molecular marker genotypes in cheatgrass ( Bromus tectorum) were compared to published data on phenotypic variation in seed dormancy, vernalization requirement, and resistance to the pathogen Ustilago bullata. Several features of cheatgrass facilitated this study: it is a recent invader in the western United States, has considerable phenotypic polymorphism, and
Correlation between molecular markers and adaptively significant genetic variation in Bromus tectorum (Poaceae), an inbreedingannual grass.
Ramakrishnan, Alisa P; Meyer, Susan E; Waters, Jennifer; Stevens, Mikel R; Coleman, Craig E; Fairbanks, Daniel J
Single sequence repeat (SSR) and amplified fragment length polymorphic (AFLP) molecular marker genotypes in cheatgrass (Bromus tectorum) were compared to published data on phenotypic variation in seed dormancy, vernalization requirement, and resistance to the pathogen Ustilago bullata. Several features of cheatgrass facilitated this study: it is a recent invader in the western United States, has considerable phenotypic polymorphism, and is an obligate self-pollinator. Forty self-pollinating lines from four populations common to the three phenotypic data sets were analyzed for molecular genetic variation using seven SSR loci and 31 AFLP loci. We examined correlations between distance matrices using the Mantel test for each pair of studies. The two molecular data sets were significantly correlated (r = 0.636). The AFLP markers often distinguished among several lines with identical SSR genotypes. The AFLP data were also significantly correlated with the phenotypic data (r values from 0.4640 to 0.5658), but the SSR data were much more highly correlated (r values from 0.677 to 0.844). The difference between molecular marker systems was especially notable when an outlier population from Potosi Pass, Nevada, was excluded from the analysis. These results suggest that SSR markers may be good surrogates for phenotypic traits in population genetic studies of strongly inbreeding species such as cheatgrass. PMID:21653434
RiceCAP: Development of molecular markers associated with long grain milling yield
Technology Transfer Automated Retrieval System (TEKTRAN)
U.S. rice breeders are focused on developing new cultivars that have high yield and high milling quality. Using traditional breeding methods, it takes approximately ten years to develop a new cultivar. Development of molecular markers that are closely linked to traits of economic value will increase...
Molecular markers highlight variation within and among Kentucky bluegrass varieties and accessions
Technology Transfer Automated Retrieval System (TEKTRAN)
Assessing relationships among germplasm and cultivars of Kentucky bluegrass (Poa pratensis L.) is limited to field evaluations or a small set of molecular markers. To improve the efficiency of characterizing Kentucky bluegrass cultivars and germplasm, this study was designed to develop a larger set...
This work focuses on analysis of organic molecular markers in airborne particulate matter (PM) by Gas Chromatography/Ion Trap Mass Spectrometry (GC/IT MS). The particulate samples used in the method development were collected as PM10 in metropolitan Philadelphia during...
Molecular markers and allelic relationships of anthracnose resistance gene cluster B4 in common bean
Belén Méndez-Vigo; Cristina Rodríguez-Suárez; Astrid Pańeda; Juan José Ferreira; Ramón Giraldez
Allelism tests and molecular marker analyses were combined to characterize the genes that, proceeding from the germplasm lines 'A493' and 'A321', confer resistance to bean anthracnose in the new breeding lines 'A1220' and 'A1231', respectively, developed through backcross breeding, using the dry bean landrace 'Andecha' as the recurrent parent. Allelism tests indicate that resistance to race 38 of anthracnose in
Cloning and characterization of resistance gene candidate sequences and molecular marker development in gerbera (Gerbera hybrida)
Technology Transfer Automated Retrieval System (TEKTRAN)
Improving disease resistance has become an important breeding objective in gerbera, one of the most important floricultural crops in the world. Development and application of molecular markers are expected to assist selection of gerberas with improved disease resistance. The availability of resistan...
Prognostic molecular markers in non-small cell lung cancer
Jacek Nikli?ski; Wies?awa Nikli?ska; Jerzy Laudanski; El?bieta Chyczewska; Lech Chyczewski
Although TNM stage is the most significant prognostic parameter in lung cancer, additional parameters are required for explaining variability of survival. Hence molecular alterations in lung cancer have been extensively studied. Most prominent among them are alterations in the p53–p21 pathway, controlling the G1\\/S transition. They are the most commonly observed aberrations in non-small cell lung cancer (NSCLC). The results
[Molecular Genetic Markers of Economically Important Traits in Dairy Cattle].
Yudin, N S; Voevoda, M I
The selection efficiency of complex quantitative economically important traits in dairy cattle depends on the identification of candidate genes responsible for these traits, as well as the determination of causative DNA polymorphism in these genes. Here, we review examples of DNA polymorphisms in coding and noncoding parts of genes that are associated with milk yield, milk fat and protein contents, milk fat and protein percentages, the biochemical composition of milk, and other milk production traits. Together with data with of foreign authors, which were obtained predominantly for Holstein animals, much attention in the review is paid to domestic studies on Russian cattle breeds. Particular attention is dedicated to DNA polymorphisms in the genes encoding transcription factors, which can potentially affect a large number of traits. The results of association analyses are summarized in a table, and they present the progress of research in this area in recent years. Our analysis indicates that the majority of SNPs, which are associated with significant effects on milk production traits, are in fact in a linkage disequilibrium with yet unknown mutations. The identification of functionally significant DNA polymorphisms and other genetic factors (epimutations, VNTR) is necessary for effective marker-assisted selection and genomic selection of diary cattle breeds. PMID:26137639
Reduction of species in the wild potato Solanum section Petota series Longipedicellata: AFLP, RAPD and chloroplast SSR data.
Van Den Berg, G.; Bryan, J.; Del Rio, A.; Spooner, M.
Species boundaries were assessed with three molecular markers [AFLPs, RAPDs and chloroplast simple sequence repeats (cpSSRs)] for all six species of wild potatoes ( Solanum section Petota) assigned to ser. Longipedicellata: Solanum fendleri, S. hjertingii, S. matehualae, S. papita, S. polytrichon and S. stoloniferum. These tetraploid (2n = 4 x = 48) species grow in the southeastern United States ( S. fendleri) and Mexico (all six species), and a recent morphological analysis supported only three species: (1) S. polytrichon, (2) S. hjertingii (including S. matehualae) and (3) S. stoloniferum (including S. fendleri and S. papita). We analyzed all six species of ser. Longipedicellata (tetraploid) and also analyzed diploids in ser. Bulbocastana, ser. Pinnatisecta, ser. Polyadenia and ser. Tuberosa; tetraploids in ser. Acaulia and hexaploids in ser. Demissa. Concordant with morphological data, AFLP and RAPD results support the synonymy of S. hjertingii and S. matehualae, and completely intermix S. papita and S. fendleri. However, accessions of S. stoloniferum have a tendency to cluster but with exceptions, and S. polytrichon is completely intermixed with S. fendleri and S. papita. The cpSSRs fail to distinguish any of the species in ser. Longipedicellata. Combined morphological and molecular data support only two species in ser. Longipedicellata: S. hjertingii and S. stoloniferum. PMID:12582888
Cytogenetic and molecular markers for detecting Aegilops uniaristata chromosomes in a wheat background.
Gong, Wenping; Li, Guangrong; Zhou, Jianping; Li, Genying; Liu, Cheng; Huang, Chengyan; Zhao, Zhendong; Yang, Zujun
Aegilops uniaristata has many agronomically useful traits that can be used for wheat breeding. So far, a Triticum turgidum - Ae. uniaristata amphiploid and one set of Chinese Spring (CS) - Ae. uniaristata addition lines have been produced. To guide Ae. uniaristata chromatin transformation from these lines into cultivated wheat through chromosome engineering, reliable cytogenetic and molecular markers specific for Ae. uniaristata chromosomes need to be developed. Standard C-banding shows that C-bands mainly exist in the centromeric regions of Ae. uniaristata but rarely at the distal ends. Fluorescence in situ hybridization (FISH) using (GAA)8 as a probe showed that the hybridization signal of chromosomes 1N-7N are different, thus (GAA)8 can be used to identify all Ae. uniaristata chromosomes in wheat background simultaneously. Moreover, a total of 42 molecular markers specific for Ae. uniaristata chromosomes were developed by screening expressed sequence tag - sequence tagged site (EST-STS), expressed sequence tag - simple sequence repeat (EST-SSR), and PCR-based landmark unique gene (PLUG) primers. The markers were subsequently localized using the CS - Ae. uniaristata addition lines and different wheat cultivars as controls. The cytogenetic and molecular markers developed herein will be helpful for screening and identifying wheat - Ae. uniaristata progeny. PMID:25486537
Highly isotopically depleted isoprenoids: Molecular markers for ancient methane venting
Thiel, V.; Peckmann, J.; Seifert, R.; Wehrung, P.; Reitner, J.; Michaelis, W.
The authors propose that organic compounds found in a Miocene limestone from Marmorito (Northern Italy) are source markers for organic matter present in ancient methane vent systems (cold seeps). The limestone contains high concentrations of the tail-to-tail linked, acyclic C{sub 20} isoprenoid 2,6,11,15-tetramethylhexadecane (crocetane), a C{sub 25} homolog 2,6,10,15,19-pentamethylicosane (PME), and a distinctive glycerol ether lipid containing 3,7,11,15-tetramethylhexadecyl (phytanyl-) moieties. The chemical structures of these biomarkers indicate a common origin from archaea. Their extremely {sup 13}C-depleted isotope compositions ({delta}{sup 13}C {approximately} {minus}108 to {minus}115.6% PDB) suggest that the respective archaea have directly or indirectly introduced isotopically depleted, methane-derived carbon into their biomass. The authors postulate that a second major cluster of biomarkers showing heavier isotope values ({delta}{sup 13}C {approximately} {minus}88%) is derived from sulfate-reducing bacteria (SRB). The observed biomarkers sustain the idea that methanogenic bacteria, in a syntrophic community with SRB, are responsible for the anaerobic oxidation of methane in marine sediments. Marmorito may thus represent a conceivable ancient scenario for methane consumption performed by a defined, two-membered bacterial consortium: (1) archaea that perform reversed methanogenesis by oxidizing methane and producing CO{sub 2} and H{sub 2}; and (2) SRB that consume the resulting H{sub 2}. Furthermore, the respective organic molecules are, unlike other compounds, tightly bound to the crystalline carbonate phase. The Marmorito carbonates can thus be regarded as cold seep microbialites rather than mere antigenic carbonates.
Anthropogenic Molecular Markers: Tools to Identify the Sources and Transport Pathways of Pollutants
Takada, H.; Satoh, F.; Bothner, Michael H.; Tripp, B.W.; Johnson, C.G.; Farrington, J.W.
The activities of modern civilization have released to the oceans a wide variety of both mobilized natural compounds and synthetic compounds not found prior to modern times. Many of these compounds provide a means of identifying sources of inputs and pathways of movement of chemicals through oceanic ecosystems and serve as molecular markers of human activities. A coastal ocean (Tokyo Bay) and a deep ocean (Deep Water Dump Site 106 in the Western North Atlantic Ocean) example are presented. In the deep ocean study, the correlation between potential sewage marker, i.e. linear alkylbenzenes (LABs), and polychlorinated biphenyls (PCBs) concentrations indicates a contribution of sewage sludge PCBs to the dump site sediments.
Molecular markers of influenza B lineages and clades.
Arvia, Rosaria; Corcioli, Fabiana; Pierucci, Federica; Azzi, Alberta
Co-circulation of two influenza B virus lineages, B/Yamagata and B/Victoria, has been recognized since the late 1980s. The assessment of the prevalent lineage and the group of viruses in circulation is of importance in order to decide on the vaccine composition and evaluate its efficacy. The molecular characterization of influenza B viruses in circulation has been the aim of this study; this was approached by identifying and locating nucleotide substitutions in the influenza B virus hemagglutinin (HA) and neuraminidase (NA), specific for the lineage and/or clade. By the alignment of 3456 sequences from the influenza GISAID EpiFlu database, a high number of lineage- and group-specific nucleotide positions have been observed in the HA gene, but not in the NA gene. Additionally, an RT-PCR method has been developed, applicable directly to clinical specimens, which amplifies a short HA region that includes a group of unique molecular signatures. Twenty eight influenza B virus-positive respiratory specimens, collected in Tuscany in the seasons 2012-2013 and 2013-2014, were analyzed. The results revealed two clearly distinguishable patterns: one, more frequent, was characterized by all of the nucleotide changes associated with the B/Yamagata lineage (in most cases of Group 2), whereas the other exhibited all of the changes associated with the B/Victoria lineage. It can be concluded that the analysis of this short HA sequence can permit a rapid, highly sensitive determination of influenza B virus lineages and clades. PMID:25412364
Molecular Markers of Influenza B Lineages and Clades
Arvia, Rosaria; Corcioli, Fabiana; Pierucci, Federica; Azzi, Alberta
Co-circulation of two influenza B virus lineages, B/Yamagata and B/Victoria, has been recognized since the late 1980s. The assessment of the prevalent lineage and the group of viruses in circulation is of importance in order to decide on the vaccine composition and evaluate its efficacy. The molecular characterization of influenza B viruses in circulation has been the aim of this study; this was approached by identifying and locating nucleotide substitutions in the influenza B virus hemagglutinin (HA) and neuraminidase (NA), specific for the lineage and/or clade. By the alignment of 3456 sequences from the influenza GISAID EpiFlu database, a high number of lineage- and group-specific nucleotide positions have been observed in the HA gene, but not in the NA gene. Additionally, an RT-PCR method has been developed, applicable directly to clinical specimens, which amplifies a short HA region that includes a group of unique molecular signatures. Twenty eight influenza B virus-positive respiratory specimens, collected in Tuscany in the seasons 2012–2013 and 2013–2014, were analyzed. The results revealed two clearly distinguishable patterns: one, more frequent, was characterized by all of the nucleotide changes associated with the B/Yamagata lineage (in most cases of Group 2), whereas the other exhibited all of the changes associated with the B/Victoria lineage. It can be concluded that the analysis of this short HA sequence can permit a rapid, highly sensitive determination of influenza B virus lineages and clades. PMID:25412364
PCR markers distinguish Plantago major subspecies
K. Wolff; M. Morgan-Richards
Plantago major plants from several Scottish and Dutch locations were surveyed for their genetic variation using PCR markers, namely RAPD\\u000a analysis, anchored inter-SSR PCR, and chloroplast PCR followed by RFLP analysis. The RAPD and inter-SSR markers showed a differentiation\\u000a between the two subspecies of P. major. These results are discussed in relation to earlier results using allozyme electrophoresis, DNA fingerprinting,
DNA marker technologies and their applications in aquaculture genetics
Z. J. Liu; J. F. Cordes
The development of DNA-based genetic markers has had a revolutionary impact on animal genetics. With DNA markers, it is theoretically possible to observe and exploit genetic variation in the entire genome. Popular genetic markers in the aquaculture community include allozymes, mitochondrial DNA, RFLP, RAPD, AFLP, microsatellite, SNP, and EST markers. The application of DNA markers has allowed rapid progress in
Discovery of Molecular Markers to Discriminate Corneal Endothelial Cells in the Human Body
Yoshihara, Masahito; Ohmiya, Hiroko; Hara, Susumu; Kawasaki, Satoshi; Hayashizaki, Yoshihide; Itoh, Masayoshi; Kawaji, Hideya; Tsujikawa, Motokazu; Nishida, Kohji
The corneal endothelium is a monolayer of hexagonal corneal endothelial cells (CECs) on the inner surface of the cornea. CECs are critical in maintaining corneal transparency through their barrier and pump functions. CECs in vivo have a limited capacity in proliferation, and loss of a significant number of CECs results in corneal edema called bullous keratopathy which can lead to severe visual loss. Corneal transplantation is the most effective method to treat corneal endothelial dysfunction, where it suffers from donor shortage. Therefore, regeneration of CECs from other cell types attracts increasing interests, and specific markers of CECs are crucial to identify actual CECs. However, the currently used markers are far from satisfactory because of their non-specific expression in other cell types. Here, we explored molecular markers to discriminate CECs from other cell types in the human body by integrating the published RNA-seq data of CECs and the FANTOM5 atlas representing diverse range of cell types based on expression patterns. We identified five genes, CLRN1, MRGPRX3, HTR1D, GRIP1 and ZP4 as novel markers of CECs, and the specificities of these genes were successfully confirmed by independent experiments at both the RNA and protein levels. Notably none of them have been documented in the context of CEC function. These markers could be useful for the purification of actual CECs, and also available for the evaluation of the products derived from other cell types. Our results demonstrate an effective approach to identify molecular markers for CECs and open the door for the regeneration of CECs in vitro. PMID:25807145
Genetic diversity analysis of Zingiber Officinale Roscoe by RAPD collected from subcontinent of India
Ashraf, Kamran; Ahmad, Altaf; Chaudhary, Anis; Mujeeb, Mohd.; Ahmad, Sayeed; Amir, Mohd.; Mallick, N.
The present investigation was undertaken for the assessment of 12 accessions of Zingiber officinale Rosc. collected from subcontinent of India by RAPD markers. DNA was isolated using CTAB method. Thirteen out of twenty primers screened were informative and produced 275 amplification products, among which 261 products (94.90%) were found to be polymorphic. The percentage polymorphism of all 12 accessions ranged from 88.23% to 100%. Most of the RAPD markers studied showed different levels of genetic polymorphism. The data of 275 RAPD bands were used to generate Jaccard's similarity coefficients and to construct a dendrogram by means of UPGMA. Results showed that ginger undergoes genetic variation due to a wide range of ecological conditions. This investigation was an understanding of genetic variation within the accessions. It will also provide an important input into determining resourceful management strategies and help to breeders for ginger improvement program. PMID:24600309
Genetic relationships among some cultivars of sea buckthorn from China, Russia and Mongolia based on RAPD analysis
Chengjiang Ruan; Pei Qin; Jianwei Zheng; Zhenxiang He
Sea buckthorn (Hippophae rhamnoides) is important environmentally and as a new commercial berry crop. Fourteen cultivars of sea buckthorn from China, Russia and Mongolia were evaluated for genetic relationships using RAPD data. Nine random primers were used to generate 114 RAPD markers by PCR. Among them, 103 (90.35%) were polymorphic. The genetic similarity ranged from 0.45 to 0.80 with a
Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers (SSR).
Hasnaoui, Nejib; Buonamici, Anna; Sebastiani, Federico; Mars, Messaoud; Zhang, Dapeng; Vendramin, Giovanni G
Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In the present study, we report the development of 4 new polymorphic SSR markers. They have been used in addition to 11 SSRs previously published to investigate molecular diversity of 33 P. granatum ecotypes. Based on the multi-locus profiles, twenty-two distinctive genotypes were identified. Globally, quite low genetic diversity has been revealed, as measured by allele richness (2.83 per locus) and heterozygosity (He=0.245; Ho=0.243), reflecting the narrow genetic background of the plant material. Four synonymous groups could be detected involving 15 accessions. Results of ordination and cluster analysis suggested that almost all the Tunisian cultivars share similar genetic background, and are likely derived from a small number of introductions in ancient times. Results issued from this study provide essential information to project a pomegranate core-collection without plant material duplication and for sustainable management of pomegranate landraces at national and international level. Furthermore, these SSR markers are powerful tool for marker assisted selection (MAS) program and for QTL studies. PMID:22123180
Characterization of molecular markers in smoke from residential coal combustion in China
Xinhui Bi; Bernd R. T. Simoneit; Guoying Sheng; Jiamo Fu
The organic constituents and distributions of molecular markers emitted from a residential coal-stove burning honeycomb coal briquettes were determined in this study. The major organic components emitted directly in smoke particles were polycyclic aromatic hydrocarbons (PAHs), with abundant hydroxy-polycyclic aromatic hydrocarbons (OH-PAHs), i.e., thermally altered derivative compounds from coal combustion, UCM (unresolved complex mixture of branched and cyclic compounds), n-alkanes
Mosaic small supernumerary marker chromosome 1 at amniocentesis: prenatal diagnosis, molecular genetic analysis and literature review.
Chen, Chih-Ping; Chen, Ming; Su, Yi-Ning; Huang, Jian-Pei; Chern, Schu-Rern; Wu, Peih-Shan; Su, Jun-Wei; Chang, Shun-Ping; Chen, Yu-Ting; Lee, Chen-Chi; Chen, Li-Feng; Pan, Chen-Wen; Wang, Wayseen
We present prenatal diagnosis and molecular cytogenetic analysis of mosaic small supernumerary marker chromosome 1 [sSMC(1)]. We review the literature of sSMC(1) at amniocentesis and chromosome 1p21.1-p12 duplication syndrome. We discuss the genotype-phenotype correlation of the involved genes of ALX3, RBM15, NTNG1, SLC25A24, GPSM2, TBX15 and NOTCH2 in this case. PMID:23933412
Functionally associated molecular genetic marker map construction in perennial ryegrass ( Lolium perenne L.)
M. J. Faville; A. C. Vecchies; M. Schreiber; M. C. Drayton; L. J. Hughes; E. S. Jones; K. M. Guthridge; K. F. Smith; T. Sawbridge; G. C. Spangenberg; G. T. Bryan; J. W. Forster
A molecular marker-based map of perennial ryegrass (Lolium perenne L.) has been constructed through the use of polymorphisms associated with expressed sequence tags (ESTs). A pair-cross between genotypes from a North African ecotype and the cultivar Aurora was used to generate a two-way pseudo-testcross population. A selection of 157 cDNAs assigned to eight different functional categories associated with agronomically important
Genetic analysis of apomixis in Citrus and Poncirus by molecular markers
R. García; M. J. Asíns; J. Forner; E. A. Carbonell
Propagation of citrus rootstocks depends upon the production of clonal plants from nucellar seedlings. This makes apomixis\\u000a one of the host important traits in breeding programs for citrus rootstocks. The genetic control of apomixis was studied in\\u000a a 50-tree progeny derived from the cross C. volkameriana?P. trifoliata using 69 molecular markers and bulked segregant analysis. The proportion of nucellar seedlings
Typing Mycobacterium bovis isolates from Texas and Mexico using molecular markers
Perumaalla, Veera Shankar
Microbiology ABSTRACT Typing Mycobacterium bovis Isolates from Texas and Mexico Using Molecular Markers. (December 1995) Veera Shankar Perumaalla, B. V. Sc. & A. H. , APAU, Hyderabad, India. Chair of Advisory Committee: Dr. Thomas A. Ficht. With the rise...Murray, Dept. of Medical Microbiology and Immunology, Texas A&M University, were included in the study as controls. All isolates were grown in 20 ml of 7H9 Middlebrook broth (Difco Laboratories) supplemented with OADC enrichment media (Difco) at 37'C on a...
Quantification of the effects of molecular marker oxidation on source apportionment estimates for motor vehicles
NASA Astrophysics Data System (ADS)
Roy, Anirban A.; Wagstrom, Kristina M.; Adams, Peter J.; Pandis, Spyros N.; Robinson, Allen L.
Molecular markers are individual organic compounds used in receptor models to apportion fine particulate matter to sources. These models currently assume that molecular markers are chemically stable; however, recent laboratory experiments suggest they may be significantly oxidized on atmospherically relevant time scales. To investigate the effects of photo-oxidation, we extended a 3-D chemical transport model (PMCAMx) to simulate norhopane concentrations over the eastern United States during July 2001. Norhopane is an important molecular marker for motor vehicle exhaust. We examined eight different simulation scenarios, using different combinations of reaction rates and source profiles. The simulations including norhopane oxidation better reproduced the observed spatial patterns of norhopane concentrations than the non-reactive cases. Chemical mass balance (CMB) analysis was performed using the PMCAMx-predicted motor vehicle norhopane and elemental carbon (EC) concentrations to quantify the bias caused by oxidation on source apportionment estimates. Norhopane oxidation caused CMB to underestimate total vehicle OC by 10-50%, with larger biases in rural areas. This underestimation was largely due to changes in the amount of OC apportioned to gasoline vehicles which was reduced by as much as 100%. The OC apportioned to diesel vehicle emissions was relatively insensitive to norhopane reaction. Therefore, oxidation can substantially alter CMB estimates regarding the relative importance of gasoline and diesel vehicle emissions.
Biological pathways, candidate genes and molecular markers associated with quality-of-life domains: an update
Sprangers, Mirjam A.G.; Thong, Melissa S.Y.; Bartels, Meike; Barsevick, Andrea; Ordońana, Juan; Shi, Qiuling; Wang, Xin Shelley; Klepstad, Pĺl; Wierenga, Eddy A.; Singh, Jasvinder A.; Sloan, Jeff A.
Background There is compelling evidence of a genetic foundation of patient-reported QOL. Given the rapid development of substantial scientific advances in this area of research, the current paper updates and extends reviews published in 2010. Objectives The objective is to provide an updated overview of the biological pathways, candidate genes and molecular markers involved in fatigue, pain, negative (depressed mood) and positive (well-being/happiness) emotional functioning, social functioning, and overall QOL. Methods We followed a purposeful search algorithm of existing literature to capture empirical papers investigating the relationship between biological pathways and molecular markers and the identified QOL domains. Results Multiple major pathways are involved in each QOL domain. The inflammatory pathway has the strongest evidence as a controlling mechanism underlying fatigue. Inflammation and neurotransmission are key processes involved in pain perception and the COMT gene is associated with multiple sorts of pain. The neurotransmitter and neuroplasticity theories have the strongest evidence for their relationship with depression. Oxytocin-related genes and genes involved in the serotonergic and dopaminergic pathways play a role in social functioning. Inflammatory pathways, via cytokines, also play an important role in overall QOL. Conclusions Whereas the current findings need future experiments and replication efforts, they will provide researchers supportive background information when embarking on studies relating candidate genes and/or molecular markers to QOL domains. The ultimate goal of this area of research is to enhance patients' QOL. PMID:24604075
Evaluation of genetic diversity in Chinese kale (Brassica oleracea L. var. alboglabra Bailey) by using rapid amplified polymorphic DNA and sequence-related amplified polymorphism markers.
Zhang, J; Zhang, L G
Chinese kale is an original Chinese vegetable of the Cruciferae family. To select suitable parents for hybrid breeding, we thoroughly analyzed the genetic diversity of Chinese kale. Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) molecular markers were used to evaluate the genetic diversity across 21 Chinese kale accessions from AVRDC and Guangzhou in China. A total of 104 bands were detected by 11 RAPD primers, of which 66 (63.5%) were polymorphic, and 229 polymorphic bands (68.4%) were observed in 335 bands amplified by 17 SRAP primer combinations. The dendrogram showed the grouping of the 21 accessions into 4 main clusters based on RAPD data, and into 6 clusters based on SRAP and combined data (RAPD + SRAP). The clustering of accessions based on SRAP data was consistent with petal colors. The Mantel test indicated a poor fit for the RAPD and SRAP data (r = 0.16). These results have an important implication for Chinese kale germplasm characterization and improvement. PMID:24615113
Development of a molecular linkage map of pearl millet integrating DArT and SSR markers.
Supriya, A; Senthilvel, S; Nepolean, T; Eshwar, K; Rajaram, V; Shaw, R; Hash, C T; Kilian, A; Yadav, R C; Narasu, M L
Pearl millet is an important component of food security in the semi-arid tropics and is assuming greater importance in the context of changing climate and increasing demand for highly nutritious food and feed. Molecular tools have been developed and applied for pearl millet on a limited scale. However, the existing tool kit needs to be strengthened further for its routine use in applied breeding programs. Here, we report enrichment of the pearl millet molecular linkage map by exploiting low-cost and high-throughput Diversity Arrays Technology (DArT) markers. Genomic representation from 95 diverse genotypes was used to develop a DArT array with circa 7,000 clones following PstI/BanII complexity reduction. This array was used to genotype a set of 24 diverse pearl millet inbreds and 574 polymorphic DArT markers were identified. The genetic relationships among the inbred lines as revealed by DArT genotyping were in complete agreement with the available pedigree data. Further, a mapping population of 140 F(7) Recombinant Inbred Lines (RILs) from cross H 77/833-2 × PRLT 2/89-33 was genotyped and an improved linkage map was constructed by integrating DArT and SSR marker data. This map contains 321 loci (258 DArTs and 63 SSRs) and spans 1148 cM with an average adjacent-marker interval length of 3.7 cM. The length of individual linkage groups (LGs) ranged from 78 cM (LG 3) to 370 cM (LG 2). This better-saturated map provides improved genome coverage and will be useful for genetic analyses of important quantitative traits. This DArT platform will also permit cost-effective background selection in marker-assisted backcrossing programs as well as facilitate comparative genomics and genome organization studies once DNA sequences of polymorphic DArT clones are available. PMID:21476042
RAPD analysis of somaclonal variants derived from embryo callus cultures of peach
G. Hashmi; R. Huettel; R. Meyer; L. Krusberg; F. Hammerschlag
Peach [Prunus persica (L.) Batsch] regenerants from cv 'Sunhigh' embryo no. 156, regenerants obtained from cv 'Redhaven' embryo no. 30, and two peach cultivars 'Sunhigh' and 'Redhaven', were screened for polymorphic RAPD (Random Amplified Polymorphic DNA) markers with up to 60 10-mer primers. Although 35 primers produced results with scoreable bands, only 10 of the primers revealed polymorphism for regenerants
Nucleotide divergence between populations of trembling aspen ( Populus tremuloides ) estimated with RAPDs
Daniel K. X. Chong; Rong-Cai Yang; Francis C. Yeh
In the present study, a total of 142 trees sampled from five populations of trembling aspen (Populus tremuloides Michx.) in Alberta was analyzed by the polymerase chain reaction (PCR) with five random oligonucleotide primers. Null-allele frequencies of 28 putative RAPD loci were estimated using the given departure from Hardy-Weinberg equilibrium (FIS) previously estimated with isozyme markers for the same population.
[Low genetic differentiation and close evolutionary connection between Anas platyrhynchos and Anas poecilorhyncha: data from RAPD-PCR analysis].
Kulikova, I V; Chelomina, G N; Zhuravlev, Iu N
Using RAPD-PCR, we examined genetic diversity and phylogenetic relationships in two groups of river ducks: Anas platyrhynchos, A. poecilorhyncha, A. strepera and A. crecca, A. formosa, A. querquedula. Molecular taxon-specific markers were found for teals (A. crecca, A. formosa, A. querquedula) and gadwall (A. strepera). Each of the species examined was shown to exhibit high genetic diversity. The mean levels of intraspecific genetic polymorphism in the groups of mallards (P = 77%) and teals (P = 74.5%) were approximately equal whereas the mean interspecific genetic distances in teals were significantly higher than in mallards (D = 0.432 and D = 0.336, respectively). The levels of interspecific genetic differentiation in the species groups were also different. The genetic distances between the teal species and between gadwall and mallards were equal to 0.668-0.971 while the genetic distance between mallard A. platyrhynchos and spot-billed duck A. poecilorhyncha was 0.401, which slightly exceeds the intraspecific values for mallards (0.356-0.377). The RAPD patterns for this species pair showed high variability and a lack of fixed differences. This was adequately reflected on both intra- and interspecific differences and on phylogenetic constructions in which the morphological species did not form their own clusters but were intermixed. In contrast to mallards, the other species, which showed high genetic variability, were reliably separated in phenogenetic and phylogenetic reconstructions. The possible explanations of the low genetic differentiation of A. platyrhynchos and A. poecilorhyncha are discussed. PMID:14658340
Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations.
Giovannoni, J J; Wing, R A; Ganal, M W; Tanksley, S D
We present a general method for isolating molecular markers specific to any region of a chromosome using existing mapping populations. Two pools of DNA from individuals homozygous for opposing alleles for a targeted chromosomal interval, defined by two or more linked RFLP markers, are constructed from members of an existing mapping population. The DNA pools are then screened for polymorphism using random oligonucleotide primers and PCR (1). Polymorphic DNA bands should represent DNA sequences within or adjacent to the selected interval. We tested this method in tomato using two genomic intervals containing genes responsible for regulating pedicle abscission (jointless) and fruit ripening (non-ripening). DNA pools containing 7 to 14 F2 individuals for each interval were screened with 200 random primers. Three polymorphic markers were thus identified, two of which were subsequently shown to be tightly linked to the selected intervals. The third marker mapped to the same chromosome (11) but 45 cM away from the selected interval. A particularly attractive attribute of this method is that a single mapping population can be used to target any interval in the genome. Although this method has been demonstrated in tomato, it should be applicable to any sexually reproducing organism for which segregating populations are being used to construct genetic linkage maps. Images PMID:1684420
Screening of rice landraces for salinity tolerance at seedling stage through morphological and molecular markers.
Ali, Md Nasim; Yeasmin, Lucina; Gantait, Saikat; Goswami, Rupak; Chakraborty, Somsubhra
The present investigation was carried out to evaluate 33 rice landrace genotypes for assessment of their salt tolerance at seedling stage. Growth parameters like root length, shoot length and plant biomass were measured after 12 days of exposure to six different levels of saline solution (with electrical conductivity of 4, 6, 8, 10, 12 or 14 dS m (-1)). Genotypes showing significant interaction and differential response towards salinity were assessed at molecular level using 11 simple sequence repeats (SSR) markers, linked with salt tolerance quantitative trait loci. Shoot length, root length and plant biomass at seedling stage decreased with increasing salinity. However, relative salt tolerance in terms of these three parameters varied among genotypes. Out of the 11 SSR markers RM8094, RM336 and RM8046, the most competent descriptors to screen the salt tolerant genotypes with higher polymorphic information content coupled with higher marker index value, significantly distinguished the salt tolerant genotypes. Combining morphological and molecular assessment, four lanraces viz. Gheus, Ghunsi, Kuthiahara and Sholerpona were considered as true salt tolerant genotypes which may contribute in greater way in the development of salt tolerant genotypes in rice. PMID:25320465
Random amplified polymorphic DNA (RAPD) analysis reveals genetic relationships among the annual Cicer species
F. Ahmad
Random amplified polymorphic DNA markers were used to distinguish between nine different Cicer taxa representing the cultivated chickpea and eight other related annual wild species. Of the 75 random10-mer primers tested,\\u000a only 8 amplified genomic DNA across all the species. A total of 115 reproducibly scorable RAPD markers were generated, all\\u000a except 1 polymorphic, and these were utilized to deduce
Genetic analysis of apomixis in Citrus and Poncirus by molecular markers.
García, R; Asíns, M J; Forner, J; Carbonell, E A
Propagation of citrus rootstocks depends upon the production of clonal plants from nucellar seedlings. This makes apomixis one of the host important traits in breeding programs for citrus rootstocks. The genetic control of apomixis was studied in a 50-tree progeny derived from the cross C. volkameriana×P. trifoliata using 69 molecular markers and bulked segregant analysis. The proportion of nucellar seedlings was estimated by isoenzymatic analysis of 25 seedlings per tree for 2 consecutive years. The type of embryony (polyembryonic versus monoembryonic seeds) was also determined for fruit-yielding trees. Separate genetic maps for each parental species were developed. The integration and comparison of these maps could be accomplished using common multiallelic segregant loci. Differences in gene synteny between the two species-specific genetic maps were shown. Important distortions in the segregation of markers at several genomic regions, some of them also involving differences in the C-methylation pattern, have been observed, especially for the pollen parent. Analysis of quantitative trait loci (QTLs) revealed the presence of six genomic positions (two in P. trifoliata and four in C. volkameriana) contributing individually up to 24% of the total variation for apomixis. Within the same species, QTLs with positive and negative allele effects were present, even in the same linkage group. One of the markers associated to apomixis (Apo2) is also associated to embryony type. Therefore, the genetic control of apomictic reproduction found in citrus (nucellar embryony) is quite complex compared to what has been reported for gametophytic apomixis. Molecular markers linked to QTLs governing apomixis will be useful to assist selection of future apomictic rootstocks for citrus varieties. PMID:22665185
Using Molecular Markers to Characterize Productivity in Chinese Hamster Ovary Cell Lines
Edros, Raihana Z.; McDonnell, Susan; Al-Rubeai, Mohamed
Selection of high producing cell lines to produce maximum product concentration is a challenging and time consuming task for the biopharmaceutical industry. The identification of early markers to predict high productivity will significantly reduce the time required for new cell line development. This study identifies candidate determinants of high productivity by profiling the molecular and morphological characteristics of a panel of six Chinese Hamster Ovary (CHO) stable cell lines with varying recombinant monoclonal antibody productivity levels ranging between 2 and 50 pg/cell/day. We examined the correlation between molecular parameters and specific productivity (qp) throughout the growth phase of batch cultures. Results were statistically analyzed using Pearson correlation coefficient. Our study revealed that, overall, heavy chain (HC) mRNA had the strongest association with qp followed by light chain (LC) mRNA, HC intracellular polypeptides, and intracellular antibodies. A significant correlation was also obtained between qp and the following molecular markers: growth rate, biomass, endoplasmic reticulum, and LC polypeptides. However, in these cases, the correlation was not observed at all-time points throughout the growth phase. The repeated sampling throughout culture duration had enabled more accurate predictions of productivity in comparison to performing a single-point measurement. Since the correlation varied from day to day during batch cultivation, single-point measurement was of limited use in making a reliable prediction. PMID:24146795
Determination of specific molecular markers of biomass burning in lake sediments
NASA Astrophysics Data System (ADS)
Kirchgeorg, Torben; Schüpbach, Simon; Kehrwald, Natalie; McWethy, David; Barbante, Carlo
Fire influences regional to global atmospheric chemistry and climate. Molecular markers of biomass burning archived in lake sediments are becoming increasingly important in paleoenvironmental reconstruction and may help determine interactions between climate and fire activity. One group of these molecular markers is the monosaccharide anhydrides levoglucosan, mannosan and galactosan. Several aerosol studies and recent ice core research use these compounds as a marker for biomass burning, but studies from lake sediment cores are rare. Previous sediment methods used gas chromatography - mass spectrometry and required derivatization of samples. Here, we present a high performance anion exchange chromatography-mass spectrometry method to allow separation and detection of the three monosaccharide anhydrides in lake sediments with implications for reconstructing past biomass burning events. We validated the method by quantifying levoglucosan, mannosan and galactosan in selected sediment core samples from Lake Kirkpatrick, New Zealand. The freeze-dried, milled and homogenized sediment samples were first extracted with methanol by pressurized solvent extraction, pre-concentrated and finally separated and analyzed by high performance anion exchange chromatography-mass spectrometry. We compared these isomers with macroscopic charcoal concentrations, as charcoal is a well-known proxy for biomass burning. In addition, we applied the method to a sediment core from Lake Petén Itzá, Guatemala to prove the suitability of these markers for reconstructing biomass burning history over the entire Holocene. In the Lake Kirkpatrick samples, levoglucosan, mannosan and galactosan concentrations significantly correlate with macroscopic charcoal concentrations. The three isomers are present in samples without any macroscopic charcoal, and may reflect the presence of microscopic charcoal. Levoglucosan/mannosan and levoglucosan/(mannosan+galactosan) ratios differ between samples with high macroscopic charcoal concentrations and samples without any charcoal. These ratios may help determine not only when fires occurred, but also past changes in the primary burned vegetation. However, the possibility that these isomer ratios help differentiate changes in burned vegetation needs further evaluation. The preliminary results of the Lake Petén Itzá samples demonstrate the occurrence of all three molecular markers in the entire core, covering the past approximately 10,000 years. The three monosaccharide anhydrides levoglucosan, mannosan and galactosan may be an additional tool for reconstructing past fire events over decadal to millennial time scales in sediment cores.
TMED6-COG8 is a novel molecular marker of TFE3 translocation renal cell carcinoma
Xu, Yongcan; Rao, Qiu; Xia, Qiuyuan; Shi, Shanshan; Shi, Qunli; Ma, Henghui; Lu, Zhenfeng; Chen, Hui; Zhou, Xiaojun
TFE3 translocation renal cell carcinoma is a highly aggressive malignancy which often occurs primarily in children and young adults. The pathognomonic molecular lesion in this subtype is a translocation event involving the TFE3 transcription factor at chromosome Xp11.2. Hence, the pathological diagnosis of an Xp11.2 translocation RCC is based upon morphology, TFE3 immunohistochemistry, or genetic analyses. However, due to the false-positive immunoreactivity for TFE3 IHC and expensive for TFE3 break-apart FISH assay, additional molecular markers are necessary to help provide early diagnose and individualization treatment. Owing to recent advances in microarray and RNA-Seq, Pflueger et al. have discovered that TMED6-COG8 is dramatically increased in TFE3 translocation RCCs, compared with clear cell RCCs and papillary RCCs, implying that TMED6-COG8 might be a new molecular tumor marker of TFE3 translocation RCCs. To extend this observation, we firstly validated the TMED6-COG8 expression level by qRT-PCR in RCCs including Xp11.2 translocation RCCs (n = 5), clear cell RCCs (n = 7) and papillary RCCs (n = 5). Then, we also examined the expression level of TMED6-COG8 chimera in Xp11.2 translocation alveolar soft part sarcoma. We found that TMED6-COG8 chimera expression level was higher in Xp11.2 translocation RCCs than in ASPS (P < 0.05). What's more, the expression levels of TMED6-COG8 chimera in esophagus cancers (n = 32), gastric cancers (n = 11), colorectal cancers (n = 12), hepatocellular carcinomas (n = 10) and non-small-cell lung cancers (n = 12) were assessed. Unexpectedly, TMED6-COG8 chimera was decreased in these five human types. Therefore, our observations from this study indicated that TMED6-COG8 chimera might act as a novel diagnostic marker in Xp11.2 translocation RCCs. PMID:26045774
Evaluation of HOXB13 as a molecular marker of recurrent prostate cancer.
Jeong, Tae-O; Oh, Kyung-Jin; Xuan Nguyen, Nguyen Thi; Kim, Young-Rang; Kim, Min Soo; Lee, Sang Don; Ryu, Soo Bang; Jung, Chaeyong
Many patients with prostate cancer have disease recurrence following surgical removal of tumors and fail to respond to androgen ablation therapy. Despite the existence of a number of clinical/pathological factors, it is not possible to predict which patients will fall into this category. The results of our previous studies demonstrated that the HOXB13 homeodomain protein plays a key role in the development of prostate cancer and the progression of this malignancy. In addition, HOXB13 has been reported to predict estrogen-resistant breast cancer tumors. The purpose of this study was to investigate whether HOXB13 could be used as a molecular marker to predict prostate cancer recurrence. To examine the role of HOXB13 as a molecular marker with clinical/pathological data, the expression of HOXB13 was compared using immunohistochemistry in 57 organ-confined prostate cancer tumors obtained by radical prostatectomy. There was no significant correlation between the expression of HOXB13 and most clinical/pathological parameters, including tumor margin, invasion, pathological stage and risk level. The HOXB13 expression levels correlated with the Gleason score and there was a positive correlation with the pre-operative prostate specific antigen (PSA) levels. Accordingly, the tumor specimens from 4 patients who ultimately had biochemical failure (PSA >0.2 ng/ml), all showed a high expression of HOXB13, while their risk levels were either intermediate or high. This is the first study to report that HOXB13, together with other clinical/pathological factors, can be used as a molecular marker to predict the progression of prostate cancer. PMID:22293681
Molecular Markers Predict Distant Metastases After Adjuvant Chemoradiation for Rectal Cancer
Kim, Jun Won; Kim, Yong Bae [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Choi, Jun Jeong [Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Koom, Woong Sub [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Kim, Hoguen [Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Kim, Nam-Kyu [Department of Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Ahn, Joong Bae [Department of Medical Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Medical Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Lee, Ikjae; Cho, Jae Ho [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Keum, Ki Chang, E-mail: email@example.com [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)
Purpose: The outcomes of adjuvant chemoradiation for locally advanced rectal cancer are nonuniform among patients with matching prognostic factors. We explored the role of molecular markers for predicting the outcome of adjuvant chemoradiation for rectal cancer patients. Methods and Materials: The study included 68 patients with stages II to III rectal adenocarcinoma who were treated with total mesorectal excision and adjuvant chemoradiation. Chemotherapy based on 5-fluorouracil and leucovorin was intravenously administered each month for 6-12 cycles. Radiation therapy consisted of 54 Gy delivered in 30 fractions. Immunostaining of surgical specimens for COX-2, EGFR, VEGF, thymidine synthase (TS), and Raf kinase inhibitor protein (RKIP) was performed. Results: The median follow-up was 65 months. Eight locoregional (11.8%) and 13 distant (19.1%) recurrences occurred. Five-year locoregional failure-free survival (LRFFS), distant metastasis-free survival (DMFS), disease-free survival (DFS), and overall survival (OS) rates for all patients were 83.9%, 78.7%, 66.7%, and 73.8%, respectively. LRFFS was not correlated with TNM stage, surgical margin, or any of the molecular markers. VEGF overexpression was significantly correlated with decreased DMFS (P=.045), while RKIP-positive results were correlated with increased DMFS (P=.025). In multivariate analyses, positive findings for COX-2 (COX-2+) and VEGF (VEGF+) and negative findings for RKIP (RKIP-) were independent prognostic factors for DMFS, DFS, and OS (P=.035, .014, and .007 for DMFS; .021, .010, and <.0001 for DFS; and .004, .012, and .001 for OS). The combination of both COX-2+ and VEGF+ (COX-2+/VEGF+) showed a strong correlation with decreased DFS (P=.007), and the combinations of RKIP+/COX-2- and RKIP+/VEGF- showed strong correlations with improved DFS compared with the rest of the patients (P=.001 and <.0001, respectively). Conclusions: Molecular markers can be valuable in predicting treatment outcome of adjuvant chemoradiation for rectal cancer patients.
A population genetics study of Anopheles darlingi (Diptera: Culicidae) from Colombia based on random amplified polymorphic DNA-polymerase chain reaction and amplified fragment lenght polymorphism markers
Ranulfo González; Richard Wilkerson; Marco Fidel Suárez; Felipe García; Gerardo Gallego; Heiber Cárdenas; Carmen Elisa Posso; Myriam Cristina Duque
The genetic variation and population structure of three populations of Anopheles darlingi from Colombia were studied using random amplified polymorphic markers (RAPDs) and amplified fragment length polymor- phism markers (AFLPs). Six RAPD primers produced 46 polymorphic fragments, while two AFLP primer com- binations produced 197 polymorphic fragments from 71 DNA samples. Both of the evaluated genetic markers showed the presence
Technology Transfer Automated Retrieval System (TEKTRAN)
NEOZYGITES TANAJOAE is a key natural enemy of cassava green mite in Brazil that was experimentally released in cassava fields in Benin (W. Africa) in 1988/1999. N. FLORIDANA closely resembles N. TANAJOAE but is a widespread pathogen of tetranychid mites in temperate and tropical regions. Genetic var...
Genetic modulation in Be-78 and Y Trypanosoma cruzi strains after long-term infection in Beagle dogs revealed by molecular markers.
Veloso, Vanja Maria; Guedes, Paulo Marcos da Matta; de Lana, Marta; Martins, Helen Rodrigues; Carneiro, Cláudia Martins; da Câmara, Antônia Cláudia Jácome; D'Ávila, Daniella Alchaar; Caldas, Ivo Santana; Galvăo, Lúcia Maria da Cunha; Chiari, Egler; Bahia, Maria Terezinha
The genetic profile of Trypanosoma cruzi was evaluated in parasite populations isolated from Beagle dogs experimentally infected with Be-78 and Y strains that present distinct biological and genetic characteristics. Molecular characterization of the isolates obtained 30days and 2years after infection was carried out. For typing MLEE, sequence polymorphisms of the mitochondrial cytochrome oxidase subunit II gene (COII) and RAPD profiles were used. The profiles of MLEE were the same for the parental Be-78 strains as their respective isolates. However, changes of MLEE profile were observed in two T. cruzi isolates from dogs inoculated with Y strain. Changes in the mitochondrial DNA (COII) and RAPD profiles of the Y strain were also observed. The dendogram constructed by UPGMA with RAPD results indicated two major branches. Global data show that the genetic modulation in polyclonal strains during the long-term infection occurred and was strain-dependent. This study still suggests that each host (here each dog) harbors a determinate T. cruzi population that may change or be modulated throughout long-term infection. This might to hinder the observation of correlation between the genetics of T. cruzi and their biological properties and behavior in different host species due to the complexity of the parasite-host interaction in which probably the genetic background of both should be considered. PMID:22554652
Molecular markers as a method to evaluate the movement of Hypothenemus hampei (Ferrari).
Gil, Zulma Nancy; Benavides, Pablo; Souza, Og De; Acevedo, Flor Edith; Lima, Eraldo
The objective of this research was to develop a methodology to describe the movement of the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae) in the field through: (i) the evaluation of allele variation of a microsatellite marker on polymorphic Colombian H. hampei populations; (ii) the invention of a device for releasing H. hampei adults; (iii) the standardization of a release-recapture technique for H. hampei populations; (iv) the estimation of the flight distance of the insect; and (v) the calculation of a mathematical expression that describes the movement of H. hampei in space over time. The results indicated that: (i) the microsatellite molecular marker HHK.1.6 was exclusively present in a population from Guapotá-Santander, was dominant and allows the evaluation of H. hampei movement for several generations; (ii) a device that released 88.8% of H. hampei adults in 2?s was designed; (iii) this device was used as H. hampei populations containing HHK.1.6 marker release strategy, and coffee seeds as recapture strategy; (iv) it was estimated that H. hampei adults flew as far as 65?m, however, 90% were recovered in a radius of <40?m. Finally, (v) the mathematical expression that described the movement of H. hampei in space over time was [Formula: see text], being [Formula: see text] the average number of borer beetles recaptured per tree, and x the distance in meters. This method will allow to determine the movement of H. hampei from different environmental and ecological scenarios. PMID:26078300
Delimitation of russula subgenus amoenula in Korea using three molecular markers.
Park, Myung Soo; Fong, Jonathan J; Lee, Hyun; Oh, Seung-Yoon; Jung, Paul Eunil; Min, Young Ju; Seok, Soon Ja; Lim, Young Woon
Distinguishing individual Russula species has been difficult due to extensive phenotypic plasticity and obscure morphological and anatomical discontinuities. Due to highly similar macroscopic features, such as the presence of a red-cap, species identification within the Russula subgenus Amoenula is particularly difficult. Three species of the subgenus Amoneula have been reported in Korea. We used a combination of morphology and three molecular markers, the internal transcribed spacer (ITS), 28S nuclear ribosomal large subunit (LSU), and RNA polymerase II gene (RPB2), for identification and study of the genetic diversity of Russula subgenus Amoenula in Korea. We identified only two species in Korea (R. mariae and R. violeipes); these two species were indistinguishable according to morphology and LSU, but were found to be reciprocally monophyletic species using ITS and RPB2. The markers, ITS, LSU, and RPB2, have been tested in the past for use as DNA barcoding markers, and findings of our study suggest that ITS and RPB2 had the best performance for the Russula subgenus Amoneula. PMID:24493939
Transcriptome analysis of Capsicum annuum varieties Mandarin and Blackcluster: assembly, annotation and molecular marker discovery.
Ahn, Yul-Kyun; Tripathi, Swati; Kim, Jeong-Ho; Cho, Young-Il; Lee, Hye-Eun; Kim, Do-Sun; Woo, Jong-Gyu; Cho, Myeong-Cheoul
Next generation sequencing technologies have proven to be a rapid and cost-effective means to assemble and characterize gene content and identify molecular markers in various organisms. Pepper (Capsicum annuum L., Solanaceae) is a major staple vegetable crop, which is economically important and has worldwide distribution. High-throughput transcriptome profiling of two pepper cultivars, Mandarin and Blackcluster, using 454 GS-FLX pyrosequencing yielded 279,221 and 316,357 sequenced reads with a total 120.44 and 142.54Mb of sequence data (average read length of 431 and 450 nucleotides). These reads resulted from 17,525 and 16,341 'isogroups' and were assembled into 19,388 and 18,057 isotigs, and 22,217 and 13,153 singletons for both the cultivars, respectively. Assembled sequences were annotated functionally based on homology to genes in multiple public databases. Detailed sequence variant analysis identified a total of 9701 and 12,741 potential SNPs which eventually resulted in 1025 and 1059 genotype specific SNPs, for both the varieties, respectively, after examining SNP frequency distribution for each mapped unigenes. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies. PMID:24125952
Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava
P. Stephenson; K. Edwards; S. Melzer; J. Nkumbira; U. Gullberg; K. Apel; M. Gale; J. Tohme; M. Fregene
The development of PCR-based, easily automated molecular genetic markers, such as SSR markers, are required for realistic\\u000a cost-effective marker-assisted selection schemes. This paper describes the development and characterization of 172 new SSR\\u000a markers for the cassava genome. The placement of 36 of these markers on the existing RFLP framework map of cassava is also\\u000a reported. Two similar enrichment methods were
The Species Mycobacterium africanum in the Light of New Molecular Markers
Niemann, S.; Kubica, T.; Bange, F. C.; Adjei, O.; Browne, E. N.; Chinbuah, M. A.; Diel, R.; Gyapong, J.; Horstmann, R. D.; Joloba, M. L.; Meyer, C. G.; Mugerwa, R. D.; Okwera, A.; Osei, I.; Owusu-Darbo, E.; Schwander, S. K.; Rüsch-Gerdes, S.
The findings of recent studies addressing the molecular characteristics of Mycobacterium tuberculosis complex isolates have initiated a discussion on the classification of M. africanum, especially of those isolates originating from East Africa (cluster F, subtype II) and displaying phenotypic and biochemical characteristics more similar to those of M. tuberculosis. To further address this question, we analyzed a representative collection of 63 M. tuberculosis complex strains comprising 30 M. africanum subtype I strains, 20 M. africanum subtype II strains, 10 randomly chosen M. tuberculosis isolates, and type strains of M. tuberculosis, M. bovis, and M. africanum for the following biochemical and molecular characteristics: single-nucleotide polymorphisms (SNPs) in gyrB and narGHJI and the presence or absence of RD1, RD9, and RD12. For all molecular markers analyzed, subtype II strains were identical to the M. tuberculosis strains tested. In contrast, the subtype I strains as well as the M. africanum type strain showed unique combinations of SNPs in gyrB and genomic deletions (the absence of RD9 and the presence of RD12), which proves their independence from M. tuberculosis and M. bovis. Accordingly, all subtype I strains displayed main biochemical characteristics included in the original species description of M. africanum. We conclude that the isolates from West Africa were proved to be M. africanum with respect to the phenotypic and genetic markers analyzed, while the isolates from East Africa must be regarded as phenotypic variants of M. tuberculosis (genotype Uganda). We propose the addition of the molecular characteristics defined here to the species description of M. africanum, which will allow clearer species differentiation in the future. PMID:15364975
The species Mycobacterium africanum in the light of new molecular markers.
Niemann, S; Kubica, T; Bange, F C; Adjei, O; Browne, E N; Chinbuah, M A; Diel, R; Gyapong, J; Horstmann, R D; Joloba, M L; Meyer, C G; Mugerwa, R D; Okwera, A; Osei, I; Owusu-Darbo, E; Schwander, S K; Rüsch-Gerdes, S
The findings of recent studies addressing the molecular characteristics of Mycobacterium tuberculosis complex isolates have initiated a discussion on the classification of M. africanum, especially of those isolates originating from East Africa (cluster F, subtype II) and displaying phenotypic and biochemical characteristics more similar to those of M. tuberculosis. To further address this question, we analyzed a representative collection of 63 M. tuberculosis complex strains comprising 30 M. africanum subtype I strains, 20 M. africanum subtype II strains, 10 randomly chosen M. tuberculosis isolates, and type strains of M. tuberculosis, M. bovis, and M. africanum for the following biochemical and molecular characteristics: single-nucleotide polymorphisms (SNPs) in gyrB and narGHJI and the presence or absence of RD1, RD9, and RD12. For all molecular markers analyzed, subtype II strains were identical to the M. tuberculosis strains tested. In contrast, the subtype I strains as well as the M. africanum type strain showed unique combinations of SNPs in gyrB and genomic deletions (the absence of RD9 and the presence of RD12), which proves their independence from M. tuberculosis and M. bovis. Accordingly, all subtype I strains displayed main biochemical characteristics included in the original species description of M. africanum. We conclude that the isolates from West Africa were proved to be M. africanum with respect to the phenotypic and genetic markers analyzed, while the isolates from East Africa must be regarded as phenotypic variants of M. tuberculosis (genotype Uganda). We propose the addition of the molecular characteristics defined here to the species description of M. africanum, which will allow clearer species differentiation in the future. PMID:15364975
Development of Specific Sequence-Characterized Amplified Region Markers for Detecting Histoplasma capsulatum in Clinical and Environmental Samples
Frías De León, María Guadalupe; Arenas López, Gabina; Taylor, Maria Lucia; Acosta Altamirano, Gustavo
Sequence-characterized amplified region (SCAR) markers, generated by randomly amplified polymorphic DNA (RAPD)-PCR, were developed to detect Histoplasma capsulatum selectively in clinical and environmental samples. A 1,200-bp RAPD-PCR-specific band produced with the 1281-1283 primers was cloned, sequenced, and used to design two SCAR markers, 1281-1283220 and 1281-1283230. The specificity of these markers was confirmed by Southern hybridization. To evaluate the relevance of the SCAR markers for the diagnosis of histoplasmosis, another molecular marker (M antigen probe) was used for comparison. To validate 1281-1283220 and 1281-1283230 as new tools for the identification of H. capsulatum, the specificity and sensitivity of these markers were assessed for the detection of the pathogen in 36 clinical (17 humans, as well as 9 experimentally and 10 naturally infected nonhuman mammals) and 20 environmental (10 contaminated soil and 10 guano) samples. Although the two SCAR markers and the M antigen probe identified H. capsulatum isolates from different geographic origins in America, the 1281-1283220 SCAR marker was the most specific and detected the pathogen in all samples tested. In contrast, the 1281-1283230 SCAR marker and the M antigen probe also amplified DNA from Aspergillus niger and Cryptococcus neoformans, respectively. Both SCAR markers detected as little as 0.001 ng of H. capsulatum DNA, while the M antigen probe detected 0.5 ng of fungal DNA. The SCAR markers revealed the fungal presence better than the M antigen probe in contaminated soil and guano samples. Based on our results, the 1281-1283220 marker can be used to detect and identify H. capsulatum in samples from different sources. PMID:22189121
Morphological and molecular evidence for hybridization and introgression in a willow (Salix) hybrid zone.
Hardig, T M; Brunsfeld, S J; Fritz, R S; Morgan, M; Orians, C M
Hybrid zones provide biologists with the opportunity to examine genetic and ecological interactions between differentiated populations. Accurate identification of hybrid genealogies is considered a necessary prerequisite to understanding observed patterns of hybridization-related phenomena. We analysed molecular and morphological data from individuals in a hybrid zone between two species of willows (Salix sericea Marshall and S. eriocephala Michaux) and report the use of randomly amplified polymorphic DNA (RAPD), chloroplast DNA (cpDNA), and ribosomal DNA (rDNA) markers, as well as vegetative morphology and foliar chemistry data to identify individuals in terms of hybrid genealogy and to infer the direction and extent of backcrossing and introgression within the hybrid zone. A novel version of a maximum likelihood estimate approach (developed for this study) was used to calculate hybrid index scores from RAPD marker data; this method produced results similar to those obtained using traditional arithmetic methods. Distribution of rDNA, cpDNA, and chemistry data were examined within the graphical context of RAPD-based hybrid index score histograms and principal component analyses (PCA) on RAPD and morphology data. Seven of the 21 plants classified as S. eriocephala in the field were possible introgressants. Another plant presented an unequivocal example of backcrossed S. sericea chemistry and RAPD markers. Inter- and intraspecific chloroplast diversity found within the hybrid zone suggests both historic introgression (perhaps in a glacial refugium), and contemporary hybridization. Patterns of inheritance and expression within the hybrid zone suggest that morphological characters are often not expressed in a simple additive fashion, and problems associated with both morphological and molecular data are considered. PMID:10652072
Molecular markers in commercial Bombyx mori (Lepidoptera: Bombycidae) hybrids susceptible to multiple nucleopolyhedrovirus.
Ribeiro, L F C; Zanatta, D B; Bravo, J P; Brancalhăo, R M C; Fernandez, M A
The silkworm Bombyx mori L. is particularly susceptible to virus diseases, especially B. mori nucleopolyhedrovirus (BmNPV). Disease resistance, along with high productivity, are important selection criteria for developing commercial hybrids of B. mori. We used bioassays and molecular markers linked to susceptibility/resistance to baculovirus infection to analyze the response of commercial B. mori hybrids from two companies to a geographic isolate of B. mori multiple nucleopolyhedrovirus (BmMNPV) from Paraná state in Brazil. Both of these commercial lines were highly susceptible to BmMNPV, with death rates of 92 and 94%. A polymorphic fragment of approximately ~350 bp, associated with susceptibility, and an ~800-bp fragment, associated with resistance to BmMNPV, were detected in all specimens. An additional fragment of ~480 bp, recently identified by our research team as a BmMNPV genomic sequence, was detected in the infected silkworms and could be used as a molecular marker for the diagnosis of nucleopolyhedrovirus infection. PMID:19283681
Identification of Leaf Rust Resistance Genes in Selected Egyptian Wheat Cultivars by Molecular Markers
Imbaby, I. A.; Mahmoud, M. A.; Hassan, M. E. M.; Abd-El-Aziz, A. R. M.
Leaf rust, caused by Puccinia triticina Eriks., is a common and widespread disease of wheat (Triticum aestivum L.) in Egypt. Host resistance is the most economical, effective, and ecologically sustainable method of controlling the disease. Molecular markers help to determine leaf rust resistance genes (Lr genes). The objective of this study was to identify Lr genes in fifteen wheat cultivars from Egypt. Ten genes, Lr13, Lr19, Lr24, Lr26, Lr34, Lr35 Lr36, Lr37, Lr39, and Lr46, were detected in fifteen wheat cultivars using various molecular markers. The most frequently occurring genes in fifteen Egyptian wheat cultivars were Lr13, Lr24, Lr34, and Lr36 identified in all the cultivars used, followed by Lr26 and Lr35 (93%), Lr39 (66%), Lr37 (53%), and Lr46 (26.6%) of the cultivars, and finally Lr19 was present in 33.3% of cultivars. It is concluded that there was a good variation in Lr genes carried by wheat cultivars commercially grown in Egypt. Therefore, strategies for deploying resistance genes to prolong effective disease resistance are suggested to control wheat leaf rust disease. PMID:24511291
Molecular Markers for Biomass Traits: Association, Interaction and Genetic Divergence in Silkworm Bombyx mori.
Pradeep, Appukuttannair R; Jingade, Anuradha H; Urs, Raje S
Improvement of high yielding, disease resistant silkworm strains became imminent to increase production of silk, which is a major revenue earner for sericulturists. Since environment interacts with phenotype, conventional breeding did not result in commendable yield improvement in synthetic strains of silkworm, Bombyx mori. Identification of DNA markers associated with different economically important biomass traits and its introgression could assist molecular breeding and expression of stabilized high yielding characters, but genetic basis of most quantitative traits in silkworm is poorly understood due to its polygenic control. Correlation analysis (R = 0.9) revealed significant interrelation among biomass traits viz., larval duration (TLD), larval weight (LWT), cocoon weight (CWT), shell weight (SWT), shell ratio (SR) and floss content. PCR using inter simple sequence repeat (ISSR) primers revealed 92% polymorphism among 14 tropical and temperate strains of B. mori, with average diversity index of 0.747. Stepwise multiple regression analysis (MRA) selected 35 ISSR markers positively or negatively correlated with different biomass traits, illustrated polygenic control. ISSR marker 830.8(1050bp) was significantly associated with LWT, CWT, SWT, SR and floss content, indicated its pleiotropic role. Two ISSR markers, 835.5(1950bp) and 825.9(710bp) showed significant association with floss content and TLD. These markers were segregated in F(2) generation and Chi-square test confirmed (chi(2) = ~45; P < 0.05) its genetic contribution to the associated biomass traits. Strains, with both positively and negatively correlated markers, had intermediate mean value for biomass traits (eg. SWT = 0.17 +/- 0.014 g in GNM and Moria) indicated interaction of loci in natural populations. Low yielding Indian strains grouped together by Hierarchical clustering. Chinese and Japanese strains were distributed in the periphery of ALSCAL matrix indicated convergence of genetic characters in Indian strains. Average genetic distance between Chinese strains and Indian strains (0.193) significantly (P < 0.01) varied from that between Chinese and Japanese strains. Interaction of loci and allelic substitutions induced phenotypic plasticity in temperate B. mori populations on tropic adaptation in India. These outcomes show possibility to combine favorable alleles at different QTL to increase larval, cocoon and shell weight. PMID:19662204
Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery
Background Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, functional annotation, and in silico discovery of potential molecular markers to support population and associations genetic studies, are described. Results Pyrosequencing of a young leaf cDNA library generated a total of 111,814 high quality reads, with an average length of 447 bp. De novo assembly using Newbler resulted into 3,005 tentative isotigs (including alternative transcripts). The non-assembled sequences (singletons) were clustered with CD-HIT-454 to identify natural and artificial duplicates from pyrosequencing reads, leading to 21,881 unique singletons. 15,497 out of 24,886 non-redundant sequences or unigenes, were successfully annotated against a plant protein database. A substantial number of simple sequence repeat markers (SSRs) were discovered in the assembled and annotated sequences. More than 40% of the SSR sequences were inside ORF sequences. To confirm the validity of these predicted markers, a subset of 73 SSRs selected through functional annotation evidences were successfully amplified from six seedlings DNA samples, being 14 polymorphic. Conclusions This paper is the first report that shows a highly precise representation of the mRNAs diversity present in young leaves of a native South American tree, N. nervosa, as well as its in silico deduced putative functionality. The reported Nothofagus transcriptome sequences represent a unique resource for genetic studies and provide a tool to discover genes of interest and genetic markers that will greatly aid questions involving evolution, ecology, and conservation using genetic and genomic approaches in the genus. PMID:22747958
Genetic molecular analysis of Coffea arabica (Rubiaceae) hybrids using SRAP markers.
Mishra, Manoj Kumar; Suresh, Narayana; Bhat, Asha M; Suryaprakash, Nayani; Kumar, Saya Satheesh; Kumar, Anil; Jayarama
In Coffea arabica (arabica coffee), the phenotypic as well as genetic variability has been found low because of the narrow genetic basis and self fertile nature of the species. Because of high similarity in phenotypic appearance among the majority of arabica collections, selection of parental lines for inter-varietals hybridization and identification of resultant hybrids at an early stage of plant growth is difficult. DNA markers are known to be reliable in identifying closely related cultivars and hybrids. Sequence Related Amplified Polymorphism (SRAP) is a new molecular marker technology developed based on PCR. In this paper, sixty arabica-hybrid progenies belonging to six crosses were analyzed using 31 highly polymorphic SRAP markers. The analysis revealed seven types of SRAP marker profiles which are useful in discriminating the parents and hybrids. The number of bands amplified per primer pair ranges from 6.13 to 8.58 with average number of seven bands. Among six hybrid combinations, percentage of bands shared between hybrids and their parents ranged from 66.29% to 85.71% with polymorphic bands varied from 27.64% to 60.0%. Percentage of hybrid specific fragments obtained in various hybrid combinations ranged from 0.71% to 10.86% and ascribed to the consequence of meiotic recombination. Based on the similarity index calculation, it was observed that F1 hybrids share maximum number of bands with the female parent compared to male parent. The results obtained in the present study revealed the effectiveness of SRAP technique in cultivar identification and hybrid analysis in this coffee species. PMID:21717853
Status of potential PfATP6 molecular markers for artemisinin resistance in Suriname
Background Polymorphisms within the PfATP6 gene have been indicated as potential molecular markers for artemisinin efficacy. Since 2004, the use of artemisinin combination therapy (ACT) was introduced as first-line treatment of the uncomplicated malaria cases in Suriname. The aim of this research was to determine changes in Suriname in the status of the polymorphic markers in the PfATP6 gene before and after the adoption of the ACT-regimen, particularly of the S769N mutation, which was reported to be associated with in vitro Artemether resistance in the neighboring country French Guiana. Methods The PfATP6 gene from Plasmodium falciparum parasites in Suriname was investigated in 28 samples using PCR amplification and restriction enzyme analysis, to assess and determine the prevalence of potentially interesting single nucleotide polymorphisms. The polymorphisms [L263E; A623E; S769N], which may be associated with the artemisinin resistant phenotype were characterized in parasites from three endemic regions before and after the adoption of the ACT-regimen. In addition, the status of these molecular markers was compared in paired P. falciparum isolates from patients with recurring malaria after controlled ACT. Results All the investigated samples exhibit the wild-type genotype at all three positions; L263, A623, S769. Conclusion All investigated isolates before and after the adoption of the ACT-regimen and independent of endemic region harbored the wild-type genotype for the three investigated polymorphisms. The study revealed that decreased artemisinin susceptibility could occur independent from PfATP6 mutations, challenging the assumption that artemisinin resistance is associated with these mutations in the PfATP6 gene. PMID:22966810
Molecular markers for the detection of the wheat leaf rust resistance gene Lr10 in diverse genetic backgrounds
Gabriele Schachermayr; Catherine Feuillet; Beat Keller
We recently showed that the Lr10 wheat leaf rust resistance gene cosegregated with the candidate resistance gene Lrk10 which encodes a putative receptor-like kinase. The aim of this study was to develop Lrk10-derived molecular markers for the detection of the Lr10 gene in breeding material. Different subfragments of Lrk10 were tested as RFLP markers for the Lr10 resistance gene. The
The semidwarf gene, sd-1, of rice ( Oryza sativa L.). II. Molecular mapping and marker-assisted selection
Y. G. Cho; M. Y. Eun; S. R. McCouch; Y. A. Chae
To establish the location of the semidwarf gene, sd-1, the anthocyanin activator (A), purple node (Pn), purple auricle (Pau), and the isozyme locus, EstI-2, in relation to DNA markers on the molecular linkage map of rice, 20 RFLP markers, previously mapped to the central region of chromosome 1 (McCouch et al. 1988), were mapped onto an F2 population derived from
Combustion inputs into a terrestrial archive over 265 years as evidenced by BPCA molecular markers
NASA Astrophysics Data System (ADS)
Hanke, Ulrich M.; Eglinton, Timothy I.; Wiedemeier, Daniel B.; Schmidt, Michael W. I.
Pyrogenic organic matter (PyOM) such as char and soot is produced during the incomplete combustion of biomass and fossil fuel. It is composed of condensed aromatic structures and can resist degradation processes, maybe over long periods of time. Land-use changes, industrial activity and its transport by wind and water affect the fluxes of PyOM from the source to its sedimentary archive. Investigating environmental PyOM with the molecular marker benzene polycarboxylic acid (BPCA) method provides various information about quantity, quality (BPCA distribution pattern) and about its isotopic composition (13C and 14C). Assessing PyOM quality can indicate whether it is mostly combustion condensate (soot) or combustion residue (charcoal) and potentially allow source apportionment. Our study area is the Pettaquamscutt River catchment area (35 km2), Rhode Island, U.S.A. It is located down-wind of industrial areas recording deposition of long-distance atmospheric transport as well as local catchment inputs, both from natural and anthropogenic sources. We investigated 50 samples of a sediment record over a time span of 265 years (1733-1998 AD). Previous investigations provided information on the age of deposition, the content of polycyclic aromatic hydrocarbons (PAH) as well as of the radiocarbon contents of total organic carbon (TOC) and PAH (Lima, 2004). We used the BPCA molecular marker method to quantify and characterize PyOM in the same record. First results show that quantity and quality of PyOM change over 265 years. Our investigation aims at understanding how different sources of PyOM are reflected in terrestrial archives by comparing the results of BPCA with radiocarbon-dated TOC and PAH records. Among other aspects, the PAH record reflects the Great Depression and the 1970s oil embargo in North America. We interpret the BPCA distribution patterns regarding the simultaneous shift of dominant fuels including wood, coal, petroleum and gas. Future work will include compound-specific radiocarbon analysis of BPCA molecular markers to improve our understanding of the sources and residence time of PyOM. References Lima, A.L.C., 2004. Molecular and Isotopic Records of Combustion Inputs to the Environment Over the Last 250 Years, doctoral dissertation, Massachusetts Institute of Technology/Woods Hole Oceanographic Institution (MIT/WHOI).
A Randomly Amplified Polymorphic DNA Marker Specific for the Bacillus cereus Group Is Diagnostic for Bacillus anthracis
Aiming to develop a DNA marker specific for Bacillus anthracis and able to discriminate this species from Bacillus cereus, Bacillus thuringiensis, and Bacillus mycoides, we applied the randomly amplified polymorphic DNA (RAPD) fingerprinting technique to a collection of 101 strains of the genus Bacillus, including 61 strains of the B. cereus group. An 838-bp RAPD marker (SG-850) specific for B.
Male-specific DNA markers from African catfish (Clarias gariepinus)
Balázs Kovács; Sándor Egedi; Richárd Bártfai; László Orbán
We searched for sex-specific DNA sequences in the male and female genomes of African catfish, Clarias gariepinus (Burchell, 1822) by comparative random amplified polymorphic DNA (RAPD) assays performed on pooled DNA samples. Two sex-linked\\u000a RAPD markers were identified from the male DNA pool and confirmed on individual samples, showing good agreement with phenotypic\\u000a sex. Both markers were isolated, cloned and
Utilization of molecular markers for the conservation of blood cockles, Anadara granosa (Arcidae).
Chee, S Y; Azizah, M N S; Devakie, M N
We examined genetic variation in blood cockles in an effort to obtain information useful for the sustainability, management, and the stability of this species as a major commodity in the fisheries sector. Ten populations of cockles were sampled from the north to the south of the west coast of peninsular Malaysia. The cockles were collected in collaboration with the Fisheries Research Institute, Penang. The population genetic analysis of the cockles were studied via RAPD-PCR and mtDNA sequencing. Three hundred individuals were analyzed with RAPD-PCR experiments. High gene diversity over all loci was observed (Shannon index = 0.549 ± 0.056 and Nei's gene diversity = 0.4852 ± 0.0430 among 35 loci). The second method, mtDNA sequencing, was employed to complement the information obtained from RAPD-PCR. The gene selected for mtDNA sequencing was cytochrome c oxidase I (COI). One hundred and fifty individuals were sequenced, yielding a partial gene of 585 bp. Statistical analysis showed homogeneity in general but did reveal some degree of variability between the populations in Johor and the rest of the populations. The Mantel test showed a positive but nonsignificant correlation between geographic and genetic distances (r = 0.2710, P = 0.622), as in the RAPD analysis. We propose that the homogeneity between distant populations is caused by two factors: 1) the translocation of the spats; 2) larvae are carried by current movement from the north of the peninsula to the south. The different genetic composition found in Johor could be due to pollution, mutagenic substances or physical factors such as the depth of the water column. This population genetic study is the first for this species in peninsular Malaysia. The data from this study have important implications for fishery management, conservation of blood cockles and translocation policies for aquaculture and stock enhancement programs. PMID:21732289
Typing Mycobacterium bovis isolates from Texas and Mexico using molecular markers
Perumaalla, Veera Shankar
be confirmed using additional methods such as 156110 hybridization. Arbitrary PCR priming, which is also referred as random amplified polymorphic DNA (RAPD) is another DNA fingerprinting method that relies on the presence of low stringency priming sites... for a single random primer on both strands of the DNA molecule close enough to permit PCR amplification. This technique has been successfully employed to type several fungal and bacterial infections including Mycobacterium species (1, 33, 47). A...
Fasciola hepatica: identification of molecular markers for resistant and susceptible Pseudosuccinea columella snail hosts
Alfredo Gutiérrez; Jean-Pierre Pointier; Jorge Fraga; Edouard Jobet; Sylvain Modat; R. T Pérez; Mary Yong; J Sanchez; Eric S Loker; André Théron
Protein electrophoresis, RAPD-PCR and nuclear rDNA ITS sequencing were performed to search for genetic differences between Pseudosuccinea columella snails susceptible and resistant to Fasciola hepatica infection. Of the 21 enzymatic loci analyzed in both populations, none of them exhibited neither within- or between-group variation. Such an absence of enzyme polymorphism support the hypothesis of selfing as the "prevalent" mating system
A slippery molecular assembly allows water as a self-erasable security marker
Thirumalai, Rajasekaran; Mukhopadhyay, Rahul Dev; Praveen, Vakayil K.; Ajayaghosh, Ayyappanpillai
Protection of currency and valuable documents from counterfeit continues to be a challenge. While there are many embedded security features available for document safety, they are not immune to forgery. Fluorescence is a sensitive property, which responds to external stimuli such as solvent polarity, temperature or mechanical stress, however practical use in security applications is hampered due to several reasons. Therefore, a simple and specific stimuli responsive security feature that is difficult to duplicate is of great demand. Herein we report the design of a fluorescent molecular assembly on which water behaves as a self-erasable security marker for checking the authenticity of documents at point of care. The underlying principle involves the disciplined self-assembly of a tailor-made fluorescent molecule, which initially form a weak blue fluorescence (?em?=?425?nm, ?f?=?0.13) and changes to cyan emission (?em?=?488?nm,?f?=?0.18) in contact with water due to a reversible molecular slipping motion. This simple chemical tool, based on the principles of molecular self-assembly and fluorescence modulation, allows creation of security labels and optically masked barcodes for multiple documents authentication. PMID:25940779
A slippery molecular assembly allows water as a self-erasable security marker.
Thirumalai, Rajasekaran; Mukhopadhyay, Rahul Dev; Praveen, Vakayil K; Ajayaghosh, Ayyappanpillai
Protection of currency and valuable documents from counterfeit continues to be a challenge. While there are many embedded security features available for document safety, they are not immune to forgery. Fluorescence is a sensitive property, which responds to external stimuli such as solvent polarity, temperature or mechanical stress, however practical use in security applications is hampered due to several reasons. Therefore, a simple and specific stimuli responsive security feature that is difficult to duplicate is of great demand. Herein we report the design of a fluorescent molecular assembly on which water behaves as a self-erasable security marker for checking the authenticity of documents at point of care. The underlying principle involves the disciplined self-assembly of a tailor-made fluorescent molecule, which initially form a weak blue fluorescence (?em?=?425?nm, ?f?=?0.13) and changes to cyan emission (?em?=?488?nm,?f?=?0.18) in contact with water due to a reversible molecular slipping motion. This simple chemical tool, based on the principles of molecular self-assembly and fluorescence modulation, allows creation of security labels and optically masked barcodes for multiple documents authentication. PMID:25940779
IL-32 is a molecular marker of a host defense network in human tuberculosis
Montoya, Dennis; Inkeles, Megan S.; Liu, Phillip T.; Realegeno, Susan; Teles, Rosane M. B.; Vaidya, Poorva; Munoz, Marcos A.; Schenk, Mirjam; Swindell, William R.; Chun, Rene; Zavala, Kathryn; Hewison, Martin; Adams, John S.; Horvath, Steve; Pellegrini, Matteo; Bloom, Barry R.; Modlin, Robert L.
Tuberculosis is a leading cause of infectious disease–related death worldwide; however, only 10% of people infected with Mycobacterium tuberculosis develop disease. Factors that contribute to protection could prove to be promising targets for M. tuberculosis therapies. Analysis of peripheral blood gene expression profiles of active tuberculosis patients has identified correlates of risk for disease or pathogenesis. We sought to identify potential human candidate markers of host defense by studying gene expression profiles of macrophages, cells that, upon infection by M. tuberculosis, can mount an antimicrobial response. Weighted gene coexpression network analysis revealed an association between the cytokine interleukin-32 (IL-32) and the vitamin D antimicrobial pathway in a network of interferon-?– and IL-15–induced "defense response" genes. IL-32 induced the vitamin D–dependent antimicrobial peptides cathelicidin and DEFB4 and to generate antimicrobial activity in vitro, dependent on the presence of adequate 25-hydroxyvitamin D. In addition, the IL-15–induced defense response macrophage gene network was integrated with ranked pairwise comparisons of gene expression from five different clinical data sets of latent compared with active tuberculosis or healthy controls and a coexpression network derived from gene expression in patients with tuberculosis undergoing chemotherapy. Together, these analyses identified eight common genes, including IL-32, as molecular markers of latent tuberculosis and the IL-15–induced gene network. As maintaining M. tuberculosis in a latent state and preventing transition to active disease may represent a form of host resistance, these results identify IL-32 as one functional marker and potential correlate of protection against active tuberculosis. PMID:25143364
Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques.
Leigh, F; Kalendar, R; Lea, V; Lee, D; Donini, P; Schulman, A H
The Sequence-Specific Amplification Polymorphism (S-SAP) method, and the related molecular marker techniques IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism), are based on retrotransposon activity, and are increasingly widely used. However, there have been no systematic analyses of the parameters of these methods or of the utility of different retrotransposon families in producing polymorphic, scorable fingerprints. We have generated S-SAP, IRAP, and REMAP data for three barley (Hordeum vulgare L.) varieties using primers based on sequences from six retrotransposon families (BARE-1, BAGY-1, BAGY-2, Sabrina, Nikita and Sukkula). The effect of the number of selective bases on the S-SAP profiles has been examined and the profiles obtained with eight MseI+3 selective primers compared for all the elements. Polymorphisms detected in the insertion pattern of all the families show that each can be used for S-SAP. The uniqueness of each transposition event and differences in the historic activity of each family suggest that the use of multiple retrotransposon families for genetic analysis will find applications in mapping, fingerprinting, and marker-assisted selection and evolutionary studies, not only in barley and other Hordeum species and related taxa, but also more generally. PMID:12768410
Identifying molecular markers for the sensitive detection of residual atypical teratoid rhabdoid tumor cells.
Vu-Han, Tu-Lan; Frühwald, Michael C; Hasselblatt, Martin; Kerl, Kornelius; Nagel, Inga; Obser, Tobias; Oyen, Florian; Siebert, Reiner; Schneppenheim, Reinhard
Atypical teratoid rhabdoid tumor (AT/RT), a rare and highly malignant tumor entity of the central nervous system that presents in early childhood, has a poor prognosis. AT/RTs are characterized by biallelic inactivating mutations of the gene SMARCB1 in 98% of patients; these mutations may serve as molecular markers for residual tumor cell detection in liquid biopsies. We developed a marker-specific method to detect residual AT/RT cells. Seven of 150 patient samples were selected, each with a histological and genetically ascertained diagnosis of AT/RT. Tumor tissue was either formalin fixed or fresh frozen. DNA was extracted from the patients' peripheral blood leukocytes (PBL) and cerebrospinal fluid (CSF). Multiplex ligation-dependent probe amplification, DNA sequencing, and fluorescence in situ hybridization were used to characterize the tumors' mutations. Residual tumor cell detection used mutation-specific primers and real-time PCR. The detection limit for the residual tumor cell search was 1-18%, depending on the quality of the template provided. The residual tumor cell search in PBL and CSF was negative for all seven patients. The SMARCB1 region of chromosome 22 is prone to DNA double-strand breaks. The individual breakpoints and breakpoint-specific PCR offer the option to detect minimal residual tumor cells in CSF or blood. Even if we did not detect minimal residual tumor cells in the investigated material, proof of principle for this method was confirmed. PMID:25016934
Identification of the sources of primary organic aerosols at urban schools: a molecular marker approach.
Crilley, Leigh R; Qadir, Raeed M; Ayoko, Godwin A; Schnelle-Kreis, Jürgen; Abbaszade, Gülcin; Orasche, Jürgen; Zimmermann, Ralf; Morawska, Lidia
Children are particularly susceptible to air pollution and schools are examples of urban microenvironments that can account for a large portion of children's exposure to airborne particles. Thus this paper aimed to determine the sources of primary airborne particles that children are exposed to at school by analyzing selected organic molecular markers at 11 urban schools in Brisbane, Australia. Positive matrix factorization analysis identified four sources at the schools: vehicle emissions, biomass burning, meat cooking and plant wax emissions accounting for 45%, 29%, 16% and 7%, of the organic carbon respectively. Biomass burning peaked in winter due to prescribed burning of bushland around Brisbane. Overall, the results indicated that both local (traffic) and regional (biomass burning) sources of primary organic aerosols influence the levels of ambient particles that children are exposed at the schools. These results have implications for potential control strategies for mitigating exposure at schools. PMID:24842381
Role of molecular markers in diagnosis and prognosis of renal cell carcinoma.
Martignoni, Guido; Brunelli, Matteo; Gobbo, Stefano; Remo, Andrea; Ficarra, Vincenzo; Cossu-Rocca, Paolo; Pea, Maurizio; Chilosi, Marco; Menestrina, Fabio; Cheng, Liang
It has been demonstrated that different renal cell neoplasms have characteristic morphologic and genetic features. Histologic subtyping of renal epithelial neoplasms has been shown to be of prognostic value; therefore they must be correctly classified. Although adequate sampling and a good understanding of the morphologic features usually minimize diagnostic errors, the use of immunohistochemical and chromosomal analysis on formalin-fixed, paraffin-embedded tissues can be necessary. These techniques can facilitate diagnosis on small biopsies, which are increasingly obtained from renal masses. An immunohistochemical panel including CD10, parvalbumin, AMACR, CK7 and S100A1 seems the most promising; fluorescence in situ hybridization analysis using centromeric probes to evaluate the gains and losses of the chromosomes can be helpful in selected cases. A wide variety of molecular markers have been examined, but further research is required to prove their value as prognostic tools. PMID:17375873
A multi-marker molecular signature approach for treatment-specific subgroup identification with survival outcomes.
Li, L; Guennel, T; Marshall, S; Cheung, L W-K
Delivering on the promise of personalized medicine has become a focus of the pharmaceutical industry as the era of the blockbuster drug is fading. Central to realizing this promise is the need for improved analytical strategies for effectively integrating information across various biological assays (for example, copy number variation and targeted protein expression) toward identification of a treatment-specific subgroup-identifying the right patients. We propose a novel combination of elastic net followed by a maximal ?(2) and semiparametric bootstrap. The combined approaches are presented in a two-stage strategy that estimates patient-specific multi-marker molecular signatures (MMMS) to identify and directly test for a biomarker-driven subgroup with enhanced treatment effect. This flexible strategy provides for incorporation of business-specific needs, such as confining the search space to a subgroup size that is commercially viable, ultimately resulting in actionable information for use in empirically based decision making. PMID:24637498
Investigation of Molecular Marker Lipids in Alpine Ice Cores Via Stir Bar Sorptive Extraction
NASA Astrophysics Data System (ADS)
Makou, M. C.; Eglinton, T. I.; Thompson, L. G.; Hughen, K. A.
Recently developed analytical techniques were employed to identify and quantify organic molecular markers trapped in high-altitude ice. While various compounds represent potentially useful proxies for biomass burning, vegetation type, atmospheric circulation, and anthropogenic activity, prior attempts to measure organic compounds in ice cores have typically required large volumes of sample material that are incompatible with generation of high-resolution paleoclimate records. We employed stir bar sorptive extraction (SBSE) and thermal desorption (TD), coupled with gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS), to examine the organic content of small quantities (? 30 ml) of ice. To test the utility of the approach, post-industrial ice core samples from the Huascarán and Sajama sites (Andes), the Dasuopu and Puruogangri sites (Tibetan Plateau), and Mt. Kilimanjaro (east Africa) were tested. n-Alkanes, n-alkanoic acids, n-alkyl amides and nitriles, polycyclic aromatic hydrocarbons (PAHs), and various diterpenoids were identified in this suite of cores. These marker compounds suggest inputs from biomass burning, fresh vascular plant material, and anthropogenic activities such as fossil fuel combustion. Differences in distributions of the alkyl amide and nitrile homologues between the different sites suggest a predominantly local or regional supply of organic matter. Pre-industrial samples from the Sajama and Puruogangri ice cores were also analyzed in order to assess the character of biomarker assemblages in the absence of anthropogenic contributions and investigate changes in inputs over time. PAHs and diterpenoids, which may result from biomass burning and were observed in the modern Sajama samples, occurred in two Holocene Sajama samples, but not in a last glacial sample. Enhanced inputs of terrestrial vegetation combustion biomarkers were consistent with periods of enhanced aridity in both cores. This study demonstrates the utility of SBSE, TD, and GC/TOF-MS for isolating organic compounds from small amounts of alpine ice and paves the way for development of high-resolution molecular stratigraphic records from tropical ice cores.
Highly variable microsatellite markers for the fungal and algal symbionts of the lichen Lobaria pulmonaria and challenges in developing biont-specific molecular markers for fungal associations.
Widmer, Ivo; Dal Grande, Francesco; Cornejo, Carolina; Scheidegger, Christoph
The availability of highly variable markers for the partners of a fungal symbiosis enables the integrated investigation of ecological and evolutionary processes at the symbiotic level. In this article we analyze the specificity of the first and to date only microsatellite markers that had been developed for an epiphytic lichen (Lobaria pulmonaria). We used DNA extracts from cultures of the fungal and of the green algal symbionts of L. pulmonaria as well as total DNA extracts from related Lobaria species associated with the same algal partner, and got evidence that five of the previously described microsatellite markers, proposed to be fungus-specific, are indeed alga-specific. Hence, highly variable microsatellite primer sets available for both, the algal and the fungal symbionts of L. pulmonaria are now at our hands, which allow us to investigate so far unexplored biological processes of lichen symbionts, such as codispersal and coevolution. In a broader sense, our work evaluates and discusses the challenges in developing biont-specific molecular markers for fungi forming close associations with other organisms. PMID:20943165
High throughput genome-specific and gene-specific molecular markers for erucic acid genes in Brassica napus (L.) for marker-assisted selection in plant breeding.
Rahman, Mukhlesur; Sun, Zudong; McVetty, Peter B E; Li, Genyi
A single base change in the Bn-FAE1.1 gene in the A genome and a two-base deletion in the Bn-FAE1.2 gene in the C genome produce the nearly zero content of erucic acid observed in canola. A BAC clone anchoring Bn-FAE1.1 from a B. rapa BAC library and a BAC clone anchoring Bn-FAE1.2 from a B. oleracea BAC library were used in this research. After sequencing the gene flanking regions, it was found that the dissimilarity of the flanking sequences of these two FAE1 homologs facilitated the design of genome-specific primers that could amplify the corresponding genome in allotetraploid B. napus. The two-base deletion in the C genome gene was detected as a sequence-characterized amplified region (SCAR) marker. To increase the throughput, one genome-specific primer was labeled with four fluorescence dyes and combined with 20 different primers to produce PCR products with different fragment sizes. Eventually, a super pool of 80 samples was detected simultaneously. This dramatically reduces the cost of marker detection. The single base change in the Bn-FAE1.1 gene was detected as single nucleotide polymorphic (SNP) marker with an ABI SNaPshot kit. A multiplexing primer set was designed by adding a polyT to the 5' primer end to increase SNP detection throughput through sample pooling. Furthermore, the Bn-FAE1.1 and Bn-FAE1.2 were integrated into the N8 and N13 linkage groups of our previously reported high-density sequence-related amplified polymorphism (SRAP) map, respectively. There were 124 SRAP markers in a N8 bin in which the Bn-FAE1.1 gene-specific SCAR marker was located and 46 SRAP markers in a N13 bin into which the Bn-FAE1.2 SNP marker was integrated. These three kinds of high throughput molecular markers have been successfully implemented in our canola/rapeseed breeding programs. PMID:18633592
Ribosomal DNA as molecular markers and their applications in the identification of fish parasites (Platyhelminthes: Monogenea) from India
Chaudhary, Anshu; Verma, Chandni; Singh, Hridaya Shanker
The development of molecular techniques for taxonomic analysis of monogenean parasites has led to a great increase for proper identification and factualness. These molecular techniques, in particular the use of molecular markers, have been used to identify and validate the monogenean parasites. Although, improvements in marker detection systems particularly of elements of rDNA like 18S, ITS and 28S used in monogeneans parasites have enabled great advances to be made in recent years in India. However, the molecular sequence analysis and phylogenetic relationships among the parasitic helminthes is unconventional in India. Many workers have been always questioned the validity of Indian species of monogeneans and emphasized the need to ascertain the status of species from Indian fish. Here we would like to provide additional resolution for the interpretation of use of molecular markers in study of monogeneans in India. This review provides an overview of current stage of studies in India that have been used in applying molecular techniques to monogenean.
Molecular genetic approach for identifying markers associated with yield traits in the silkworm, Bombyx mori using RFLP-STS primers.
Mohandas, T P; Sethuraman, B N; Saratchandra, B; Chatterjee, S N
Bombyx mori, the mulberry silkworm, exhibits wide variability in yield and developmental attributes. The genetics of yield expression, shown to be of polygenic nature, is poorly studied in silkworm. To identify markers associated with 10 selected yield traits, multiple regression analysis (MRA) and discriminant function analysis (DFA) were applied on 64 markers generated with eight RFLP-derived sequence-tagged-site (STS) primers on the genomic DNA of 20 silkworm stocks of different origin and diverse yield potential. The analyses led to the identification of ten markers showing significant association with the different yield traits. The markers could classify the stocks according to yield potential, irrespective of their origin and status of diapause. Trait means were significantly different for stocks with and with out the associated marker. The inheritance of a marker G2(1300bp), selected at the first step of MRA for five yield traits was shown to segregate in 1:1 ratio in the F2 progeny from a cross between two divergent stocks. The relevance of the STS primers is discussed in the context of applying multiple regression model for identifying markers associated with yield expression and suitability for molecular breeding work in B. mori for yield improvement. PMID:15609576
Evaluation of molecular markers for discriminating Gonatocerus morrilli (Hymenoptera: Mymaridae): a biological control agent for Homalodisca vitripennis
Technology Transfer Automated Retrieval System (TEKTRAN)
We tested the utility of molecular markers for distinguishing between two closely related species, Gonatocerus morrilli (Howard) and G. walkerjonesi, S. Triapitsyn, to evaluate whether post-release G. morrilli specimens could be discriminated in the field. Initially, post-release specimens from Cal...
Genetic mapping of Z chromosome and identification of W chromosome-specific markers in the silkworm, Bombyx mori.
Nagaraja, G M; Mahesh, G; Satish, V; Madhu, M; Muthulakshmi, M; Nagaraju, J
In the silkworm, Bombyx mori, the female is the heterogametic (ZW) sex and the male is homogametic (ZZ). The female heterogamety is a typical situation in the insect order Lepidoptera. Although the W chromosome in silkworm is strongly female determining, no W-linked gene for a morphological character has been found on it. The Z chromosome carries important traits of economic value as well as genes for various phenotypic traits, but only 2% of molecular information based on its relative size is known. Studies conducted so far indicate that the Z-linked genes are not dosage compensated. In the present study, we constructed a genetic map of randomly amplified polymorphic DNA fragments (RAPD), simple sequence repeats (SSR), and fluorescent intersimple sequence repeat PCR (FISSR) markers for the Z chromosome using a backcross mapping population. A total of 16 Z-linked markers were identified, characterized, and mapped using od, a recessive trait for translucent skin as an anchor marker yielding a total recombination map of 334.5 cM. The linkage distances obtained suggested that the markers were distributed throughout the Z chromosome. Four RAPD and four SSR markers that were linked to W chromosome were also identified. The proposed mapping approach should be useful to identify and map sex-linked traits in the silkworm. The economic and evolutionary significance of Z- and W-linked genes in silkworm, in particular, and lepidopterans, in general, is discussed. PMID:15931240
The Development of 7E Chromosome-Specific Molecular Markers for Thinopyrum elongatum Based on SLAF-seq Technology
Chen, Shiqiang; Huang, Zefeng; Dai, Yi; Qin, Shuwen; Gao, Yingying; Zhang, Lulu; Gao, Yong; Chen, Jianmin
Thinopyrum elongatum is an important relative of wheat, it is favored by many researchers for the disease resistant genes that exist in its E genome. Some studies have showed that the 7E chromosome of Th. elongatum contains resistance genes related to Fusarium head blight and wheat rust. Therefore, developing 7E chromosome-specific molecular markers linked to resistance genes will provide an important tool for exploring and using the resistant genes of Th. elongatum. In addition, it would greatly contribute in the effort to cultivate disease-resistant wheat varieties. Featured in high throughput, high-accuracy and low-cost, SLAF-seq technology has been widely used in molecular breeding, system evolution, and germplasm resource detection. Based on SLAF-seq, 518 specific fragments on the 7E chromosome of Th. elongatum were successfully amplified. A total of 135 primers were designed according to 135 randomly selected fragments, and 89 specific molecular markers of Th. elongatum were developed, with efficiencies up to 65.9%. These markers were all detected in a variety of materials, and they are all proved to be specific and stable. These markers can be used not only for detecting the 7E chromosome of Th. elongatum but also for providing an important theoretical and practical basis for wheat breeding by marker-assisted selection (MAS). This paper reports the first application of SLAF-seq technology with a high success rate in developing specific molecular markers for Th. elongatum, providing a strong case for the application of this new technology. PMID:23762296
Mitochondrial DNA and RAPD polymorphisms in the haploid mite Brevipalpus phoenicis (Acari: Tenuipalpidae).
Rodrigues, J C V; Gallo-Meagher, M; Ochoa, R; Childers, C C; Adams, B J
Brevipalpus phoenicis (Geijskes) (Acari: Tenuipalpidae) is recognized as the vector of citrus leprosis virus that is a significant problem in several South American countries. Citrus leprosis has been reported from Florida in the past but no longer occurs on citrus in North America. The disease was recently reported in Central America, suggesting that B. phoenicis constitutes a potential threat to the citrus industries of North America and the Caribbean. Besides B. phoenicis, B. obovatus Donnadieu, and B. californicus (Banks) have been incriminated as vectors of citrus leprosis virus and each species has hundreds of host plants. In this study, Brevipalpus mite specimens were collected from different plants, especially citrus, in the States of Florida (USA) and Săo Paulo (Brazil), and reared on citrus fruit under standard laboratory conditions. Mites were taken from these colonies for DNA extraction and for morphological species identification. One hundred and two Random Amplified Polymorphic DNA (RAPD) markers were scored along with amplification and sequencing of a mitochondrial cytochrome oxidase subunit I gene fragment (374 bp). Variability among the colonies was detected with consistent congruence between both molecular data sets. The mites from the Florida and Brazilian colonies were morphologically identified as belonging to B. phoenicis, and comprise a monophyletic group. These colonies could be further diagnosed and subdivided geographically by mitochondrial DNA analysis. PMID:15651525
Identification of ISSR markers associated with productivity traits in silkworm, Bombyx moni L.
Chatterjee, S N; Mohandas, T P
Bombyx mori L., commonly recognised around the world as the mulberry silkworm, is characterized by a wide variability in yield and developmental traits, which have been proven through conventional genetic analysis to be of polygenic nature. A large number of morpho-biochemical traits and RFLP and RAPD markers are mapped on different linkage groups, but to this point very little attention has been given to unravelling the genetics of yield traits. To address this issue, polymorphic profiles of 147 markers generated with 12 ISSR primers on the genomic DNA of 20 silkworm stocks of diverse yield status were subjected to multiple regression and discriminant function analyses (DFA). This led to the identification of eight markers generated by six primers, which demonstrated high beta-coefficient indices of -0.451 to -0.940. Furthermore, a significant difference between the yield traits for stocks with and without the specific marker could also be established. The inheritance pattern of one marker, L13800bp, identified at the first step of selection of markers through stepwise regression analyses for five yield parameters is discussed in the context of applying multiple regression analysis for establishing association, if not linkage, between a group of DNA markers and a particular yield trait of polygenic nature and using such markers in molecular marker-assisted breeding programs. PMID:12834060
Widespread utility of highly informative AFLP molecular markers across divergent shark species.
Zenger, Kyall R; Stow, Adam J; Peddemors, Victor; Briscoe, David A; Harcourt, Robert G
Population numbers of many shark species are declining rapidly around the world. Despite the commercial and conservation significance, little is known on even the most fundamental aspects of their population biology. Data collection that relies on direct observation can be logistically challenging with sharks. Consequently, molecular methods are becoming increasingly important to obtain knowledge that is critical for conservation and management. Here we describe an amplified fragment length polymorphism method that can be applied universally to sharks to identify highly informative genome-wide polymorphisms from 12 primer pairs. We demonstrate the value of our method on 15 divergent shark species within the superorder Galeomorphii, including endangered species which are notorious for low levels of genetic diversity. Both the endangered sand tiger shark (Carcharodon taurus, N = 18) and the great white shark (Carcharodon carcharias, N = 7) displayed relatively high levels of allelic diversity. A total of 59 polymorphic loci (H(e) = 0.373) and 78 polymorphic loci (H(e) = 0.316) were resolved in C. taurus and C. carcharias, respectively. Results from other sharks (e.g., Orectolobus ornatus, Orectolobus sp., and Galeocerdo cuvier) produced remarkably high numbers of polymorphic loci (106, 94, and 86, respectively) from a limited sample size of only 2. A major constraint to obtaining much needed genetic data from sharks is the time-consuming process of developing molecular markers. Here we demonstrate the general utility of a technique that provides large numbers of informative loci in sharks. PMID:17150982
Population Genetic Structure of Two Threatened Dragonfly Species (Odonata: Anisoptera) as Revealed by RAPD Analysis
Mónica A. Amorín; Marta Vila; Adolfo C. Rivera
\\u000a The riverine odonates Macromia splendens and Oxygastra curtisii were included in the European Habitats directive as taxa of special concern. Nevertheless, there is almost no genetic information\\u000a about them. We assessed the genetic diversity and population structuring among several Northwest Iberian locations where these\\u000a species occur. For this, we examined the genetic pattern revealed by RAPD markers in four locations
Application of rapd in the determination of genetic fidelity in micropropagated Drosera plantlets
Anna Kawiak; Ewa ?ojkowska
Summary Random amplified polymorphic DNA (RAPD) markers were used to verify the clonal fidelity of two micropropagated Drosera species, D. anglica and D. binata, which were regenerated by adventitious budding from leaf explants and shoot tips, respectively. Twenty arbitrary decamers\\u000a were used to screen 15 randomly selected plantlets of each species. No genetic variation was detected among D. binata regenerants, whereas
A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech ( Fagus sylvatica L.)
M. Scalfi; M. Troggio; P. Piovani; S. Leonardi; G. Magnaschi; G. G. Vendramin; P. Menozzi
The genetic linkage map of European beech ( Fagus sylvatica L.) that we report here is the first to our knowledge. Based on a total of 312 markers (28 RAPDs, 274 AFLPs, 10 SSRs) scored in 143 individuals from a F 1 full-sib family. Two maps (one for each parent) were constructed according to a "two-way pseudo-testcross" mapping strategy. In
Molecular marker characterization and source appointment of particulate matter and its organic aerosols.
Choi, Jong-Kyu; Ban, Soo-Jin; Kim, Yong-Pyo; Kim, Yong-Hee; Yi, Seung-Muk; Zoh, Kyung-Duk
This study was carried out to identify possible sources and to estimate their contribution to total suspended particle (TSP) organic aerosol (OA) contents. A total of 120 TSP and PM2.5 samples were collected simultaneously every third day over a one-year period in urban area of Incheon, Korea. High concentration in particulate matters (PM) and its components (NO3(-), water soluble organic compounds (WSOCs), and n-alkanoic acids) were observed during the winter season. Among the organics, n-alkanes, n-alkanoic acids, levoglucosan, and phthalates were major components. Positive matrix factorization (PMF) analysis identified seven sources of organic aerosols including combustion 1 (low molecular weight (LMW)-polycyclic aromatic hydrocarbons (PAHs)), combustion 2 (high molecular weight (HMW)-PAHs), biomass burning, vegetative detritus (n-alkane), secondary organic aerosol 1 (SOA1), secondary organic aerosol 2 (SOA2), and motor vehicles. Vegetative detritus increased during the summer season through an increase in biogenic/photochemical activity, while most of the organic sources were prominent in the winter season due to the increases in air pollutant emissions and atmospheric stability. The correlation factors were high among the main components of the organic carbon (OC) in the TSP and PM2.5. The results showed that TSP OAs had very similar characteristics to the PM2.5 OAs. SOA, combustion (PAHs), and motor vehicle were found to be important sources of carbonaceous PM in this region. Our results imply that molecular markers (MMs)-PMF model can provide useful information on the source and characteristics of PM. PMID:26022138
[Markers for non-invasive molecular genetic diagnosis of oncourological diseases].
Mikha?lenko, D S; Perepechin, D V; Apolikhin, O I; Efremov, G D; Sivkov, A V
Currently, there is accumulated mass of data on the molecular-genetic disorders in prostate cancer (PCa), bladder cancer (BC) and renal cancer (RC). Tumor cells in these diseases are present in the urine sediment; their number is sufficient for molecular genetic analysis that makes possible the development of noninvasive diagnosis of oncourological diseases. A characteristic feature of PCa includes the overexpression of the PCA3 gene; assay kit Progensa™ to quantify such overexpression has been developed; approximately 50% of tumors express a TMPRSS2-ERG chimeric oncogene. Combined analysis of PCA3 and TMPRSS2-ERG allows to detect PCa with a diagnostic accuracy of 84%, which is significantly higher than that of prostate specific antigen test. As a potential markers of BC, there are somatic mutations in FGFR3, PIK3CA, TERT genes in urine sediment, which are found in this disease with a frequency of about 60, 30 and 50%, respectively. The basis of the test system for DNA diagnosis of BC in urine sediment may include a definition of a combination of mutations in these genes with microsatellite instability. Aberrant methylation of the 5'-regulatory regions of tumor suppressor genes, integrated in the panel, also is considered as a tool in the diagnosis of RC (VHL, RASSF1, RARB2, CDH1), PCa (GSTP1, PTGS2, LGALS3) and BC (RASSF1, APC, SFRP2) after standardization of panels of loci investigated, sample preparation methods, bisulfite conversion, and the design of primers and probes. Thus, a test systems for molecular genetic diagnosis of oncourological diseases in urine sediment are currently available or may be developed in the near future. PMID:25807773
Genetic rearrangements of six wheat-agropyron cristatum 6P addition lines revealed by molecular markers.
Han, Haiming; Bai, Li; Su, Junji; Zhang, Jinpeng; Song, Liqiang; Gao, Ainong; Yang, Xinming; Li, Xiuquan; Liu, Weihua; Li, Lihui
Agropyron cristatum (L.) Gaertn. (2n?=?4x?=?28, PPPP) not only is cultivated as pasture fodder but also could provide many desirable genes for wheat improvement. It is critical to obtain common wheat-A. cristatum alien disomic addition lines to locate the desired genes on the P genome chromosomes. Comparative analysis of the homoeologous relationships between the P genome chromosome and wheat genome chromosomes is a key step in transferring different desirable genes into common wheat and producing the desired alien translocation line while compensating for the loss of wheat chromatin. In this study, six common wheat-A. cristatum disomic addition lines were produced and analyzed by phenotypic examination, genomic in situ hybridization (GISH), SSR markers from the ABD genomes and STS markers from the P genome. Comparative maps, six in total, were generated and demonstrated that all six addition lines belonged to homoeologous group 6. However, chromosome 6P had undergone obvious rearrangements in different addition lines compared with the wheat chromosome, indicating that to obtain a genetic compensating alien translocation line, one should recombine alien chromosomal regions with homoeologous wheat chromosomes. Indeed, these addition lines were classified into four types based on the comparative mapping: 6PI, 6PII, 6PIII, and 6PIV. The different types of chromosome 6P possessed different desirable genes. For example, the 6PI type, containing three addition lines, carried genes conferring high numbers of kernels per spike and resistance to powdery mildew, important traits for wheat improvement. These results may prove valuable for promoting the development of conventional chromosome engineering techniques toward molecular chromosome engineering. PMID:24595330
Molecular Assay for Detection of Genetic Markers Associated with Decreased Susceptibility to Cephalosporins in Neisseria gonorrhoeae.
Peterson, S W; Martin, I; Demczuk, W; Bharat, A; Hoang, L; Wylie, J; Allen, V; Lefebvre, B; Tyrrell, G; Horsman, G; Haldane, D; Garceau, R; Wong, T; Mulvey, M R
The incidence of antimicrobial-resistant Neisseria gonorrhoeae continues to rise in Canada; however, antimicrobial resistance data are lacking for approximately 70% of gonorrhea infections that are diagnosed directly from clinical specimens by nucleic acid amplification tests (NAATs). We developed a molecular assay for surveillance use to detect mutations in genes associated with decreased susceptibility to cephalosporins that can be applied to both culture isolates and clinical samples. Real-time PCR assays were developed to detect single nucleotide polymorphisms (SNPs) in ponA, mtrR, penA, porB, and one N. gonorrhoeae-specific marker (porA). We tested the real-time PCR assay with 252 gonococcal isolates, 50 nongonococcal isolates, 24 N. gonorrhoeae-negative NAAT specimens, and 34 N. gonorrhoeae-positive NAAT specimens. Twenty-four of the N. gonorrhoeae-positive NAAT specimens had matched culture isolates. Assay results were confirmed by comparison with whole-genome sequencing data. For 252 N. gonorrhoeae strains, the agreement between the DNA sequence and real-time PCR was 100% for porA, ponA, and penA, 99.6% for mtrR, and 95.2% for porB. The presence of ?2 SNPs correlated with decreased susceptibility to ceftriaxone (sensitivities of >98%) and cefixime (sensitivities of >96%). Of 24 NAAT specimens with matched cultures, the agreement between the DNA sequence and real-time PCR was 100% for porB, 95.8% for ponA and mtrR, and 91.7% for penA. We demonstrated the utility of a real-time PCR assay for sensitive detection of known markers for the decreased susceptibility to cephalosporins in N. gonorrhoeae. Preliminary results with clinical NAAT specimens were also promising, as they correlated well with bacterial culture results. PMID:25878350
Establishment of a proteome profile and identification of molecular markers for mouse spermatogonial stem cells
Zhou, Quan; Guo, Yueshuai; Zheng, Bo; Shao, Binbin; Jiang, Min; Wang, Gaigai; Zhou, Tao; Wang, Lei; Zhou, Zuomin; Guo, Xuejiang; Huang, Xiaoyan
Spermatogonial stem cells (SSCs) are undifferentiated cells that are required to maintain spermatogenesis throughout the reproductive life of mammals. Although SSC transplantation and culture provide a powerful tool to identify the mechanisms regulating SSC function, the precise signalling mechanisms governing SSC self-renewal and specific surface markers for purifying SSCs remain to be clearly determined. In the present study, we established a steady SSC culture according to the method described by Shinohara's lab. Fertile progeny was produced after transplantation of cultured SSCs into infertile mouse testis, and the red fluorescence exhibited by the culture cell membranes was stably and continuously transmitted to the offspring. Next, via advanced mass spectrometry and an optimized proteomics platform, we constructed the proteome profile, with 682 proteins expressed in SSCs. Furthermore bioinformatics analysis showed that the list contained several known molecules that are regulated in SSCs. Several nucleoproteins and membrane proteins were chosen for further exploration using immunofluorescence and RT-PCR. The results showed that SALL1, EZH2, and RCOR2 are possibly involved in the self-renewal mechanism of SSCs. Furthermore, the results of tissue-specific expression analysis showed that Gpat2 and Pld6 were uniquely and highly expressed in mouse testes and cultured SSCs. The cellular localization of PLD6 was further explored and the results showed it was primarily expressed in the spermatogonial membrane of mouse testes and cultured SSCs. The proteins identified in this study form the basis for further exploring the molecular mechanism of self-renewal in SSCs and for identifying specific surface markers of SSCs. PMID:25352495
Comparative analysis of seeded and vegetative biotype buffalograsses based on phylogenetic relationship using ISSRs, SSRs, RAPDs, and SRAPs.
Budak, H; Shearman, R C; Parmaksiz, I; Dweikat, I
Buffalograss [ Buchloe dactyloides (Nutt.) Englem.] is the only native grass that is being used extensively as a turfgrass in the Great Plains region. Its low-growth habit, drought resistance, and low-maintenance requirement make it attractive as a turfgrass species. Our objective was to obtain an overview on the genetic relatedness among and within seeded and vegetative biotype buffalograsses using inter-simple sequence repeats (ISSRs), random amplified polymorphic DNA (RAPDs), sequence-related amplified polymorphisms (SRAPs), and simple sequence repeats (SSRs) markers that were derived from related species (maize, pearl millet, sorghum, and sugarcane). Twenty individuals per cultivar were genotyped using 30 markers from each marker system. All buffalograss cultivars were uniquely fingerprinted by all four marker systems. Mean genetic similarities were estimated at 0.52, 0.51, 0.62, and 0.57 using SSRs, ISSRs, SRAPs, and RAPDs, respectively. Two main clusters separating the seeded-biotype from the vegetative-biotype cultivars were produced using UPGMA analysis. Further subgroupings were unequivocal. The Mantel test resulted in a very good fit (SRAP=0.92, ISSR=0.90) to good fit (RAPD=0.86, SSR=0.88) of cophenetic values. Comparing the four marker systems to each other, RAPD and SRAP similarity indices were highly correlated ( r=0.73), while Spearman's rank correlation coefficient between RAPDs and SSRs was r=0.24 and between ISSRs and SSRs was r=0.66. A genotype-assignment analytical approach might be useful for cultivar identification and property rights protection. Polymorphic SRAPs were abundant and demonstrated genetic diversity among closely related cultivars. PMID:15024466
Genetic and interval mapping of the bovine X chromosome for quantitative trait loci using microsatellite markers
Yeh, Chen-Chen
probes can only be used for closely related species, (2) the level of polymorphism is higher than RFLPs, (3) the process is simpler and faster, and (4) RAPD requires small amounts of 19 genomic DNA for PCR amplification. RAPDs need only 2 to 4 hours... markers for gene mapping (ORITA et al. 1989; KITAJIMA 1994). Random-amplified polymorphic DNA fragments (RAPD) / Arbitrary- primer (AP) PCR: The RAPD technique is based on the use of primers of arbitrary nucleotide sequence to amplify random segments...
Evaluation of RAPD-PCR and protein profile analysis to differentiate Vibrio harveyi strains prevalent along the southwest coast of India.
Maiti, Biswajit; Shekar, Malathi; Khushiramani, Rekha; Karunasagar, Iddya; Karunasagar, Indrani
Sixty five isolates of Vibrio harveyi were subjected to random amplified polymorphic DNA (RAPD)-PCR analysis and protein profiling to investigate the genetic variability among V. harveyi prevalent along the coast and also assess the discriminating ability of these two molecular methods. A total of 10 RAPD primers were assayed for their specificity in detecting V. harveyi, of which only two primers: PM3 and CRA25 were highly reproducible and found suitable for use in RAPD-PCR. The genetic diversity among V. harveyi isolates assessed by RAPD-PCR using PM3 primer yielded 35 different RAPD patterns which clustered the isolates into 15 groups at 72% similarity level. Similarly, RAPD-PCR with CRA25 clustered the 38 patterns into 10 groups at 74% similarity. The discriminatory index (D) value calculated for RAPD fingerprints generated with PM3 and CRA25 were 0.90 and 0.85, respectively. On the other hand, molecular typing of V. harveyi using whole cell proteins generated profiles that showed no major difference indicating the technique to be not useful in typing strains of this bacterium. However, a few of the isolates showed the presence of unique band of 28 kDa that needs to be further investigated to understand the role of the protein in disease process if any. PMID:20086292
Molecular Linkage Mapping and Marker-Trait Associations with NlRPT, a Downy Mildew Resistance Gene in Nicotiana langsdorffii
Zhang, Shouan; Gao, Muqiang; Zaitlin, David
Nicotiana langsdorffii is one of two species of Nicotiana known to express an incompatible interaction with the oomycete Peronospora tabacina, the causal agent of tobacco blue mold disease. We previously showed that incompatibility is due to the hypersensitive response (HR), and plants expressing the HR are resistant to P. tabacina at all stages of growth. Resistance is due to a single dominant gene in N. langsdorffii accession S-4-4 that we have named NlRPT. In further characterizing this unique host-pathogen interaction, NlRPT has been placed on a preliminary genetic map of the N. langsdorffii genome. Allelic scores for five classes of DNA markers were determined for 90 progeny of a "modified backcross" involving two N. langsdorffii inbred lines and the related species N. forgetiana. All markers had an expected segregation ratio of 1:1, and were scored in a common format. The map was constructed with JoinMap 3.0, and loci showing excessive transmission distortion were removed. The linkage map consists of 266 molecular marker loci defined by 217 amplified fragment length polymorphisms (AFLPs), 26 simple-sequence repeats (SSRs), 10 conserved orthologous sequence markers, nine inter-simple sequence repeat markers, and four target region amplification polymorphism markers arranged in 12 linkage groups with a combined length of 1062?cM. NlRPT is located on linkage group three, flanked by four AFLP markers and one SSR. Regions of skewed segregation were detected on LGs 1, 5, and 9. Markers developed for N. langsdorffii are potentially useful genetic tools for other species in Nicotiana section Alatae, as well as in N. benthamiana. We also investigated whether AFLPs could be used to infer genetic relationships within N. langsdorffii and related species from section Alatae. A phenetic analysis of the AFLP data showed that there are two main lineages within N. langsdorffii, and that both contain populations expressing dominant resistance to P. tabacina. PMID:22936937
Molecular markers for the identification and global tracking of whitefly vector-Begomovirus complexes.
Brown, J K
Recent unprecedented upsurges in populations of the whitefly Bemisia tabaci (Genn.) have drawn much attention to its worldwide importance as an insect pest and as the vector of emergent begomoviruses (Family: Geminiviridae; Genus: Begomovirus). Several begomoviruses that are considered 'new' and others previously regarded as minor pathogens have been linked to recent epidemics. Recent studies have revealed much variation in begomoviruses, despite the view that DNA-containing viruses do not rapidly accumulate mutations. Also, certain B. tabaci 'variants' are known that more effectively or selectively transmit certain begomoviruses and exhibit biotic differences that may influence their spread. Patterns of distribution and dissemination of begomoviruses transmitted by B. tabaci are poorly understood because standardized molecular-based tracking methods have not been available. Understanding virus/whitefly vector/host plant interrelationships in the context of emerging problems can be achieved only by linking predicted evolutionary histories with epidemiology using molecular phylogenetic approaches. Identification and validation of informative molecular sequences are essential initial steps in this process. Genus-wide degenerate polymerase chain reaction (PCR) primers have been developed to amplify and sequence the 'core' region of the coat protein open reading frame (ORF) (V1), permitting 'universal' detection and provisional virus identification by comparisons with described viral genotypes. In subsequent studies reported here, several potentially informative viral ORFs and a non-coding region are explored. Of particular use for expanding diversity studies are group- or virus-specific sequences that can be targeted by utilizing newly available core CP sequences, or additional conserved regions around which broad spectrum primers can be designed to target variable sequences in key ORFs or non-coding regions. Prospective markers under exploration were selected with a basis in the most highly conserved viral ORFs, CP (V1) and a portion of replication-associated protein (REP) (L1/C1), and a key non-coding sequence that contain sufficient variability and/or virus-specific sequences, and are consequently of potential epidemiological relevance. Because B. tabaci occurs as a cryptic species, or species complex, that exhibits biotic polymorphism, yet morphological invariance, traditional morphologically based identification is impossible. An overriding complication to establishing molecular markers for identifying whitefly vector variants is that whitefly sequences in general, have not been available. However, recent work has shown that a partial mitochondria cytochrome oxidase I (mt COI) sequence separates vector variants with a basis in geographical origin, suggesting it is useful for further exploring variability and the phylogenetic history of whiteflies on a large scale. Here, the utility of whitefly mt COI nucleotides (nt) sequences is illustrated for inferring relationships between B. tabaci collected from major world regions. Used collectively, these approaches permit investigations of the patterns of distribution and dissemination of begomovirus-whitefly vector complexes for the first time. Ultimately, more immediate recognition of exotic viruses and whitefly vectors and early detection of upsurges in vector populations and of emerging viruses will be possible. PMID:11137175
Mitochondrial DNA damage: molecular marker of vulnerable nigral neurons in Parkinson's disease.
Sanders, Laurie H; McCoy, Jennifer; Hu, Xiaoping; Mastroberardino, Pier G; Dickinson, Bryan C; Chang, Christopher J; Chu, Charleen T; Van Houten, Bennett; Greenamyre, J T
DNA damage can cause (and result from) oxidative stress and mitochondrial impairment, both of which are implicated in the pathogenesis of Parkinson's disease (PD). We therefore examined the role of mitochondrial DNA (mtDNA) damage in human postmortem brain tissue and in in vivo and in vitro models of PD, using a newly adapted histochemical assay for abasic sites and a quantitative polymerase chain reaction (QPCR)-based assay. We identified the molecular identity of mtDNA damage to be apurinic/apyrimidinic (abasic) sites in substantia nigra dopamine neurons, but not in cortical neurons from postmortem PD specimens. To model the systemic mitochondrial impairment of PD, rats were exposed to the pesticide rotenone. After rotenone treatment that does not cause neurodegeneration, abasic sites were visualized in nigral neurons, but not in cortex. Using a QPCR-based assay, a single rotenone dose induced mtDNA damage in midbrain neurons, but not in cortical neurons; similar results were obtained in vitro in cultured neurons. Importantly, these results indicate that mtDNA damage is detectable prior to any signs of degeneration - and is produced selectively in midbrain neurons under conditions of mitochondrial impairment. The selective vulnerability of midbrain neurons to mtDNA damage was not due to differential effects of rotenone on complex I since rotenone suppressed respiration equally in midbrain and cortical neurons. However, in response to complex I inhibition, midbrain neurons produced more mitochondrial H2O2 than cortical neurons. We report selective mtDNA damage as a molecular marker of vulnerable nigral neurons in PD and suggest that this may result from intrinsic differences in how these neurons respond to complex I defects. Further, the persistence of abasic sites suggests an ineffective base excision repair response in PD. PMID:24981012
Gene Expression Profiles in Cells of Peripheral Blood Identify New Molecular Markers of Acute Pancreatitis
Bluth, Martin; Lin, Yin-yao; Zhang, Hong; Viterbo, Dominick; Zenilman, Michael
Introduction Blood leukocytes play a major role in mediating local and systemic inflammation during acute pancreatitis. We hypothesize that peripheral blood mononuclear cells (PBMC) in circulation exhibit unique changes in gene expression, and could provide a "reporter" function that reflects the inflammatory response in pancreas of acute pancreatitis. Methods To determine specific changes in blood leukocytes during acute pancreatitis, we studied gene transcription profile of in peripheral blood mononuclear cells (PBMC) in a rat model of experimental pancreatitis (sodium taurocholate). Normal rats, saline controls and a model of septic shock were used as a controls. cRNA obtained from PBMC of each group (n = 3) were applied to Affymetrix rat genome DNA Gene Chip Arrays. Results From the 8,799 rat genes analyzed, 140 genes showed unique significant changes in their expression in PBMC during the acute phase of pancreatitis, but not in sepsis. Among the 140 genes, 57 were upregulated, while 69 were downregulated. Platelet-derived growth factor receptor, prostaglandin E2 receptor and phospholipase D1 are among the top upregulated genes. Others include genes involved in G protein-coupled receptor and TGF-?-mediated signaling pathways, while genes associated with apoptosis, glucocorticoid receptors and even the cholecystokinin receptor are downregulated. Conclusions Microarray analysis in transcriptional profiling of PBMC showed that genes that are uniquely related to molecular and pancreatic function display differential expression in acute pancreatitis. Profiling genes obtained from an easily accessible source during severe pancreatitis may identify surrogate markers for disease severity. PMID:18347268
Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei
NASA Astrophysics Data System (ADS)
Yu, Yang; Zhang, Xiaojun; Liu, Jingwen; Li, Fuhua; Huang, Hao; Li, Yijun; Liu, Xiaolin; Xiang, Jianhai
Selective breeding of the Pacific white shrimp Litopenaeus vannamei during the last decade has produced new varieties exhibiting high growth rates and disease resistance. However, the identification of new varieties of shrimps from their phenotypic characters is difficult. This study introduces a new approach for identifying varieties of shrimps using molecular markers of microsatellites and mitochondrial control region sequences. The method was employed to identify a new selected variety, Kehai No. 1 (KH-1), from three representative stocks (control group): Zhengda; Tongwei; and a stock collected from Fujian Province, which is now cultured in mainland China. By pooled genotyping of KH-1 and the control group, five microsatellites showing differences between KH-1 and the control group were screened out. Individual genotyping data confirmed the results from pooled genotyping. The genotyping data for the five microsatellites were applied to the assignment analysis of the KH-1 group and the control group using the partial Bayesian assignment method in GENECLASS2. By sequencing the mitochondrial control regions of individuals from the KH-1 and control group, four haplotypes were observed in the KH-1 group, whereas 14 haplotypes were obtained in the control group. By combining the microsatellite assignment analysis with mitochondrial control region analysis, the average accuracy of identification of individuals in the KH-1 group and control group reached 89%. The five selected microsatellite loci and mitochondrial control region sequences were highly polymorphic and could be used to distinguish new selected varieties of L. vannamei from other populations cultured in China.
Molecular characterization of sour orange (Citrus aurantium) accessions and their relatives using SSR and SRAP markers.
Polat, I; Kacar, Y A; Yesiloglu, T; Uzun, A; Tuzcu, O; Gulsen, O; Incesu, M; Kafa, G; Turgutoglu, E; Anil, S
Citrus production with its many varieties is of importance since it provides economically important products for Turkish exports. Sour orange is a rootstock commonly used for propagating the different scion varieties. Knowledge of the genetic diversity of the rootstock accessions would be useful in order to improve citrus breeding programs. We studied genetic relationships and diversity of 51 accessions of sour orange (Citrus aurantium) and their relatives using SSR (simple sequence repeat) and SRAP (sequence-related amplified polymorphism) molecular markers. Twenty-one SRAP primer combinations were tested on these accessions and relatives, producing 167 polymorphic fragments, with a mean of 8.0 and a mean polymorphism information content value of 0.47. Seventeen SSR primers also produced 30 polymorphic fragments, with a mean of 1.4 per primer and a mean polymorphism information content value of 0.39. The unweighted pair-group method with arithmetic average analysis using combined SSR and SRAP data showed a similarity range from 0.71 to 1.00 among the accessions. In the cluster analysis, sour orange relatives were indicated as a separate group from sour orange. 'Macrophylla' and 'Mexican lime' were the accessions most distinct (0.71) from the others. We conclude that genetic diversity in these sour orange accessions is lower and some of them were identical. PMID:23079821
Stathmin is a potential molecular marker and target for the treatment of gastric cancer
Liu, Xiaolin; Liu, Hairong; Liang, Jing; Yin, Beibei; Xiao, Junjuan; Li, Junwei; Feng, Dongfeng; Li, Yan
Objective: This study is to investigate the expression levels of stathmin in tissues of gastric cancer, and evaluate the therapeutic effects of stathmin antisense oligodeoxynucleotide (ASODN) and/or docetaxel in human gastric cancer cells. Methods: Immunohistochemistry was performed to detect the expression levels of stathmin in gastric cancer and adjacent tissues. Stathmin ASODN was transfected into gastric cancer SGC 7901 cell lines. The cell proliferation was assessed with the MTT assay, and the inhibitory rates were calculated. RT-PCR and Western blot analysis were performed to detect the mRNA and protein expression levels of stathmin, respectively. The synergistic effects of stathmin ASODN and docetaxel were evaluated. The efficacy and clinical benefit rates of the treatment of docetaxel combined with stathmin evaluation were investigated and compared. Results: Our results showed that the expression of stathmin was elevated in gastric cancer tissues, indicating a possible association between the stathmin expression and the disease occurrence. The MTT assay and tumor growth experiment revealed that stathmin ASODN significantly inhibited the proliferation of gastric cancer cells, both in vitro and in vivo. Furthermore, stathmin ASDON enhanced the inhibitory effects of docetaxel on the proliferation of gastric cancer cells, indicating a synergistic effect for the combination treatment. Importantly, docetaxel treatment was more effective for stathmin-negative gastric cancer patients, compared with stathmin-positive patients. Conclusion: Stathmin expression provides evidence for the treatment planning for gastric cancers. Stathmin might be a potential molecular marker and target for the treatment of gastric cancer.
Molecular Screening of Blast Resistance Genes in Rice using SSR Markers
Singh, A. K.; Singh, P. K.; Arya, Madhuri; Singh, N. K.; Singh, U. S.
Rice Blast is the most devastating disease causing major yield losses in every year worldwide. It had been proved that using resistant rice varieties would be the most effective way to control this disease. Molecular screening and genetic diversities of major rice blast resistance genes were determined in 192 rice germplasm accessions using simple sequence repeat (SSR) markers. The genetic frequencies of the 10 major rice blast resistance genes varied from 19.79% to 54.69%. Seven accessions IC337593, IC346002, IC346004, IC346813, IC356117, IC356422 and IC383441 had maximum eight blast resistance gene, while FR13B, Hourakani, Kala Rata 1–24, Lemont, Brown Gora, IR87756-20-2-2-3, IC282418, IC356419, PKSLGR-1 and PKSLGR-39 had seven blast resistance genes. Twenty accessions possessed six genes, 36 accessions had five genes, 41 accessions had four genes, 38 accessions had three genes, 26 accessions had two genes, 13 accessions had single R gene and only one accession IC438644 does not possess any one blast resistant gene. Out of 192 accessions only 17 accessions harboured 7 to 8 blast resistance genes. PMID:25774106
Molecular Screening of Blast Resistance Genes in Rice using SSR Markers.
Singh, A K; Singh, P K; Arya, Madhuri; Singh, N K; Singh, U S
Rice Blast is the most devastating disease causing major yield losses in every year worldwide. It had been proved that using resistant rice varieties would be the most effective way to control this disease. Molecular screening and genetic diversities of major rice blast resistance genes were determined in 192 rice germplasm accessions using simple sequence repeat (SSR) markers. The genetic frequencies of the 10 major rice blast resistance genes varied from 19.79% to 54.69%. Seven accessions IC337593, IC346002, IC346004, IC346813, IC356117, IC356422 and IC383441 had maximum eight blast resistance gene, while FR13B, Hourakani, Kala Rata 1-24, Lemont, Brown Gora, IR87756-20-2-2-3, IC282418, IC356419, PKSLGR-1 and PKSLGR-39 had seven blast resistance genes. Twenty accessions possessed six genes, 36 accessions had five genes, 41 accessions had four genes, 38 accessions had three genes, 26 accessions had two genes, 13 accessions had single R gene and only one accession IC438644 does not possess any one blast resistant gene. Out of 192 accessions only 17 accessions harboured 7 to 8 blast resistance genes. PMID:25774106
Glutamine synthetase sequence evolution in the mycobacteria and their use as molecular markers for Actinobacteria speciation
Hayward, Don; van Helden, Paul D; Wiid, Ian JF
Background Although the gene encoding for glutamine synthetase (glnA) is essential in several organisms, multiple glnA copies have been identified in bacterial genomes such as those of the phylum Actinobacteria, notably the mycobacterial species. Intriguingly, previous reports have shown that only one copy (glnA1) is essential for growth in M. tuberculosis, while the other copies (glnA2, glnA3 and glnA4) are not. Results In this report it is shown that the glnA1 and glnA2 encoded glutamine synthetase sequences were inherited from an Actinobacteria ancestor, while the glnA4 and glnA3 encoded GS sequences were sequentially acquired during Actinobacteria speciation. The glutamine synthetase sequences encoded by glnA4 and glnA3 are undergoing reductive evolution in the mycobacteria, whilst those encoded by glnA1 and glnA2 are more conserved. Conclusion Different selective pressures by the ecological niche that the organisms occupy may influence the sequence evolution of glnA1 and glnA2 and thereby affecting phylogenies based on the protein sequences they encode. The findings in this report may impact the use of similar sequences as molecular markers, as well as shed some light on the evolution of glutamine synthetase in the mycobacteria. PMID:19245690
Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales.
Keim, Paul; Van Ert, Matthew N; Pearson, Talima; Vogler, Amy J; Huynh, Lynn Y; Wagner, David M
Precise identification of Bacillus anthracis isolates has aided forensic and epidemiological analyses of natural anthrax cases, bioterrorism acts and industrial scale accidents by state-sponsored bioweapons programs. Because there is little molecular variation among B. anthracis isolates, identifying and using rare variation is crucial for precise strain identification. We think that mutation is the primary diversifying force in a clonal, recently emerged pathogen, such as B. anthracis, since mutation rate is correlated with diversity on a per locus basis. While single nucleotide polymorphisms (SNPs) are rare, their detection is facilitated by whole genome discovery approaches. As highly stable phylogenetic markers, SNPs are useful for identifying long branches or key phylogenetic positions. Selection of single, diagnostic "Canonical SNPs" (canSNPs) for these phylogenetic positions allows for efficient and defining assays. We have taken a nested hierarchal strategy for subtyping B. anthracis, which is consistent with traditional diagnostics and applicable to a wide range of pathogens. Progressive hierarchical resolving assays using nucleic acids (PHRANA) uses a progression of diagnostic genomic loci that are initially highly stable but with low resolution and, ultimately, very unstable but with high resolution. This approach mitigates the need for data weighting and provides both a deeply rooted phylogenetic hypothesis and high resolution discrimination among closely related isolates. PMID:15450200
Intraspecific chromosomal and genetic polymorphism in Brassica napus L. detected by cytogenetic and molecular markers.
Amosova, Alexandra V; Zemtsova, Lyudmila V; Grushetskaya, Zoya E; Samatadze, Tatiana E; Mozgova, Galina V; Pilyuk, Yadviga E; Volovik, Valentina T; Melnikova, Natalia V; Zelenin, Alexandr V; Lemesh, Valentina A; Muravenko, Olga V
The application of DNA intercalator 9-aminoacridine allowed us to increase the resolution of chromosome C-banding and DAPI-banding patterns and to investigate chromosomal polymorphism in karyotypes of seven spring and six winter rape varieties. It was shown that the pericentromeric and intercalary C-bands of most of the chromosomes in spring rape were smaller in size and less polymorphic than those of winter rape. More 26S and 5S rDNA sites were found in the winter rape karyotypes than the spring varieties. Separate or colocalized 26S and 5S rDNA sites were revealed on chromosomes 4, 5, 6, 8, 10, 14, 15, 16 and 18. Intervarietal and intravarietal polymorphism of the number and chromosomal localization of rDNA sites were detected. The generalized idiogram of chromosomes of 13 Brassica napus varieties with account of all possibilities of C-banding patterns as well as localization of 26S and 5S rDNA sites were constructed. Polymorphism of the examined molecular and cytogenetic markers as well as the heterozygosis level of FAE1.1 gene controlling erucic acid synthesis in rapeseed was higher in the winter varieties than in the spring ones. The obtained data were in a atisfactory agreement with increased tolerance to environmental stress conditions of winter rape. PMID:24840830
Molecular markers linked to papaya ring spot virus resistance and Fusarium race 2 resistance in melon.
Brotman, Yariv; Kovalski, Irina; Dogimont, Catherine; Pitrat, Michel; Portnoy, Vitaly; Katzir, Nurit; Perl-Treves, Rafael
In melon, the Fom-1 gene confers monogenic resistance against the soil-borne fungus Fusarium oxysporum f. sp. melonis, races 0 and 2, while the closely linked Prv gene specifies resistance against the papaya ring spot virus. Markers linked to these resistance (R) genes were identified using two recombinant inbred line populations, derived from crosses between Cucumis melo Vedrantais and C. melo PI 161375, and between C. melo Vedrantais and C. melo PI 414723, respectively. Using bulked segregant analysis, as well as systematic scoring of the mapping populations, we developed two amplified fragment length polymorphism markers, two random amplified polymorphic DNA markers and five restriction fragment length polymorphism (RFLP) markers linked to this locus. Four of the RFLP sequences bear homology to nucleotide-binding site-leucine-rich repeat R genes, indicating the presence of a significant R-gene cluster in this locus. Our study provides the most closely linked markers published so far for these important traits. It also improves the resolution of the whole linkage group IX, which was difficult to order in our previous studies. Two of the markers were converted to cleaved amplified polymorphic sequence markers to facilitate their application in marker-assisted selection. Testing these two markers in several melon lines revealed different marker haplotypes in the melon germplasm and supported multiple, independent origin of the Fusarium races 0 and 2 resistance trait. PMID:15551034
Genetic and withaferin A analysis of Iranian natural populations of Withania somnifera and W. coagulans by RAPD and HPTLC.
Mirjalili, Mohammad Hossein; Fakhr-Tabatabaei, Seyyed Mohammad; Alizadeh, Houshang; Ghassempour, Alireza; Mirzajani, Fateme
For successful conservation and breeding of a medicinal species, it is important to evaluate its genetic diversity as well as its content of phytochemical compounds. The aim of the present study was to investigate the genetic variation of Iranian natural populations of W. somnifera and W. coagulans, using the RAPD (random amplified polymorphic DNA) markers, and their withaferin A content. Using 16 RAPD primers, a total of 282 RAPD bands were achieved. The highest and lowest percentages of polymorphism were observed with primers OPAD-15 (100.0%) and OPC-06 (75.0%), respectively. Cluster analysis of the genotypes was performed based on data from polymorphic RAPD bands, using Dice's similarity coefficient and the UPGMA clustering method. Variations in the RAPD results were found to reflect geographical distribution and genetic factors of the plant populations. The HPTLC analysis of the studied samples revealed the presence of withaferin A in W. coagulans and W. somnifera. Moreover, the concentration of withaferin A had a range from 2.2 to 32.5 microg/g DW and was higher in the aerial part than in the root in all used samples. The results of the present study show that there is a high level of variation in the Iranian natural population of Withania, which is significant for conservation and breeding programs to improve production of withaferin A. PMID:19413110
[Construction of AFLP molecular markers linkage map and localization of green cocoon gene in silkworm (Bombyx mori)].
Zhao, Ai-Chun; Lu, Cheng; Li, Bin; Pu, Xiao-Ying; Zhou, Ze-Yang; Xiang, Zhong-Huai
Based on an improved method of AFLP, AFLP markers were employed for construction of a linkage map and localization of Gc gene used a set of 44 backcross lines( BC1) of silkworm ( Bombyx mori) as a mapping population. In this work, all together 3 956 bands were obtained by 28 pairs of primers and 141.3 bands each primer pair on average. Among them 2 836 bands were in good agreement with the segregation pattern. A total of 1 018 (25.7%) polymorphic AFLP markers were detected. The 693 (68.1%) of polymorphic markers with 1:1 segregation ratio ( P < or = 0.05) were obtained. Furthermore,The analytical model was based on the backcross type and the parameters were set as following: LOD = 3.0, maximum recombination value of 0. 20 and use the command ' group', 'compare', 'try', 'map' and 'ripple' to construct the linkage maps. 407 of the 693 loci were chi2 tested in agreement with 1:1 segregation were divided into 33 linkages by Mapmaker/Exp(Version 3.0), with a total map distance of 3 676.7 cM and a mean distance of 9.1 cM between markers. The morphological gene Gc was located between L-P4T6-107 and L-PT6T4-84 on linkage group 22. In addition, 286 markers were not included in the linkage groups. The efficiency of loci mapping was 58.7%. Among the 33 linkage groups, the morphological marker Gc classically localized on linkage group 15 was relocated on linkage group 22 on the map, suggesting that this molecular linkage group corresponds to linkage group 15 on the linkage map based on morphological characters. All these have laid an important base for the marker assisted breeding of the silkworm. PMID:15481532
Temporal trends of molecular markers associated with artemether-lumefantrine tolerance\\/resistance in Bagamoyo district, Tanzania
M. Malmberg; B. Ngasala; P. E. Ferreira; E. Larsson; I. Jovel; A. Hjalmarsson; M. Petzold; Z. Premji; J. P. Gil; A. Bjorkman; A. Martensson
BACKGROUND: Development and spread of Plasmodium falciparum resistance to artemisinin-based combination therapy (ACT) constitutes a major threat to recent global malaria control achievements. Surveillance of molecular markers could act as an early warning system of ACT-resistance before clinical treatment failures are apparent. The aim of this study was to analyse temporal trends of established genotypes associated with artemether-lumefantrine tolerance\\/resistance before
Identification of molecular markers for the detection of the yellow rust resistance gene Yr17 in wheat
Olivier Robert; Christine Abelard; Françoise Dedryver
The Yr17 gene, which is present in many European wheat cultivars, displays yellow rust resistance at the seedling stage. The\\u000a gene introduced into chromosome 2A from Aegilops ventricosa was previously found to be closely linked (0.5 cM) to leaf and\\u000a stem rust resistance genes Lr37 and Sr38, respectively. The objective of this study was to identify molecular markers linked\\u000a to the
Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stability testing
Paul Arens; Carmen Mansilla; Daniël Deinum; Laetitia Cavellini; André Moretti; Sophie Rolland; Hanneke van der Schoot; David Calvache; Fernando Ponz; Cécile Collonnier; René Mathis; Diederik Smilde; Carole Caranta; Ben Vosman
Molecular markers linked to phenotypically important traits are of great interest especially when traits are difficult and\\/or\\u000a costly to be observed. In tomato where a strong focus on resistance breeding has led to the introgression of several resistance\\u000a genes, resistance traits have become important characteristics in distinctness, uniformity and stability (DUS) testing for\\u000a Plant Breeders Rights (PBR) applications. Evaluation of
Genetic dissection of root growth in rice (Oryza sativa L.).II: mapping quantitative trait loci using molecular markers
A. H. Price; A. D. Tomos
Drought is a major abiotic stress of upland rice, and good root growth has been associated with drought avoidance. We report\\u000a on the genetic mapping of root growth traits in an F2 population derived from two drought-resistant rice varieties, 'Bala' and 'Azucena'. Restriction fragment length polymorphism\\u000a (RFLP) between the parents was 32%, and a molecular map with 71 marker loci
Prediction of hybrid performance in maize using molecular markers and joint analyses of hybrids and parental inbreds
Tobias A. Schrag; Jens Möhring; Albrecht E. Melchinger; Barbara Kusterer; Baldev S. Dhillon; Hans-Peter Piepho; Matthias Frisch
The identification of superior hybrids is important for the success of a hybrid breeding program. However, field evaluation\\u000a of all possible crosses among inbred lines requires extremely large resources. Therefore, efforts have been made to predict\\u000a hybrid performance (HP) by using field data of related genotypes and molecular markers. In the present study, the main objective\\u000a was to assess the
A computational procedure for functional characterization of potential marker genes from molecular data: Alzheimer's as a case study
Margherita Squillario; Annalisa Barla
Background A molecular characterization of Alzheimer's Disease (AD) is the key to the identification of altered gene sets that lead to\\u000a AD progression. We rely on the assumption that candidate marker genes for a given disease belong to specific pathogenic pathways,\\u000a and we aim at unveiling those pathways stable across tissues, treatments and measurement systems. In this context, we analyzed\\u000a three
Identification and cloning of molecular markers for UV-B tolerant gene in wild sugarcane ( Saccharum spontaneum L.)
Yuan Li; Yongmei He; Yanqun Zu; Fangdong Zhan
Previously we have selected wild sugarcane (Saccharum spontaneum L.) sterile lines that are tolerant or susceptible to UV-B radiation based on response index (RI) in a field screening test. The RI was established according to plant height, tiller number, leaf index, total biomass and brix under enhanced ultraviolet-B (UV-B, 280–310nm) radiation. In this experiment, molecular markers linked to the UV-B
Sex determination in 58 bird species and evaluation of CHD gene as a universal molecular marker in bird sexing.
Vucicevic, Milos; Stevanov-Pavlovic, Marija; Stevanovic, Jevrosima; Bosnjak, Jasna; Gajic, Bojan; Aleksic, Nevenka; Stanimirovic, Zoran
The aim of this research was to test the CHD gene (Chromo Helicase DNA-binding gene) as a universal molecular marker for sexing birds of relatively distant species. The CHD gene corresponds to the aim because of its high degree of conservation and different lengths in Z and W chromosomes due to different intron sizes. DNA was isolated from feathers and the amplification of the CHD gene was performed with the following sets of polymerase chain reaction (PCR) primers: 2550F/2718R and P2/P8. Sex determination was attempted in 284 samples of 58 bird species. It was successful in 50 bird species; in 16 of those (Alopochen aegyptiacus, Ara severus, Aratinga acuticaudata, Bucorvus leadbeateri, Cereopsis novaehollandiae, Columba arquatrix, Corvus corax, C. frugilegus, Cyanoliseus patagonus, Guttera plumifera, Lamprotornis superbus, Milvus milvus, Neophron percnopterus, Ocyphaps lophotes, Podiceps cristatus, and Poicephalus senegalus), it was carried out for the first time using molecular markers and PCR. It is reasonable to assume that extensive research is necessary to define the CHD gene as a universal molecular marker for successful sex determination in all bird species (with exception of ratites). The results of this study may largely contribute to the aim. PMID:22553188
An update of the Courtot × Chinese Spring intervarietal molecular marker linkage map for the QTL detection of agronomic traits in wheat
P. Sourdille; T. Cadalen; H. Guyomarc'h; J. Snape; M. Perretant; G. Charmet; C. Boeuf; S. Bernard; M. Bernard
We made an update of the intervarietal molecular marker linkage map of the wheat genome developed using a doubled-haploid (DH) population derived from the cross between the cultivars 'Courtot' and 'Chinese Spring'. This map was constructed using 187 DH lines and 659 markers. The genome was well covered (more than 95%) except for chromosomes from homoeologous group 4 and chromosomes
Technology Transfer Automated Retrieval System (TEKTRAN)
To aid in identifying key predators of Proconiini sharpshooter species present in California, we developed and tested molecular diagnostic markers for the glassy-winged sharpshooter Homalodisca coagulata (Say) and smoke-tree sharpshooter Homalodisca liturata (Ball) (Homoptera: Cicadellidae: Proconii...
Molecular markers of trichloroethylene-induced toxicity in human kidney cells
Lash, Lawrence H. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States)]. E-mail: firstname.lastname@example.com; Putt, David A. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States); Hueni, Sarah E. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States); Horwitz, Beth P. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States)
Difficulties in evaluation of trichloroethylene (TRI)-induced toxicity in humans and extrapolation of data from laboratory animals to humans are due to the existence of multiple target organs, multiple metabolic pathways, sex-, species-, and strain-dependent differences in both metabolism and susceptibility to toxicity, and the lack or minimal amount of human data for many target organs. The use of human tissue for mechanistic studies is thus distinctly advantageous. The kidneys are one target organ for TRI and metabolism by the glutathione (GSH) conjugation pathway is responsible for nephrotoxicity. The GSH conjugate is processed further to produce the cysteine conjugate, S-(1,2-dichlorovinyl)-L-cysteine (DCVC), which is the penultimate nephrotoxic species. Confluent, primary cultures of human proximal tubular (hPT) cells were used as the model system. Although cells in log-phase growth, which are undergoing more rapid DNA synthesis, would give lower LD{sub 50} values, confluent cells more closely mimic the in vivo proximal tubule. DCVC caused cellular necrosis only at relatively high doses (>100 {mu}M) and long incubation times (>24 h). In contrast, both apoptosis and enhanced cellular proliferation occurred at relatively low doses (10-100 {mu}M) and early incubation times (2-8 h). These responses were associated with prominent changes in expression of several proteins that regulate apoptosis (Bcl-2, Bax, Apaf-1, Caspase-9 cleavage, PARP cleavage) and cellular growth, differentiation and stress response (p53, Hsp27, NF-{kappa}B). Effects on p53 and Hsp27 implicate function of protein kinase C, the mitogen activated protein kinase pathway, and the cytoskeleton. The precise pattern of expression of these and other proteins can thus serve as molecular markers for TRI exposure and effect in human kidney.
Molecular markers of yolk sac fry development in nine families of lake trout.
Vuori, Kristiina A; Paavilainen, Tiia; Nikinmaa, Mikko; Czesny, Sergiusz; Rinchard, Jacques
Salmonids in certain areas of North America and northern Europe suffer from reproductive disturbances manifested through the death of yolk sac fry. These disturbances are referred to as early mortality syndrome (EMS) in the Great Lakes region and M74 in the Baltic Sea. Both of these syndromes have been associated with reduced concentrations of thiamine in affected females and their eggs. However, large variations in signs and mortality, both within and between the individual syndromes, have been reported. Yolk sac fry mortality (M74) in Atlantic salmon Salmo salar has been shown to be associated with reduced DNA binding of the hypoxia-inducible transcription factor 1 (HIF-1), reduced production of vascular endothelial growth factor (VEGF) protein, decreased capillary density, and down-regulation of adult-type globin gene transcription (which is responsible for the protein part of adult hemoglobin). One of the main effects of all of these changes is reduced oxygen transport to the tissues of affected fry. In this study, the developmental patterns of HIF-1 DNA binding, VEGF protein expression, and adult-type globin gene transcription were analyzed in nine family groups of Lake Michigan lake trout Salvelinus namaycush. The results indicate that HIF-1 DNA binding and globin gene transcription increase from hatch to the end of yolk sac stage. Interindividual and between-family biological variations were detected, especially in VEGF protein expression and globin gene transcription. Our results demonstrate the possibility of using these molecular markers in investigating the etiology of EMS and making comparisons between the mechanisms of different salmonid yolk sac fry mortalities. PMID:20218502
Subtracted diversity array identifies novel molecular markers including retrotransposons for fingerprinting Echinacea species.
Olarte, Alexandra; Mantri, Nitin; Nugent, Gregory; Pang, Edwin C K
Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA) for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH) was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea. PMID:23940565
Subtracted Diversity Array Identifies Novel Molecular Markers Including Retrotransposons for Fingerprinting Echinacea Species
Olarte, Alexandra; Mantri, Nitin; Nugent, Gregory; Pang, Edwin C. K.
Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA) for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH) was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea. PMID:23940565
Molecular markers indicate different dynamics of leaves and roots during litter decomposition
NASA Astrophysics Data System (ADS)
Altmann, Jens; Jansen, Boris; Palviainen, Marjo; Kalbitz, Karsten
Up to now there is only a poor understanding of the sources contributing to organic carbon in forest soils, especially the contribution of leaves and roots. Studies of the last 2 decades have shown that methods like pyrolysis and CuO oxidation are suitable tools to trace back the main contributors of organic matter in water, sediments and soils. Lignin derived monomers, extractable lipids, cutin and suberin derived compounds have been used frequently for identification of plant material. However, for the selection of suitable biomarker the decomposition patterns and stability of these compounds are of high importance but they are only poorly understood. In this study we focused on following questions: (I) Which compounds are characteristic to identify certain plant parts and plant species? (II) How stable are these compounds during the first 3 years of litter decomposition? We studied the chemical composition of samples from a 3-year litterbag decomposition experiment with roots and leaves of spruce, pine and birch which was done in Finland. Additionally to mass loss, carbon and nitrogen contents, free lipids were extracted; by alkaline hydrolysis non extractable lipids were gained. The extracts were analyzed afterwards by GC-MS, the insoluble residues were analyzed by curie-point Pyrolysis GC-MS. In addition to the identification and quantification of a variety of different compounds and compound ratios we used statistical classification methods to get deeper insights into the patterns of leaf and root-derived biomarkers during litter decomposition. The mass loss was largely different between the litter species and we always observed larger mass loss for leaf-derived litter in comparison to root derived litter. This trend was also observed by molecular analysis. The increase of the ratio of vanillic acid to vanillin was correlated to the mass loss of the samples over time. This shows that the degree of decomposition of plant material was linked with the degree of lignin degradation. Preliminary results show, that we were able to distinguish the different species and plant parts using various approaches, e.g., abundance and patterns of different substances and different ratios of compounds. The polyesters suberin and cutin were particularly useful to differentiate between roots and leaves. We conclude that knowledge of the decomposition patterns of molecular markers will largely improve the identification power of organic matter sources in soils.
The potential of hypoxia markers as target for breast molecular imaging – a systematic review and meta-analysis of human marker expression
Background Molecular imaging of breast cancer is a promising emerging technology, potentially able to improve clinical care. Valid imaging targets for molecular imaging tracer development are membrane-bound hypoxia-related proteins, expressed when tumor growth outpaces neo-angiogenesis. We performed a systematic literature review and meta-analysis of such hypoxia marker expression rates in human breast cancer to evaluate their potential as clinically relevant molecular imaging targets. Methods We searched MEDLINE and EMBASE for articles describing membrane-bound proteins that are related to hypoxia inducible factor 1? (HIF-1?), the key regulator of the hypoxia response. We extracted expression rates of carbonic anhydrase-IX (CAIX), glucose transporter-1 (GLUT1), C-X-C chemokine receptor type-4 (CXCR4), or insulin-like growth factor-1 receptor (IGF1R) in human breast disease, evaluated by immunohistochemistry. We pooled study results using random-effects models and applied meta-regression to identify associations with clinicopathological variables. Results Of 1,705 identified articles, 117 matched our selection criteria, totaling 30,216 immunohistochemistry results. We found substantial between-study variability in expression rates. Invasive cancer showed pooled expression rates of 35% for CAIX (95% confidence interval (CI): 26-46%), 51% for GLUT1 (CI: 40-61%), 46% for CXCR4 (CI: 33-59%), and 46% for IGF1R (CI: 35-70%). Expression rates increased with tumor grade for GLUT1, CAIX, and CXCR4 (all p < 0.001), but decreased for IGF1R (p < 0.001). GLUT1 showed the highest expression rate in grade III cancers with 58% (45-69%). CXCR4 showed the highest expression rate in small T1 tumors with 48% (CI: 28-69%), but associations with size were only significant for CAIX (p < 0.001; positive association) and IGF1R (p = 0.047; negative association). Although based on few studies, CAIX, GLUT1, and CXCR4 showed profound lower expression rates in normal breast tissue and benign breast disease (p < 0.001), and high rates in carcinoma in situ. Invasive lobular carcinoma consistently showed lower expression rates (p < 0.001). Conclusions Our results support the potential of hypoxia-related markers as breast cancer molecular imaging targets. Although specificity is promising, combining targets would be necessary for optimal sensitivity. These data could help guide the choice of imaging targets for tracer development depending on the envisioned clinical application. PMID:24206539
Technology Transfer Automated Retrieval System (TEKTRAN)
Marker-assisted selection (MAS) can provide an effective and efficient breeding tool for maintaining and enhancing disease resistance. For common bean, PCR-based RAPD and SCAR markers linked with more than 20 major genes conditioning resistance to angular leaf spot, anthracnose, ashy stem blight, be...
DNA Fingerprinting of Jute Germplasm by RAPD
Mohammad Belayat Hossain; Samiul Haque; Haseena Khan
The genotype characteristic of cultivars was investigated, along with varieties of both of the jute species, Corchorus olitorius and Corchorus capsularis, in the germplasm collection at the Bangladesh Jute Research Institute (BJRI). DNA fingerprinting was generated for 9 different varieties and 12 accessions of jute cultivars by using random amplified polymorphic DNA (RAPD). A total of 29 arbitrary oligonucleotide primers
Rose germplasm identification and analysis with RAPD markers
Jan, Chih-Hui
The genus Rosa consists of more than 100 species distributed widely throughout the northern hemisphere. It has been classified into four subgenera, Eurosa, Platyrhodon, Hesperhodos and Hulthemia. The subgenus Eurosa includes ...
Rose germplasm identification and analysis with RAPD markers
Jan, Chih-Hui
The genus Rosa consists of more than 100 species distributed widely throughout the northern hemisphere. It has been classified into four subgenera, Eurosa, Platyrhodon, Hesperhodos and Hulthemia. The subgenus Eurosa includes 11 sections. The other...
Microsatellite primed-PCR to select molecular markers for Tuber species
Antonella Amicucci; Chiara Guidi; Lucia Potenza; Vilberto Stocchi
The direct microsatellite-primed PCR and the RAMPO techniques were applied to detect inter-specific polymorphisms in Tuber species and to select species specific fragments. A T. borchii marker was identified and specific primers were selected.
Molecular cloning and characterization of markers and cytokines for equid myeloid cells
Falko Steinbach; Robert Stark; Sherif Ibrahim; Eman Abd-El Gawad; Hanns Ludwig; Jakob Walter; Ulrich Commandeur; Susanne Mauel
The myeloid cell system comprises of monocytes, macrophages (M?), dendritic cells (DC), Kupffer cells, osteoclasts or microglia and is also known as the mononuclear phagocytic system (MPS). Essential cytokines to differentiate or activate these cells include GM-CSF or IL-4. Important markers for characterization include CD1, CD14, CD68, CD163 and CD206. All these markers, however, were not cloned or further characterized
A high-density molecular map for ryegrass (Lolium perenne) using AFLP markers
P. F. Bert; G. Charmet; P. Sourdille; M. D. Hayward; F. Balfourier
AFLP markers have been successfully employed for the development of a high-density linkage map of ryegrass (Lolium\\u000a perenne L.) using a progeny set of 95 plants from a testcross involving a doubled-haploid tester. This genetic map covered 930 cM\\u000a in seven linkage groups and was based on 463 amplified fragment length polymorphism (AFLP) markers using 17 primer pairs,\\u000a three isozymes
Genetic variation of jointed goatgrass (Aegilops cylindrica Host.) from Iran using RAPD-PCR and SDS-PAGE of seed proteins.
Farkhari, M; Naghavi, M R; Pyghambari, S A; Sabokdast
Genetic variation of 28 populations of jointed goatgrass (Aegilops cylindrica Host.), collected from different parts of Iran, were evaluated using both RAPD-PCR and SDS-PAGE of seed proteins. The diversity within and between populations for the three-band High Molecular Weight (HMW) subunits of glutenin pattern were extremely low. Out of 15 screened primers of RAPD, 14 primers generated 133 reproducible fragments which among them 92 fragments were polymorphic (69%). Genetic similarity calculated from the RAPD data ranged from 0.64 to 0.98. A dendrogram was prepared on the basis of a similarity matrix using the UPGMA algorithm and separated the 28 populations into two groups. Confusion can happen between populations with the same origin as well as between populations of very diverse geographical origins. Our results show that compare to seed storage protein, RAPD is suitable for genetic diversity assessment in Ae. cylindrica populations. PMID:19090190
Characterization of Listeria monocytogenes and Listeria innocua from a vegetable processing plant by RAPD and REA
V. Aguado; A. I. Vitas; I. Garc??a-Jalón
The incidence of Listeria monocytogenes in a vegetable processing plant was investigated over a 23-month period. Frozen ready-to-eat vegetable samples, well as the plant environment, were sampled. The molecular subtyping techniques, Random Amplified Polymorphic DNA (RAPD) and Restriction Endonuclease Analyses (REA), were performed to help investigate the origin and routes of Listeria dissemination.The low and sporadic incidence of L. monocytogenes
Taxonomic relationships in Astragalus sections Hololeuce and Synochreati (Fabaceae): evidence from RAPD-PCR and SDS-PAGE of seed proteins
Leyla Açik; Murat Ekici; Ayten Çelebi
Taxonomic status of the Turkish members of the sections Hololeuce and Synochreati of Astragalus (Fabaceae) was analysed using variation of morphological features, seed proteins and RAPD markers. Dendrograms based on Nei's genetic distance method UPGMA were used to compare the species. The results of cluster analysis were in broad agreement with morphological classifications of these species, and they were slightly
Essential oil composition and preliminary molecular study of four Hungarian Thymus species.
Pluhár, Zsuzsanna; Kocsis, Marianna; Kuczmog, Anett; Csete, S; Simkó, Hella; Sárosi, Szilvia; Molnár, P; Horváth, Györgyi
Chemical and genetic differences of twenty taxa belonging to four Thymus species were studied in order to determine whether molecular characters and essential oil components could be used as taxonomic markers and to examine the correlation between them. Plant samples, representing different taxa and geographic regions, were collected from experimentally grown populations. Essential oil samples were analysed by GC/MS and cluster analysis of volatile composition resulted in segregation of thymol chemotypes from sesquiterpenic ones. Thymol was characteristic for all the populations of Thymus glabrescens and T. pannonicus as well as for certain taxa belonging to T. praecox and T. pulegioides. Sesquiterpenes occurred in only two taxa of T. glabrescens, in each sample of T. praecox and in three taxa of T. pulegioides. Plant samples were analysed by random amplified polymorphic DNA (RAPD). The obtained dendrogram revealed high gene diversity. The 13 primers resulted 114 polymorphic RAPD bands, and the average percentage of polymorphism was 80.8%. The RAPD dendogram showed separation neither at interspecific nor at interpopulational levels. Therefore, further specific molecular studies involving more taxa are suggested. Partial correlation have been found between molecular and chemical assessments. PMID:22453802
Development of ITS sequence based molecular marker to distinguish, Tribulus terrestris L. (Zygophyllaceae) from its adulterants.
Balasubramani, Subramani Paranthaman; Murugan, Ramar; Ravikumar, Kaliamoorthy; Venkatasubramanian, Padma
Tribulus terrestris L. (Zygophyllaceae) is one of the highly traded raw drugs and also used as a stimulative food additive in Europe and USA. While, Ayurvedic Pharmacopoeia of India recognizes T. terrestris as Goksura, Tribulus lanuginosus and T. subramanyamii are also traded by the same name raising issues of quality control. The nuclear ribosomal RNA genes and ITS (internal transcribed spacer) sequence were used to develop species-specific DNA markers. The species-specific markers efficiently amplified 295bp for T. terrestris (TT1F and TT1R), 300bp for T. lanuginosus (TL1F and TL1R) and 214bp for T. subramanyamii (TS1F and TS1R). These DNA markers can be used to distinguish T. terrestris from its adulterants. PMID:20083169
A potential species-specific molecular marker suggests interspecific hybridization between sibling species Littorina arcana and L. saxatilis (Mollusca, Caenogastropoda) in natural populations.
Mikhailova, Natalia A; Gracheva, Yulia A; Backeljau, Thierry; Granovitch, Andrey I
Three sister species of rough periwinkles, viz. Littorina saxatilis (Olivi 1792), L. arcana (Hannaford Ellis 1978) and L. compressa (Jeffreys 1865) from the Barents Sea (Russia), the White Sea (Russia) and the Norwegian Sea (Norway) were studied. The identification of two sibling species L. saxatilis and L. arcana is often difficult as both species have extremely similar shell morphology and reproductive systems. Only mature females can be unambiguously distinguished, with a jelly gland present in female L. arcana, but which is replaced by a brood pouch containing developing embryos in L. saxatilis. No clear-cut diagnostic features have been found to discriminate between males or juveniles of the two species. The very first diagnostic DNA marker (DNA fragment A2.8, 271 bp length) for L. arcana and L. saxatilis separation was developed. The marker was derived from apparently species-specific L. arcana DNA fragments obtained via Random Amplified Polymorphic DNA (RAPD) analysis. This fragment was cloned and sequenced, whereupon specific primers were designed and the amplification was surveyed in a large number of morphologically well-identified females of both species. Subsequently, the specific DNA marker was used for the identification of male L. arcana and partners in copulating pairs. In this way, we obtained evidence of possible interspecific hybridization between the sibling species L. arcana and L. saxatilis living in sympatry in natural populations: the presence of A2.8 fragment in 12% of morphologically well identified L. saxatilis females and its absence in 14% of morphologically well identified L. arcana females. The A2.8 fragment never amplified in L. saxatilis from sites without L. arcana. The A2.8 fragment did not amplify in L. compressa, not even in microsympatric populations, and we did not observe interspecific copulations between L. arcana and L. compressa. PMID:19690967
Random amplified polymorphic DNA (RAPD) detection of dwarf off-types inmicropropagated Cavendish (Musa spp. AAA) bananas
Olivia P. Damasco; Glenn C. Graham; Robert J. Henry; Steve W. Adkins; Mike K. Smith; Ian D Godwin
A RAPD marker specific to the dwarf off-type (hereafter known as dwarf) from micropropagation of Cavendish banana (Musa spp. AAA) cultivars New Guinea Cavendish and Williams was identified following an analysis of 57 normal (true-to-type) and 59 dwarf plants generated from several different micropropagation events. Sixty-six random decamer primers were used in the initial screen, of which 19 (28.8%) revealed
Genetic diversity within a range of cultivars and landraces of flax ( Linum usitatissimum L.) as revealed by RAPDs
Yong-Bi Fu; Axel Diederichsen; K. W. Richards; Gregory Peterson
Analysis of the extent and distribution of genetic diversity incrop plants is essential for optimizing sampling and breedingstrategies. We used random amplified polymorphic DNA (RAPD)markers to assess genetic diversity and relationships in 22 Canadiancultivars, 29 selected world cultivars and 10 landraces of flax(Linum usitatissimum L.). RAPDvariation was generally low and more variation was detected among,than within, the investigated flax accessions.
Molecular markers reveal only two mud crab species of genus Scylla (Brachyura: Portunidae) in Indian coastal waters.
Mandal, Anup; Varkey, Mathews; Sobhanan, Sobha Pindaniyil; Mani, Anjali Kottayil; Gopalakrishnan, Achamveetil; Kumaran, Ganesh; Sethuramalingam, Arulraj; Srinivasan, Pandiarajan; Samraj, Yohannan Chellema Thampi
The taxonomic ambiguity of the Indian mud crab (genus Scylla de Hann 1833) is still a cause of concern as several papers have been published with misleading identification. This is the first attempt to resolve the taxonomic uncertainty of the mud crab commonly available in Indian coastal waters using molecular genetic markers (ITS-1 and sequencing of COI gene) combined with traditional morphometry. Additionally, we developed a PCR method by which Indian mud crab species can be identified rapidly and effectively. The results clearly indicate that the green morph of the Indian mud crab is Scylla serrata and the brown morph is S. olivacea. The S. serrata commonly mentioned in the literature from India is S. olivacea; the S. tranquebarica noted by many Indian researchers should belong to S. serrata. Caution should be taken when interpreting or implementing the biological, molecular, and aquaculture data in the literature. PMID:24699826
[RAPD analysis of plant pathogenic coryneform bacteria].
Yin, Yan-Ni; Chen, Yong-Fang; Li, Shi-Mo; Guo, Jian-Hua
RAPD analysis was used for the taxonomy of plant pathogenic coryneform bacteria, especially for the classification of two new pathogens (Curtobacterium flaccumfaciens pv. basellae pv. nov. and Curtobacterium flaccumfaciens pv. beticola pv. nov.). 20 random primers were screened from 50 ones to detect polymorphism among the total strains used. 80.4% were polymorphic bands among the 225 ones produced. The results of pairwise similarity and UPGMA cluster analysis suggest that the two new pathovars of sugar beet (Beta vulgaris var. saccharifera) and malabar spinach (Basella rubra) are genetically close related with Curtobacterium flacumfaciens, and the minimal similarity coefficient is 0.6511. According to the RAPD analysis and previous research, some newly made taxonomic changes of the plant pathogenic coryneform bacteria are discussed. PMID:16496687
Survey of Paramecium duboscqui using three markers and assessment of the molecular variability in the genus Paramecium.
Boscaro, Vittorio; Fokin, Sergei I; Verni, Franco; Petroni, Giulio
The genus Paramecium (phylum Ciliophora) is one of the best-known among protozoa. Nevertheless, the knowledge on the diversity and distribution of species within this genus was remarkably scarce until recent times. In the last years a constantly growing amount of data has formed, especially on the distribution of species and the characterization of molecular markers. Much effort has been made on detecting clades inside each morphospecies, which could suggest the presence of sibling species complexes as in the famous case of Paramecium aurelia. In this work we present new data on Paramecium duboscqui, one of the morphospecies that have not yet been surveyed employing DNA sequences as markers. We obtained data from nine strains sampled around the world, using the three most commonly employed markers (18S rRNA gene, ITS1-5.8S-ITS2 and COI gene sequences). Moreover, we compared our results with those already available for other Paramecium species, and performed phylogenetic analyses for the entire genus. We also expanded the knowledge on the ITS2 secondary structure and its usefulness in studies on Paramecium. Our approach, that considers the data of all the species together, highlighted some characteristic patterns as well as some ambiguities that should be further investigated. PMID:22982632
Identification of incompatibility alleles and characterisation of molecular markers genetically linked to the A incompatibility locus in the white rot fungus Pleurotus ostreatus
Luis Larraya; María M. Peńas; Gumer Pérez; Cruz Santos; Enrique Ritter; Antonio G. Pisabarro; Lucía Ramírez
Pleurotus ostreatus is a hetertothallic homobasidiomycete whose mating is controlled by a bifactorial tetrapolar genetic system. Although this\\u000a mechanism is well accepted, there is a lack of knowledge about its molecular basis, as the incompatibility loci have not been\\u000a cloned and sequenced. As a first step towards the elucidation of the molecular structure of the A-type incompatibility locus, molecular markers
Use of molecular markers in breeding for soluble solids content in tomato — a re-examination
S. D. Tanksley; J. Hewitt
Through earlier breeding efforts, portions of the genome of the wild species Lycopersicon chmielewskii have been introgressed into the cultivated tomato (Rick 1974). These introgressed chromosomal segments have been reported to increase soluble solids in fruit of certain tomato varieties (Rick 1974). Recently, two of the introgressed segments have been identified with RFLP markers and tested for effects on soluble
Genetic Stock Identification of Steelhead in the Columbia River Basin: An Evaluation of Different Molecular Markers
Gary A. Winans; Melanie M. Paquin; Donald M. Van Doornik; Bruce M. Baker; Perry Thornton; Dan Rawding; Anne Marshall; Paul Moran; Steven Kalinowski
Protein genetic markers (allozymes) have been used during the last decade in a genetic stock identification (GSI) program by state and federal management agencies to monitor stocks of steelhead Oncorhynchus mykiss in the Columbia River basin. In this paper we report new data for five microsatellite and three intron loci from 32 steelhead populations in the three upriver evolutionarily significant
Molecular characterization of peach [Prunus persica (L.) Batsch] germplasm in the United States using microsatellite markers
Technology Transfer Automated Retrieval System (TEKTRAN)
Peach [Prunus persica (L.) Batsch] is an important medicinal fruit with immense health benefits and antioxidant activity. In this study, microsatellite markers were used as DNA fingerprinting tools for the identification and characterization of peach germplasm in the United States. Eleven microsatel...
Molecular markers to determine ecological fate of Bacillus thuringiensis subsp. kurstaki
Technology Transfer Automated Retrieval System (TEKTRAN)
Bacillus thuringiensis ("Bt") is a ubiquitous soil bacterium with entomopathogenic properties. One strain, Bt subsp. kurstaki ("Btk"), is highly toxic to lepidopteran larvae and used in many commercial products for biological pest control. We designed a set of DNA markers that successfully identifi...
A clinical, cytogenetic, FISH and molecular study of supernumerary marker 15 chromosomes
Dennis, N.R. [Princess Anne Hospital, Southampton (United Kingdom); Crolla, J.A.; Harvey, J.F. [Salisbury District Hospital (United Kingdom)
We studied 17 patients with supernumerary marker chromosomes shown by fluorescent in situ hybridization (FISH) with the 15-centromere specific probe pTRA-25 to be 15-derived. Genetic constitution of the marker chromosomes was investigated using FISH, Southern blot analysis and PCR for proximal and distal loci on 15q as well as conventional cytogenetics. Eight of the 17 patients were mentally retarded. Six of the eight carried a de novo marker 15 containing one or two doses of loci known to be in or near the Prader-Willi/Angelman (PWS/AS) region, whereas none of the nine non-retarded patients had duplications of this region, and only two of the eight whose parents were available had a de novo marker. None of the mentally retarded patients had PWS or AS. In two retarded patients (one de novo, one familial) there was no duplication of the PWS/AS region. Uniparental disomy affecting the normal 15 homologs was excluded in 10 of the patients, including all eight with mental retardation.
Molecular fossils and other organic markers as palaeoenvironmental indicators of the Messinian Calcare di Base
Paris-Sud XI, Université de
biological signatures: algae, bacteria and higher plants. Organic markers together with sedimentary evidence in Earth history: the Messinian Salinity Crisis. This occurred in a complex palaeogeographic environment Salinity Crisis are still intensely debated. An exhaustive and thorough review of the depositional
Identification of molecular markers associated with low chill/heat tolerance in raspberry
Technology Transfer Automated Retrieval System (TEKTRAN)
New genetic markers were developed which are linked to cold and heat tolerant raspberries. Raspberry is a cool season crop, and as such, cannot tolerate the high temperatures of the South during the normal growing season. Expanding the commercial growth range of raspberry production to the southern...
Molecular detection of clinical colorectal cancer metastasis: how should multiple markers be put to use?
Michael Conzelmann; Ulrich Linnemann; Martin R. Berger
Background and aims Up to 45% of colorectal cancer (CRC) patients will develop local recurrence or metastasis following curative resection. The latter is due to cells shed from the primary carcinoma prior to or during surgery. The aim of this study was to contribute toward a "rational"-approach for detecting these disseminated tumor cells (DTC) using a combination of independent markers
RAPD analysis of the interspecific somatic hybrids: Solanum bulbocastanum (+) S. tuberosum.
Bo?towicz, Danuta; Szczerbakowa, Anna; Wielgat, Bernard
The diploid Mexican species S. bulbocastanum (blb) was used as a source of late blight resistance in somatic hybridization with the potato (S. tuberosum, tbr) dihaploid H-8105. The produced 2x blb (+) 2x tbr H-8105 somatic hybrids did not retain the blb parent's characteristic high resistance to P. infestans. The revealed aneuploidy of blb (+) tbr H-8105 hybrids indicated a possible loss of individual blb chromosome(s) carrying the resistance genes. Four hybrid clones differing in terms of their ploidy, morphology and growth potential were analysed for the presence of all twelve blb chromosomes (linkage groups). The RAPD markers assigned to particular chromosomes were selected on the basis of the linkage map of S. bulbocastanum constructed by Naess et al., Mol. Gen. Genom. 265 (2001) 694-704. Of the 86 markers analysed, twelve (14%) were common for blb and H-8105, while 34 (40%) and 40 (46%) markers were specific for the blb and H-8105 genome, respectively; this confirms the differences between the nuclear genomes of the two species. Seventeen markers (20%) present in one or the other parent were absent in the hybrids, and only one new marker was found in the hybrids. The poorly growing, aneuploid and chimeric hybrids had the same band profiles as the well growing, morphologically normal hybrids, except for two bands that were present only in normal hybrids. The presence of eleven blb linkage groups in the blb (+) tbr H-8105 hybrids was confirmed. The markers specific for the second linkage group (chromosome 2) of blb were not present in the RAPD patterns of the somatic hybrids analysed, suggesting a loss or rearrangement of this chromosome in the combined nuclear genome of the hybrids. PMID:15809686
Identification and mapping of molecular markers linked to rust resistance genes located on chromosome 1RS of rye using wheat-rye translocation lines
R. Mago; W. Spielmeyer; G. Lawrence; E. Lagudah; J. Ellis; A. Pryor
The short arm of rye (Secale cereale) chromosome 1 has been widely used in breeding programs to incorporate new disease resistance genes into wheat. Using wheat-rye translocation and recombinant lines, molecular markers were isolated and mapped within chromosomal regions of 1RS carrying rust resistance genes Lr26, Sr31, Yr9 from 'Petkus' and SrR from 'Imperial' rye. RFLP markers previously mapped to
Chromosomal regions associated with segregation distortion of molecular markers in F 2 ?, backcross, doubled haploid, and recombinant inbred populations in rice ( Oryza sativa L.)
Y. Xu; L. Zhu; J. Xiao; N. Huang; S. R. McCouch
Chromosomal regions associated with marker segregation distortion in rice were compared based on six molecular linkage maps.\\u000a Mapping populations were derived from one interspecific backcross and five intersubspecific (indica?\\/?japonica) crosses, including two F2 populations, two doubled haploid (DH) populations, and one recombinant inbred (RI) population. Mapping data for each population\\u000a consisted of 129–629 markers. Segregation distortion was determined based on
Molecular Diversity in Ukrainian Melon Collection as Revealed by AFLP and Microsatellite Markers
Technology Transfer Automated Retrieval System (TEKTRAN)
Thirty-eight melon accessions, which are of primary breeding importance in the Ukraine, were analyzed for diversity. These collections represent a major non-US and non-west Europe source of melon germplasm that have not yet been subjected to molecular characterization. Molecular diversity was esti...
Applications of molecular markers and DNA sequences in identifying fungal pathogens of cool season grain legumes
Technology Transfer Automated Retrieval System (TEKTRAN)
Molecular techniques have now been widely applied in many disciplines of biological sciences including fungal identification in microbial ecology and plant pathology. In plant pathology, it is now common to use molecular techniques to identify and study plant pathogens of many agronomic and horticul...
Development of reliable molecular markers to detect non- pathogenic binucleate Rhizoctonia isolates (AG-G) using PCR
Non-pathogenic binucleate Rhizoctonia species (BNR) belonging to the anastomosis group AG-G are commonly associated with members of the Rhizoctonia solani complex. They provide eective protection to young bean seedlings against root rot caused by R. solani AG-4. Both fungi are morphologically similar and it is dicult to dierentiate between them without using laborious conventional techniques. RAPD assays were carried out
RGA-ILP, a new type of functional molecular markers in bread wheat
Ronghua Zhou; Jizeng Jia; Lifeng Gao
Markers targeting intron length polymorphism of resistance gene analogues (RGA-ILP) are not only expected to be more polymorphic\\u000a than those designed from conserved exons, but also have potential resistance gene function. Based on known domains of resistance\\u000a genes, more than 900 wheat RGAs were mined from public databases. Two hundred and seventy-eight intron-containing RGA candidates\\u000a were predicted based on rice
Molecular Characterization of Tree Peony Germplasm Using Sequence-Related Amplified Polymorphism Markers
Xiao Yan Han; Liang Sheng Wang; Qing Yan Shu; Zheng An Liu; Su Xia Xu; Takuya Tetsumura
This study examined 63 tree peony specimens, consisting of 3 wild species and 63 cultivars, using sequence-related amplified\\u000a polymorphism (SRAP) markers for the purpose of detecting genomic polymorphisms. Bulk DNA samples from each specimen were evaluated\\u000a with 23 SRAP primer pairs. Among the 296 different amplicons, 262 were polymorphic. The maximum parsimony, neighbor-joining,\\u000a and unweighted pair-group method using arithmetic average
Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution
Bhandari, Vaibhav; Naushad, Hafiz S.; Gupta, Radhey S.
The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs) among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning of whether the Darwinian model of evolution is applicable to prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) and conserved signature proteins (CSPs) for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs) initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies. PMID:22919687
Genetic polymorphism and taxonomic infrastructure of the Pleurotus eryngii species-complex as determined by RAPD analysis, isozyme profiles and ecomorphological characters.
Zervakis, G I; Venturella, G; Papadopoulou, K
The Pleurotus eryngii species-complex includes populations of choice edible mushrooms, growing in the greater Mediterranean area in close association with different genera of plants of the family Apiaceae. Their distinct host-specialization served as the principal criterion for the discrimination of several taxa; however, the genetic relationships among the various P. eryngii ecotypes remain ambiguous. In the present study, 46 Pleurotus strains with a wide range of geographical origins were isolated from Eryngium spp., Ferula communis, Cachrys ferulacea, Thapsia garganica and Elaeoselinum asclepium subsp. asclepium, and were subjected to isozyme and random amplified polymorphic DNA-PCR (RAPD) analysis. The 16 enzyme activities tested were controlled by 28 loci, 11 of which were monomorphic. Host-exclusive zymograms for the Aph (acid phosphatase) and Phe-1 (dopa-phenoloxidase) loci were obtained from Pleurotus strains associated with C. ferulacea. Allele frequencies, genetic diversity and mean diversity were high for isolates from Eryngium spp. and Ferula communis. In RAPD analysis, the use of five primers allowed the production of 45 (out of 48) polymorphic bands, while four molecular markers specific for the identification of Pleurotus strains growing on E. asclepium subsp. asclepium and C. ferulacea were obtained. The Pleurotus strains produced 35 distinct electrophoretic types and 42 RAPD patterns, which independently permitted the separation of the fungal populations into five clusters in accordance with their host-specificity. In addition, the evaluation of the principal ecological and morphological characters provided further evidence for discriminating between P. nebrodensis growing on C. ferulacea and the rest of the host-associated populations. The latter represent taxa at the varietal level: P. eryngii var. eryngii, P. eryngii var. ferulae and P. eryngii var. elaeoselini. The position of taxa of dubious validity, such as P. hadamardii and P. fossulatus, is discussed in relation to the new findings. All Mediterranean Pleurotus populations growing on umbellifers seem to have recently diverged through a sympatric speciation process, that is based on both intrinsic reproductive barriers and extrinsic ecogeographical factors. PMID:11700370
Selective DNA Pooling for Determination of Linkage between a Molecular Marker and a Quantitative Trait Locus
Darvasi, A.; Soller, M.
Selective genotyping is a method to reduce costs in marker-quantitative trait locus (QTL) linkage determination by genotyping only those individuals with extreme, and hence most informative, quantitative trait values. The DNA pooling strategy (termed: ``selective DNA pooling'') takes this one step further by pooling DNA from the selected individuals at each of the two phenotypic extremes, and basing the test for linkage on marker allele frequencies as estimated from the pooled samples only. This can reduce genotyping costs of marker-QTL linkage determination by up to two orders of magnitude. Theoretical analysis of selective DNA pooling shows that for experiments involving backcross, F(2) and half-sib designs, the power of selective DNA pooling for detecting genes with large effect, can be the same as that obtained by individual selective genotyping. Power for detecting genes with small effect, however, was found to decrease strongly with increase in the technical error of estimating allele frequencies in the pooled samples. The effect of technical error, however, can be markedly reduced by replication of technical procedures. It is also shown that a proportion selected of 0.1 at each tail will be appropriate for a wide range of experimental conditions. PMID:7896115
Week 6: Restriction sites, RAPDs, microsatellites, likelihood, hidden Markov models
Borenstein, Elhanan
Week 6: Restriction sites, RAPDs, microsatellites, likelihood, hidden Markov models Genome 570 February, 2010 Week 6: Restriction sites, RAPDs, microsatellites, likelihood, hidden Markov models p.1, likelihood, hidden Markov models p.2/62 #12;Number of sequences in a restriction site location Nk = r k 3k
Genetic diversity of alligator weed in China by RAPD analysis
Cheng-Yuan Xu; Wen-Ju Zhang; Cui-Zhang Fu; Bao-Rong Lu
Random amplified polymorphic DNA (RAPD) was applied to analyze geneticdiversity of an invasive weedy species, alligator weed (Alternantheraphiloxeroides (Martius) Grisebach), collected from eight differentsites in southern China. Amplified by 108 RAPD primers, 391 bands wereidentified from samples collected from three of the eight sites withconsiderably large spatial intervals, but no genetic variation was detectedamong the samples. A total number of
Highly variable microsatellite markers for the fungal and algal symbionts of the lichen Lobaria pulmonaria and challenges in developing biont-specific molecular markers for fungal associations
Ivo Widmer; Francesco Dal Grande; Carolina Cornejo; Christoph Scheidegger
The availability of highly variable markers for the partners of a fungal symbiosis enables the integrated investigation of ecological and evolutionary processes at the symbiotic level. In this article we analyze the specificity of the first and to date only microsatellite markers that had been developed for an epiphytic lichen (Lobaria pulmonaria). We used DNA extracts from cultures of the
Sequence characterization, in silico mapping and cytosine methylation analysis of markers linked to apospory in Paspalum notatum.
Podio, Maricel; Rodríguez, María P; Felitti, Silvina; Stein, Juliana; Martínez, Eric J; Siena, Lorena A; Quarin, Camilo L; Pessino, Silvina C; Ortiz, Juan Pablo A
In previous studies we reported the identification of several AFLP, RAPD and RFLP molecular markers linked to apospory in Paspalum notatum. The objective of this work was to sequence these markers, obtain their flanking regions by chromosome walking and perform an in silico mapping analysis in rice and maize. The methylation status of two apospory-related sequences was also assessed using methylation-sensitive RFLP experiments. Fourteen molecular markers were analyzed and several protein-coding sequences were identified. Copy number estimates and RFLP linkage analysis showed that the sequence PnMAI3 displayed 2-4 copies per genome and linkage to apospory. Extension of this marker by chromosome walking revealed an additional protein-coding sequence mapping in silico in the apospory-syntenic regions of rice and maize. Approximately 5 kb corresponding to different markers were characterized through the global sequencing procedure. A more refined analysis based on sequence information indicated synteny with segments of chromosomes 2 and 12 of rice and chromosomes 3 and 5 of maize. Two loci associated with apomixis locus were tested in methylation-sensitive RFLP experiments using genomic DNA extracted from leaves. Although both target sequences were methylated no methylation polymorphisms associated with the mode of reproduction were detected. PMID:23271945
Molecular Phylogeny of a tick, Ixodes granulatus (Acari: Ixodidae) based on cytochrome oxidase subunit I (COI) marker
NASA Astrophysics Data System (ADS)
Lah, Ernieenor Faraliana Che; Yaakop, Salmah; Ahamad, Mariana; George, Ernna; Nor, Shukor Md
Identification of a local species of tick, Ixodes granulatus from the family Ixodidae is essential because it has potential to be vector for spotted fever group (SFG) rickettsia and tick thypus. The aim of this study is to portray the relationships among several populations of I. granulatus collected from different species of animal hosts and localities in Peninsular Malaysia. Polymerase Chain Reaction was conducted by amplifying mitochondrial DNA marker, namely cytochrome oxidase subunit I (COI) sequences from 15 individual ticks that attached to five different hosts caught from three different localities. Confirmation of the species identity was accomplished using BLAST program. Neighbor-joining (NJ) and Maximum Parsimony (MP) tree based on COI sequences were constructed by using PAUP 4.0b10 to identify the relationship among species. The result of this study showed a high genetic heterogeneity between I. granulatus and other species of the same genus (7.2-23.7%). Furthermore, a low intraspecific variation was observed among the species of I. granulatus collected from different localities (0-3.7%). This study produced the first establishment of molecular marker for clarifying genetic species variation and diversity of local I. granulatus tick which contribute to the control of tick-borne infections.
Molecular identification and phylogenetic relationship of green algae, Spirogyra ellipsospora (Chlorophyta) using ISSR and rbcL markers.
Wongsawad, Pheravut; Peerapornpisal, Yuwadee
Spirogyra is found in a wide range of habitats, including small stagnant water bodies, rivers, and streams. Spirogyra ellipsospora is common in northern Thailand. Species identification of the Spirogyra species based only on morphological characteristics can be difficult. A reliable and accurate method is required to evaluate genetic variations. This study aims to apply molecular approaches for the identification of S. ellipsospora using microsatellites and rbcL markers. Based on DNA sequencing, the rbcL gene was sequenced and the data was analyzed using the BLAST (Basic Local Alignment Search Tool) program in the NCBI (National Center for Biotechnology Information) database. The sequence of S. ellipsospora from this study revealed definitive identity matches in the range of 99% for the consensus sequences of S. ellipsospora. The 10 primers of ISSR could be amplified by 92 amplification fragments. The DNA fragments and the rbcL sequence data grouped the Spirogyra specimens into two distinct clusters. PMID:25313288
The genotypes of citrus tristeza virus isolates from China revealed by sequence analysis of multiple molecular markers.
Wu, Guan-Wei; Pan, Song; Wang, Guo-Ping; Tang, Min; Liu, Yong; Yang, Fan; Hong, Ni
The genotypes of ten citrus tristeza virus (CTV) isolates from central China were determined by examining multiple molecular markers (MMMs) using 11 primer pairs. The results revealed that one isolate contained a single T30 genotype, two isolates contained a single VT genotype, and the other seven isolates were mixtures of two or more genotypes. Sequence analysis of amplified MMMs showed a high genetic diversity in Chinese CTV populations. The genotypes resembling T36, RB and B165 were identified from Chinese CTV isolates for the first time. Our results suggest that genotype assignment of CTV cannot be based solely on the amplification profiles of MMMs, and sequencing of MMMs is required. PMID:22987316
Development of microsatellite markers from an enriched genomic library for genetic analysis of melon (Cucumis melo L.)
Ritschel, Patricia Silva; Lins, Tulio Cesar de Lima; Tristan, Rodrigo Lourenço; Buso, Gláucia Salles Cortopassi; Buso, José Amauri; Ferreira, Márcio Elias
Background Despite the great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in melon (Cucumis melo L.) and cucurbit species. The development of microsatellite markers will have a major impact on genetic analysis and breeding of melon, especially on the generation of marker saturated genetic maps and implementation of marker assisted breeding programs. Genomic microsatellite enriched libraries can be an efficient alternative for marker development in such species. Results Seven hundred clones containing microsatellite sequences from a Tsp-AG/TC microsatellite enriched library were identified and one-hundred and forty-four primer pairs designed and synthesized. When 67 microsatellite markers were tested on a panel of melon and other cucurbit accessions, 65 revealed DNA polymorphisms among the melon accessions. For some cucurbit species, such as Cucumis sativus, up to 50% of the melon microsatellite markers could be readily used for DNA polymophism assessment, representing a significant reduction of marker development costs. A random sample of 25 microsatellite markers was extracted from the new microsatellite marker set and characterized on 40 accessions of melon, generating an allelic frequency database for the species. The average expected heterozygosity was 0.52, varying from 0.45 to 0.70, indicating that a small set of selected markers should be sufficient to solve questions regarding genotype identity and variety protection. Genetic distances based on microsatellite polymorphism were congruent with data obtained from RAPD marker analysis. Mapping analysis was initiated with 55 newly developed markers and most primers showed segregation according to Mendelian expectations. Linkage analysis detected linkage between 56% of the markers, distributed in nine linkage groups. Conclusions Genomic library microsatellite enrichment is an efficient procedure for marker development in melon. One-hundred and forty-four new markers were developed from Tsp-AG/TC genomic library. This is the first reported attempt of successfully using enriched library for microsatellite marker development in the species. A sample of the microsatellite markers tested proved efficient for genetic analysis of melon, including genetic distance estimates and identity tests. Linkage analysis indicated that the markers developed are dispersed throughout the genome and should be very useful for genetic analysis of melon. PMID:15149552
Molecular Characterization of Cultivated Bromeliad Accessions with Inter-Simple Sequence Repeat (ISSR) Markers
Zhang, Fei; Ge, Yaying; Wang, Weiyong; Yu, Xinying; Shen, Xiaolan; Liu, Jianxin; Liu, Xiaojing; Tian, Danqing; Shen, Fuquan; Yu, Yongming
Bromeliads are of great economic importance in flower production; however little information is available with respect to genetic characterization of cultivated bromeliads thus far. In the present study, a selection of cultivated bromeliads was characterized via inter-simple sequence repeat (ISSR) markers with an emphasis on genetic diversity and population structure. Twelve ISSR primers produced 342 bands, of which 287 (~84%) were polymorphic, with polymorphic bands per primer ranging from 17 to 34. The Jaccard's similarity ranged from 0.08 to 0.89 and averaged ~0.30 for the investigated bromeliads. The Bayesian-based approach, together with the un-weighted paired group method with arithmetic average (UPGMA)-based clustering and the principal coordinate analysis (PCoA), distinctly grouped the bromeliads from Neoregelia, Guzmania, and Vriesea into three separately clusters, well corresponding with their botanical classifications; whereas the bromeliads of Aechmea other than the recently selected hybrids were not well assigned to a cluster. Additionally, ISSR marker was proven efficient for the identification of hybrids and bud sports of cultivated bromeliads. The findings achieved herein will further our knowledge about the genetic variability within cultivated bromeliads and therefore facilitate breeding for new varieties of cultivated bromeliads in future as well. PMID:22754348
Molecular characterization of cultivated bromeliad accessions with Inter-Simple Sequence Repeat (ISSR) Markers.
Zhang, Fei; Ge, Yaying; Wang, Weiyong; Yu, Xinying; Shen, Xiaolan; Liu, Jianxin; Liu, Xiaojing; Tian, Danqing; Shen, Fuquan; Yu, Yongming
Bromeliads are of great economic importance in flower production; however little information is available with respect to genetic characterization of cultivated bromeliads thus far. In the present study, a selection of cultivated bromeliads was characterized via inter-simple sequence repeat (ISSR) markers with an emphasis on genetic diversity and population structure. Twelve ISSR primers produced 342 bands, of which 287 (~84%) were polymorphic, with polymorphic bands per primer ranging from 17 to 34. The Jaccard's similarity ranged from 0.08 to 0.89 and averaged ~0.30 for the investigated bromeliads. The Bayesian-based approach, together with the un-weighted paired group method with arithmetic average (UPGMA)-based clustering and the principal coordinate analysis (PCoA), distinctly grouped the bromeliads from Neoregelia, Guzmania, and Vriesea into three separately clusters, well corresponding with their botanical classifications; whereas the bromeliads of Aechmea other than the recently selected hybrids were not well assigned to a cluster. Additionally, ISSR marker was proven efficient for the identification of hybrids and bud sports of cultivated bromeliads. The findings achieved herein will further our knowledge about the genetic variability within cultivated bromeliads and therefore facilitate breeding for new varieties of cultivated bromeliads in future as well. PMID:22754348
Identification of two novel waxy alleles and development of their molecular markers in sorghum.
Lu, Yuangen; Zhao, Ganlin; Li, Yan; Fan, Jing; Ding, Guoxiang; Zhao, Jiqun; Ni, Xianlin; Xu, Yongju; Wang, Wenming
High amylopectin grains of waxy sorghum have a high economic value in the food and bioenergy industries because of their increased starch digestibility and higher ethanol conversion rate compared with wild-type sorghum grains. Mutation in the granule-bound starch synthase (GBSS) gene contributes to the waxy phenotype. Two classes of waxy alleles, wx(a) and wx(b), have been characterized previously. In the present work, we identified two novel types of waxy mutations in the sorghum GBSS gene, designated as wx(c) and wx(d). The wx(c) allele has a G deletion at the 5' splicing site of the ninth intron, causing a shift of the 5' cleavage site; in turn, a reading frame shift occurred and resulted in an early translation termination. The wx(d) allele contained a mutation at the 3' splicing site of the 10th intron, which led to a splicing site shift and resulted in the deletion of five amino acids (GTGKK) in the predicted translation product. Furthermore, cleaved amplified polymorphic sequence (CAPS) markers were developed to detect the wx(c) and wx(d) alleles. With these markers, classification of waxy alleles was performed in nearly 100 sorghum accessions from our breeding program. Most waxy sorghum cultivars in China were either wx(a) or wx(c), implying that these two mutations are preferentially maintained during domestic selection in glutinous sorghum production. PMID:23789996
Prediction of body mass index in mice using dense molecular markers and a regularized neural network.
Okut, Hayrettin; Gianola, Daniel; Rosa, Guilherme J M; Weigel, Kent A
Bayesian regularization of artificial neural networks (BRANNs) were used to predict body mass index (BMI) in mice using single nucleotide polymorphism (SNP) markers. Data from 1896 animals with both phenotypic and genotypic (12 320 loci) information were used for the analysis. Missing genotypes were imputed based on estimated allelic frequencies, with no attempt to reconstruct haplotypes based on family information or linkage disequilibrium between markers. A feed-forward multilayer perceptron network consisting of a single output layer and one hidden layer was used. Training of the neural network was done using the Bayesian regularized backpropagation algorithm. When the number of neurons in the hidden layer was increased, the number of effective parameters, ?, increased up to a point and stabilized thereafter. A model with five neurons in the hidden layer produced a value of ? that saturated the data. In terms of predictive ability, a network with five neurons in the hidden layer attained the smallest error and highest correlation in the test data although differences among networks were negligible. Using inherent weight information of BRANN with different number of neurons in the hidden layer, it was observed that 17 SNPs had a larger impact on the network, indicating their possible relevance in prediction of BMI. It is concluded that BRANN may be at least as useful as other methods for high-dimensional genome-enabled prediction, with the advantage of its potential ability of capturing non-linear relationships, which may be useful in the study of quantitative traits under complex gene action. PMID:21481292
Screening of molecular markers linked to dwarf trait in crape myrtle by bulked segregant analysis.
Ye, Y J; Liu, Y; Cai, M; He, D; Shen, J S; Ju, Y Q; Bian, X M; Pan, H T; Zhang, Q X
Plant height is one of the most important traits of plant architecture as it modulates both economic and ornamental values. Crape myrtle (Lagerstroemia indica L.) is a popular ornamental woody plant because of its long-lasting mid-summer bloom, rich colors, and diversified plant architecture. These traits also make it an ideal model of woody species for genetic analysis of many ornamental traits. To understand the inheritance of plant height and screen for genes modulating plant height in Lagerstroemia, segregation of the plant height trait was analyzed using the F1 population of L. fauriei (standard) x L. indica 'Pocomoke' (dwarf) with 96 seedlings, while dwarf genes were screened using the bulked segregant analysis method, combined with 28 amplified fragment length polymorphism primers and 41 simple sequence repeat primers. The results showed that the dwarf trait of crape myrtle was controlled by a major gene and modified by minor genes. An amplified fragment length polymorphism marker, M53E39-92, which was 23.33 cM from the loci controlling the dwarf trait, was screened. These results provide basic information for marker-assisted selection in Lagerstromia and cloning of dwarf genes in future studies. PMID:25966210
Genetic analysis of two Portuguese populations of Ruditapes decussatus by RAPD profiling
NASA Astrophysics Data System (ADS)
Pereira, Jorge C.; Chaves, Raquel; Leităo, Alexandra; Matias, Domitilia; Guedes-Pinto, Henrique
The clam Ruditapes decussatus is commercially important in the south of Portugal. The random amplified polymorphic DNA (RAPD) technique was applied to assess the genetic diversity and population structure of two Portuguese populations occurring in the Ria Formosa (Faro) and the Ria de Alvor, respectively. Twenty-five individuals of each population were investigated by RAPD profiles. Genetic diversity within populations, measured by the percentage of polymorphic loci ( %P), varied between 68.57% (Alvor) and 73.88% (Faro). Shannon's information index ( H) and Nei's gene diversity ( h) were 0.281 and 0.176, respectively, for the Alvor population and 0.356 and 0.234 for the Faro population. Overall, genetic variation within R. decussatus populations was high. The total genetic diversity ( H T) was explained by a low variation between populations ( G ST = 0.145), which is consistent with high gene flow ( N m = 2.9). The analysis of molecular variance (AMOVA) showed that 65% of variability is within populations and 35% between populations (?PT = 0.345; P ? 0.001). The value of Nei's genetic distance was 0.0881, showing a low degree of population genetic distance, despite the different geographic origin. This is the first study on the population genetics of R. decussatus by RAPD technique. The results may be useful for restocking programs and aquaculture.
Molecular hierarchy of mammary differentiation yields refined markers of mammary stem cells
dos Santos, Camila O.; Rebbeck, Clare; Rozhkova, Elena; Valentine, Amy; Samuels, Abigail; Kadiri, Lolahon R.; Osten, Pavel; Harris, Elena Y.; Uren, Philip J.; Smith, Andrew D.; Hannon, Gregory J.
The partial purification of mouse mammary gland stem cells (MaSCs) using combinatorial cell surface markers (Lin?CD24+CD29hCD49fh) has improved our understanding of their role in normal development and breast tumorigenesis. Despite the significant improvement in MaSC enrichment, there is presently no methodology that adequately isolates pure MaSCs. Seeking new markers of MaSCs, we characterized the stem-like properties and expression signature of label-retaining cells from the mammary gland of mice expressing a controllable H2b-GFP transgene. In this system, the transgene expression can be repressed in a doxycycline-dependent fashion, allowing isolation of slowly dividing cells with retained nuclear GFP signal. Here, we show that H2b-GFPh cells reside within the predicted MaSC compartment and display greater mammary reconstitution unit frequency compared with H2b-GFPneg MaSCs. According to their transcriptome profile, H2b-GFPh MaSCs are enriched for pathways thought to play important roles in adult stem cells. We found Cd1d, a glycoprotein expressed on the surface of antigen-presenting cells, to be highly expressed by H2b-GFPh MaSCs, and isolation of Cd1d+ MaSCs further improved the mammary reconstitution unit enrichment frequency to nearly a single-cell level. Additionally, we functionally characterized a set of MaSC-enriched genes, discovering factors controlling MaSC survival. Collectively, our data provide tools for isolating a more precisely defined population of MaSCs and point to potentially critical factors for MaSC maintenance. PMID:23580620
Molecular characterization of Buffalograss germplasm using sequence-related amplified polymorphism markers.
Budak, H; Shearman, R C; Parmaksiz, I; Gaussoin, R E; Riordan, T P; Dweikat, I
Buffalograss [ Buchloe dactyloides (Nutt.) Englem] germplasm has a broad resource of genetic diversity that can be used for turfgrass, forage and conservation. Buffalograss is the only native grass that is presently used as a turfgrass in the Great Plains region of North America. Its low growth habit, drought tolerance and reduced requirement for fertilizer and pesticides contribute to interest in its use. The objectives of this study were to use sequence-related amplified polymorphism (SRAP) markers in the evaluation of genetic diversity and phenetic relationships in a diverse collection of 53 buffalograss germplasms, and to identify buffalograss ploidy levels using flow cytometry. Based on their DNA contents, buffalograss genotypes were grouped into four sets, corresponding to their ploidy levels. Thirty-four SRAP primer combinations were used. This is the first report of the detection of differentiating diploid, tetraploid, pentaploid and hexaploid buffalograss genotypes, representing diverse locations of origin, using SRAP markers. Cluster analysis by the unweighted pair-group method with arithmetic averages based on genetic similarity matrices indicated that there were eight clusters. The coefficients of genetic distance among the genotypes ranged from 0.33 up to 0.99 and averaged D=0.66. The genetic diversity estimate, He, averaged 0.35. These results demonstrated that genotypes with potential traits for turfgrass improvement could readily be distinguished, based on SRAP. The use of PCR-based technologies such as SRAP is an effective tool for estimating genetic diversity, identifying unique genotypes as new sources of alleles for enhancing turf characteristics, and for analyzing the evolutionary and historical development of cultivars at the genomic level in a buffalograss breeding program. PMID:13679978
Diagnostic value of molecular markers for Lr genes and characterization of leaf rust resistance of German winter wheat cultivars with regard to the stability of vertical resistance
Albrecht Serfling; Ilona Krämer; Volker Lind; Edgar Schliephake; Frank Ordon
Breeding for resistance is an efficient strategy to manage wheat leaf rust caused by Puccinia triticina f. sp. tritici. However, a prerequisite for the directed use of Lr genes in breeding and the detection of new races virulent to these Lr genes is a detailed knowledge on Lr genes present in wheat cultivars. Therefore, respective molecular markers for 18 Lr
Evaluation of molecular markers for discriminating Gonaterocerus morrilli: A biological control agent imported from the origin of the glassy-winged sharpshooter
Technology Transfer Automated Retrieval System (TEKTRAN)
We examined the utility of molecular markers for discriminating between two very closely related species, Gonatocerus morrilli (Howard) (imported from Texas) and G. walkerjonesi S. Triapitsyn (native to California), to determine whether post-release G. morrilli specimens could be detected and discri...
Genetic analysis and molecular mapping of maize (Zea mays L.) stalk rot resistant gene Rfg1.
Yang, D E; Zhang, C L; Zhang, D S; Jin, D M; Weng, M L; Chen, S J; Nguyen, H; Wang, B
One single pathogen Fusarium graminearum Schw. was inoculated to maize inbred lines 1,145 (Resistant) and Y331 (Susceptive), and their progenies of F(1), F(2) and BC(1)F(1) populations. Field statistical data revealed that all of the F(1) individuals were resistant to the disease and that the ratio of resistant plants to susceptive plants was 3:1 in the F(2) population, and 1:1 in the BC(1)F(1 )population. The results revealed that a single dominant gene controls the resistance to F. graminearum Schw. The resistant gene to F. graminearum Schw. was denominated as Rfg1 according to the standard principle of the nomenclature of the plant disease resistant genes. RAPD (randomly amplified polymorphic DNA) combined with BSA (bulked segregant analysis) analysis was carried out in the developed F(2) and BC(1)F(1 )populations, respectively. Three RAPD products screened from the RAPD analysis with 820 Operon 10-mer primers showed the linkage relation with the resistant gene Rfg1. The three RAPD amplification products (OPD-20(1000), OPA-04(1100) and OPY-04(900)) were cloned and their copy numbers were determined. The results indicated that only OPY-04(900) was a single-copy sequence. Then, OPY-04(900) was used as a probe to map the Rfg1 gene with a RIL F(7) mapping population provided by Henry Nguyen, which was developed from the cross "S3xMo17". Rfg1 was primarily mapped on chromosome 6 between the two linked markers OPY-04(900) and umc21 (Bin 6.04-6.05). In order to confirm the primary mapping result, 25 SSR (simple sequence repeat) markers and six RFLP (restriction fragment length polymorphism) markers in the Rfg1 gene-encompassing region were selected, and their linkage relation with Rfg1 was analyzed in our F(2) population. Results indicated that SSR marker mmc0241 and RFLP marker bnl3.03 are flanking the Rfg1 gene with a genetic distance of 3.0 cM and 2.0 cM, respectively. This is the first time to name and to map a single resistant gene of maize stalk rot through a single pathogen inoculation and molecular marker analysis. PMID:14647897
Identification of a Genetic Marker That Discriminates Ocean-Type and Stream-Type Chinook Salmon in the Columbia River Basin
Charlotte Rasmussen; Carl O. Ostberg; David R. Clifton; James L. Holloway; Russell J. Rodriguez
A marker based on randomly amplified polymorphic DNA (RAPD), OT-38, was discovered that nonlethally discriminates between stream-type and ocean-type populations of chinook salmon Oncorhynchus tshawytscha in the Columbia River basin, including the threatened fall-run (ocean-type) and spring-run (stream-type) Snake River populations. This marker was developed by amplifying chinook salmon genomic DNA with a single RAPD primer, sequencing the termini of
Molecular characterization and population structure of the macaw palm, Acrocomia aculeata (Arecaceae), ex situ germplasm collection using microsatellites markers.
Lanes, Éder C M; Motoike, Sérgio Y; Kuki, Kacilda N; Nick, Carlos; Freitas, Renata D
The Acrocomia aculeata is one of the most promising plants for sustainable production of renewable energy. In order to understand patterns of the distribution of the allelic diversity of A. aculeata ex situ germplasm collection, the present study investigated the hypothesis that the genetic variability of the accessions may match their geographical origin. A genotypic analysis of 77 A. aculeata accessions was conducted with 6 simple sequence repeat markers. A high degree of molecular diversity among the accessions was found, with an average of 9 alleles per locus and a polymorphic information content with a mean of 0.76. A total of 4 clusters was identified by the Bayesian analysis of population structure. The highest subpopulation diversity was identified in Pop1, mainly formed by accessions from State of Mato Grosso do Sul. The populations Pop2A, Pop2B, and Pop2C, all from the State of Minas Gerais, showed high genetic variability as determined by a higher F st, and a wide genetic variance, which were identified within and among the population by analysis of molecular variance. Based on our results and on Vavilov's theory on crop origins, one possible diversity center for A. aculeata is proposed to be in a region in southeast Brazil. PMID:25425677
Morphological and molecular profiling of Spirogyra from northeastern and northern Thailand using inter simple sequence repeat (ISSR) markers
Wongsawad, Pheravut; Peerapornpisal, Yuwadee
Green algae, Spirogyra (Chlorophyta), are found in a wide range of habitats including small stagnant water bodies, rivers, and streams. Species identification of Spirogyra based on morphological characteristics has proven to be a difficult process. An accurate identification method is required to evaluate genetic variations. This study is aimed at investigating the molecular profiling of 19 samples of Spirogyra from northern and northeastern Thailand. The morphological characteristics of each sample were recorded, viz. cell dimensions (width and length), along with the number and arrangement of chloroplast spirals/pyrenoids. With regard to a correlation of the biological and ecological parameters, conductivity was clearly significantly related to the number of pyrenoids. While DO is negatively related to the number of chloroplast spirals. Molecular studies with 10 ISSR primers were amplified to examine the DNA fingerprints. Morphological characters were determined to be significantly different by revealing 5 traits (P < 0.05) for all specimens. In addition, the DNA markers of all specimens were investigated using 10 ISSR primers. The results show that the PCR technique amplified 108 fragments. An analysis of the DNA fragments grouped all samples by ISRR-PCR, which were then separated into two groups according to their distribution. PMID:26150742
Expanding Character Sampling for Ciliate Phylogenetic Inference Using Mitochondrial SSU-rDNA as a Molecular Marker
Dunthorn, Micah; Foissner, Wilhelm; Katz, Laura A.
Molecular systematics of ciliates, particularly at deep nodes, has largely focused on increasing taxon sampling using the nuclear small subunit rDNA (nSSU-rDNA) locus. These previous analyses have generally been congruent with morphologically-based classifications, although there is extensive non-monophyly at many levels. However, caution is needed in interpreting these results as nSSU-rDNA is just a single molecular marker. Here the mitochondrial small subunit rDNA (mtSSU-rDNA) is evaluated for deep ciliate nodes using the Colpodea as an example. Overall, well-supported nodes in the mtSSU-rDNA and concatenated topologies are well supported in the nSSU-rDNA topology; e.g., the non-monophyly of the Cyrtolophosidida. The two moderately-to well-supported incongruences between the loci are the placement of the Sorogenida and Colpoda aspera. Our analyses of mtSSU-rDNA support the conclusion, originally derived from nSSU-rDNA, that the morphological characters used in taxonomic circumscriptions of the Colpodea represent a mixture of ancestral and derived states. This demonstration of the efficacy of the mtSSU-rDNA will enable phylogenetic reconstructions of deep nodes in the ciliate tree of life to move from a single-locus to a multi-locus approach. PMID:20708960
Uses of molecular markers for understanding modern and historical ecosystems (Invited)
NASA Astrophysics Data System (ADS)
Friesen, V. L.
Information on current and historical population sizes and movements is important for understanding many aspects of ecosystem ecology such as responses to climate change. Such information can be surprisingly difficult to acquire, but can be estimated from clues contained in an organism's DNA. Recent revolutions in molecular genetics, including direct sequencing and efficient mutation-detection methods, enable extraction of sequence information from even very small or ancient specimens. Furthermore, theoretical advances such as coalescent theory and molecular assignments are providing powerful tools to unlock secrets about changes in numbers, distributions and movements. Combination of these approaches with other types of data promises to provide especially useful insights into modern and paleoecosystems. I will provide examples of these applications from recent studies in ornithology.
Temporal trends of molecular markers associated with artemether-lumefantrine tolerance/resistance in Bagamoyo district, Tanzania
Background Development and spread of Plasmodium falciparum resistance to artemisinin-based combination therapy (ACT) constitutes a major threat to recent global malaria control achievements. Surveillance of molecular markers could act as an early warning system of ACT-resistance before clinical treatment failures are apparent. The aim of this study was to analyse temporal trends of established genotypes associated with artemether-lumefantrine tolerance/resistance before and after its deployment as first-line treatment for uncomplicated malaria in Tanzania 2006. Methods Single nucleotide polymorphisms in the P. falciparum multidrug resistance gene 1 (pfmdr1) N86Y, Y184F, D1246Y and P. falciparum chloroquine transporter gene (pfcrt) K76T were analysed from dried blood spots collected during six consecutive studies from children with uncomplicated P. falciparum malaria in Fukayosi village, Bagamoyo District, Tanzania, between 2004–2011. Results There was a statistically significant yearly increase of pfmdr1 N86, 184F, D1246 and pfcrt K76 between 2006–2011 from 14% to 61% (yearly OR = 1.38 [95% CI 1.25-1.52] p < 0.0001), 14% to 35% (OR = 1.17 [95% CI 1.07-1.30] p = 0.001), 54% to 85% (OR = 1.21 [95% CI 1.03-1.42] p = 0.016) and 49% to 85% (OR = 1.33 [95% CI 1.17-1.51] p < 0.0001), respectively. Unlike for the pfmdr1 SNP, a significant increase of pfcrt K76 was observed already between 2004–2006, from 26% to 49% (OR = 1.68 [95% CI 1.17-2.40] p = 0.005). From 2006 to 2011 the pfmdr1 NFD haplotype increased from 10% to 37% (OR = 1.25 [95% CI 1.12-1.39] p < 0.0001), whereas the YYY haplotype decreased from 31% to 6% (OR = 0.73 [95% CI 0.56-0.98] p = 0.018). All 390 successfully analysed samples had one copy of the pfmdr1 gene. Conclusion The temporal selection of molecular markers associated with artemether-lumefantrine tolerance/resistance may represent an early warning sign of impaired future drug efficacy. This calls for stringent surveillance of artemether-lumefantrine efficacy in Tanzania and emphasizes the importance of molecular surveillance as a complement to standard in vivo trials. PMID:23506218
Technology Transfer Automated Retrieval System (TEKTRAN)
To address the lack of available molecular markers for cotton, Cotton Incorporated has spearheaded an initiative to create the Cotton Microsatellite Database (CMD), and several groups are actively involved in projects to generate, screen and map cotton molecular markers. CMD is a centralized databas...
A genetic linkage map of papaya based on randomly amplified polymorphic DNA markers
S. N. Sondur; R. M. Manshardt; J. I. Stiles
A genetic linkage map of papaya (Carica papaya L.) was constructed using randomly amplified polymorphic DNA (RAPD) markers and a F2 population derived from a University of Hawaii UH breeding line 356 x 'Sunrise' cross. A total of 596 10-mer primers were screened, and 96 polymorphisms were detected. At LOD 4.0, 62 of these markers mapped to 11 linkage groups
[RAPD variation in two trematode species (Fasciola hepatica and Dicrocoelium dendriticum) from a single cattle population].
Morozova, E V; Ryskov, A P; Semenova, S K
The method of random DNA amplification by PCR with arbitrary primers (RAPD-PCR) was used for the description and estimation of genetic variation in two trematode species, Fasciola hepatica (n = 21) and Dicrocoelium dendriticum (n = 8). The studied trematodes were liver parasites of five cattle individuals belonging to the same herd. To study the F. hepatica population, five primers were selected, which revealed 320 RAPD markers in five samples of parasites isolated from five different host individuals. Using 87 RAPD markers, a comparison of variation was conducted between F. hepatica and D. dendriticum samples from the same host individual. Based on the estimates of RAPD variation for the individual samples of parasites collected from each of five host individuals and for the total F. hepatica population, standard indices of genetic similarity (S), diversity (H), polymorphism (P), and population subdivision (FST) were calculated. From the indices of similarity in pairs (S), dendrograms were constructed, which reflect genetic relationship between the representatives of two species and between F. hepatica individuals isolated from the same or different host individuals. It was revealed that polymorphism level (P) varied within a range of 35.5 to 83.2% in the studied F. hepatica population and reached 95.1% in the studied D. dendriticum population. Two different trematode species that simultaneously parasitize the same host animal were characterized by similar estimates of polymorphism and genetic diversity and by similar topology of genetic similarity dendrograms. The degree of genetic similarity between F. hepatica and D. dendriticum was significantly lower (20%) than between five F. hepatica samples (41.4%) that formed two unequal clusters. Each of these clusters represents a heterogeneous group consisting of parasites collected from three or four host individuals. In the individual samples of parasites related to each of the studied host individuals, the indices of genetic similarity (S) and diversity (H) varied within a range of 43.3 to 64.8% and 25.1 to 56.6%, respectively. In the total F. hepatica sample, the estimates of intraspecific variation, the topology of dendrograms, and the FST index (7.4%) indicate the absence of clear genetic differentiation between the samples of parasites isolated from different host individuals. Possible reasons for the high level of genetic variation in the studied trematode populations and the genetic consequences of host--parasite interaction are discussed. PMID:12244701
Molecular characterization of Syrian date palm cultivars using plasmid-like DNA markers.
Haider, N; Nabulsi, I
Date palm (Phoenix dactylifera L.) is one of the most important domesticated fruit trees in the Near East and North African countries. This tree has been, for several decades, in serious threat of being completely destroyed by the "Bayoud" disease caused by Fusarium oxysporum f. sp. albedinis. In this study, 18 Syrian date palm cultivars and four male trees were analyzed according to the identity of mitochondrial plasmid-like DNAs. A PCR strategy that employs plasmid-like DNAs-specific primer pair was used. These primers amplify a product of either 373-bp or 265-bp that corresponds to the S-(Bayoud-susceptible) or the R-plasmid (Bayoud-resistant), respectively. Generated data revealed that only six cultivars ('Medjool', 'Ashrasi', 'Gish Rabi', 'Khineze', and yellow- and red-'Kabkab') have the S-plasmid, suggesting their susceptibility to the fusariosis, while the remaining 12 cultivars and the four male trees contain the R-plasmid, suggesting their resistance to the fusariosis. The PCR process applied here has been proved efficient for the rapid screening for the presence of the S and R DNAs in Syrian date palm. PCR markers developed in this study could be useful for the screening of date palm lines growing in the field. The availability of such diagnostic tool for plasmid characterization in date palm would also be of great importance in establishing propagation and breeding programs of date palm in Syria. PMID:22568006
Molecular characterization and differentiation of five horse breeds raised in Algeria using polymorphic microsatellite markers.
Berber, N; Gaouar, S; Leroy, G; Kdidi, S; Tabet Aouel, N; Saďdi Mehtar, N
In this study, genetic analyses of diversity and differentiation were performed on five horse breeds raised in Algeria (Barb, Arab-Barb, Arabian, Thoroughbred and French Trotter). All microsatellite markers were highly polymorphic in all the breeds. A total of 123 alleles from 14 microsatellite loci were detected in 201 horses. The average number of alleles per locus was the highest in the Arab-Barb horses (7.86) and lowest in the thoroughbred breed (5.71), whereas the observed and expected heterozygosities per breed ranged from 0.71 (Thoroughbred) to 0.752 (Barb) and 0.71 (Thoroughbred) to 0.77 (Arab-Barb), respectively. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (FST ). Three different approaches for evaluating the genetic relationships were applied. Genetic distances, the factorial correspondence analysis and structure analysis showed that a significant amount of genetic variation is maintained in the native horse populations and the other breeds. The Barb and Arab-Barb breeds seem to be the most genetically related and support the decision to consider the breeds as same population. PMID:24834806
Molecular markers reveal infestation dynamics of the bed bug (Hemiptera: Cimicidae) within apartment buildings.
Booth, Warren; Saenz, Virna L; Santangelo, Richard G; Wang, Changlu; Schal, Coby; Vargo, Edward L
The bed bug, Cimex lectularius L. (Hemiptera: Cimicidae), has experienced an extraordinary global resurgence in recent years, the reasons for which remain poorly understood. Once considered a pest of lower socioeconomic classes, bed bugs are now found extensively across all residential settings, with widespread infestations established in multiapartment buildings. Within such buildings, understanding the population genetic structure and patterns of dispersal may prove critical to the development of effective control strategies. Here, we describe the development of 24 high-resolution microsatellite markers through next generation 454 pyrosequencing and their application to elucidate infestation dynamics within three multistory apartment buildings in the United States. Results reveal contrasting characteristics potentially representative of geographic or locale differences. In Raleigh, NC, an infestation within an apartment building seemed to have started from a single introduction followed by extensive spread. In Jersey City, NJ, two or more introductions followed by spread are evident in two buildings. Populations within single apartments in all buildings were characterized by high levels of relatedness and low levels of diversity, indicative of foundation from small, genetically depauperate propagules. Regardless of the number of unique introductions, genetic data indicate that spread within buildings is extensive, supporting both active and human-mediated dispersal within and between adjacent rooms or apartments spanning multiple floors. PMID:22679860
Distribution of Mytilus taxa in European coastal areas as inferred from molecular markers
NASA Astrophysics Data System (ADS)
Kijewski, T.; ?mietanka, B.; Zbawicka, M.; Gosling, E.; Hummel, H.; Wenne, R.
The genetic constitution of mussels ( Mytilus spp.) was studied by means of three nuclear (Me 15/16, EF-bis, ITS) and one mtDNA (ND2-COIII) marker on a large European scale. In addition to a sharp cline between Atlantic and Mediterranean M. galloprovincialis, we observed a clear genetic distinction between the Black Sea and Mediterranean populations and a higher incidence of M. trossulus than reported so far in northern European populations. The frequency of M. galloprovincialis nuclear alleles was high along the Iberian Peninsula and decreased abruptly along the French coasts with a high frequency of M. edulis alleles in the Bay of Biscay, The Netherlands, Germany, Iceland, Barents and White Seas, and with little evidence of introgression between the two taxa. M. trossulus alleles were observed in the Baltic Sea and Danish Straits as expected. In addition, occurrence of M. trossulus alleles in cold waters of Iceland, Barents Sea and White Sea is reported for the first time.
Isolation and characterization of novel microsatellite markers for molecular genetic diversity in Siganus fuscescens.
Ning, Y F; Li, Z B; Li, Q H; Dai, G; Shangguan, J B; Yuan, Y; Huang, Y S
The rabbitfish Siganus fuscescens is an economically valuable species that is widely distributed throughout the estuaries, intertidal, and offshore coasts of the Indo-Pacific and eastern Mediterranean. Ten novel microsatellite loci from the genome of S. fuscescens were developed using the fast isolation protocol with amplified fragment length polymorphism of sequences containing repeats. Polymorphisms in these 10 microsatellite markers were determined from 32 wild individuals. The number of alleles per locus and the polymorphism information content ranged from 2 to 5 and from 0.059 to 0.668, respectively. The observed and expected heterozygosities varied from 0.063 to 0.781 and from 0.062 to 0.731, respectively. Although 1 locus (LZY-X7, P < 0.005) showed significant deviation from the Hardy-Weinberg equilibrium, no deviations were detected in the other 9 loci. These microsatellite loci may be useful for further population genetic studies, conservation studies, population structure assessment, and linkage map construction of S. fuscescens. PMID:25729939
Retrotransposon-based molecular markers for analysis of genetic diversity within the Genus Linum.
Melnikova, Nataliya V; Kudryavtseva, Anna V; Zelenin, Alexander V; Lakunina, Valentina A; Yurkevich, Olga Yu; Speranskaya, Anna S; Dmitriev, Alexey A; Krinitsina, Anastasia A; Belenikin, Maxim S; Uroshlev, Leonid A; Snezhkina, Anastasiya V; Sadritdinova, Asiya F; Koroban, Nadezda V; Amosova, Alexandra V; Samatadze, Tatiana E; Guzenko, Elena V; Lemesh, Valentina A; Savilova, Anastasya M; Rachinskaia, Olga A; Kishlyan, Natalya V; Rozhmina, Tatiana A; Bolsheva, Nadezhda L; Muravenko, Olga V
SSAP method was used to study the genetic diversity of 22 Linum species from sections Linum, Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons FL9 and FL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism of Fl1a, Fl1b, and Cassandra insertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation of Linum species. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sections Dasylinum, Stellerolinum, Adenolinum, and Linum. All species of sect. Adenolinum clustered apart from species of sect. Linum. The data confirmed the accuracy of the separation in these sections. Members of section Linum are not as closely related as members of other sections, so taxonomic revision of this section is desirable. L. usitatissimum accessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization of Cassandra retrotransposon in Linum species was determined. PMID:25243121
Detection of self-incompatible oilseed rape plants (Brassica napus L.) based on molecular markers for identification of the class I S haplotype
Havlícková, Lenka; Jozová, Eva; Klíma, Miroslav; Kucera, Vratislav; Curn, Vladislav
The selection of desirable genotypes with recessive characteristics, such as self-incompatible plants, is often difficult or even impossible and represents a crucial barrier in accelerating the breeding process. Molecular approaches and selection based on molecular markers can allow breeders to overcome this limitation. The use of self-incompatibility is an alternative in hybrid breeding of oilseed rape. Unfortunately, stable self-incompatibility is recessive and phenotype-based selection is very difficult and time-consuming. The development of reliable molecular markers for detecting desirable plants with functional self-incompatible genes is of great importance for breeders and allows selection at early stages of plant growth. Because most of these reliable molecular markers are based on discrimination of class I S-locus genes that are present in self-compatible plants, there is a need to use an internal control in order to detect possible PCR inhibition that gives false results during genotyping. In this study, 269 double haploid F2 oilseed rape plants obtained by microspore embryogenesis were used to verify the applicability of an improved PCR assay based on the detection of the class I SLG gene along with an internal control. Comparative analysis of the PCR genotyping results vs. S phenotype analysis confirmed the applicability of this molecular approach in hybrid breeding programs. This approach allows accurate detection of self-incompatible plants via a different amplification profile. PMID:25249779
Detection of self-incompatible oilseed rape plants (Brassica napus L.) based on molecular markers for identification of the class I S haplotype.
Havlícková, Lenka; Jozová, Eva; Klíma, Miroslav; Kucera, Vratislav; Curn, Vladislav
The selection of desirable genotypes with recessive characteristics, such as self-incompatible plants, is often difficult or even impossible and represents a crucial barrier in accelerating the breeding process. Molecular approaches and selection based on molecular markers can allow breeders to overcome this limitation. The use of self-incompatibility is an alternative in hybrid breeding of oilseed rape. Unfortunately, stable self-incompatibility is recessive and phenotype-based selection is very difficult and time-consuming. The development of reliable molecular markers for detecting desirable plants with functional self-incompatible genes is of great importance for breeders and allows selection at early stages of plant growth. Because most of these reliable molecular markers are based on discrimination of class I S-locus genes that are present in self-compatible plants, there is a need to use an internal control in order to detect possible PCR inhibition that gives false results during genotyping. In this study, 269 double haploid F2 oilseed rape plants obtained by microspore embryogenesis were used to verify the applicability of an improved PCR assay based on the detection of the class I SLG gene along with an internal control. Comparative analysis of the PCR genotyping results vs. S phenotype analysis confirmed the applicability of this molecular approach in hybrid breeding programs. This approach allows accurate detection of self-incompatible plants via a different amplification profile. PMID:25249779
A mitochondrial molecular marker, ori-rep-tra, for differentiation of yeast species.
Piskur, J; Mozina, S S; Stenderup, J; Pedersen, M B
Yeasts exhibit various mechanisms for the inheritance of their mitochondrial genomes. Differences among these mechanisms are based on variations within nuclear as well as mitochondrial genetic elements. Here we report diagnostic differences in the presence of biologically active mitochondrial intergenic sequences, ori-reptra, among related yeasts in the genera Saccharomyces, Arxiozyma, Debaryomyces, Kluyveromyces, Pachytichospora, Torulaspora, and Zygosaccharomyces. A molecular probe containing ori-rep-tra can be employed specifically for the differentiation and identification of isolates belonging to the species complex Saccharomyces sensu stricto. PMID:7618892
Molecular phylogeography of Angiostrongylus cantonensis (Nematoda: Angiostrongylidae) and genetic relationships with congeners using cytochrome b gene marker.
Yong, Hoi-Sen; Eamsobhana, Praphathip; Song, Sze-Looi; Prasartvit, Anchana; Lim, Phaik-Eem
Angiostrongylus cantonensis is an important emerging zoonotic parasite causing human eosinophilic meningitis (or meningoencephalitis) in many parts of the world. To-date there is only a single study using mitochondrial cytochrome b (CYTB) gene to determine its genetic structure in eight geographical localities in Thailand. The present study examined the molecular phylogeography of this rat lungworm and its phylogenetic relationship with congeners using CYTB gene marker. A total of 15 CYTB haplotypes was found in 37 sequences from 14 geographical localities (covering north, west, east, central and south regions) in Thailand. These CYTB haplotypes were distinct from those of A. cantonensis for China and Hawaii. In Thailand, some CYTB haplotypes appeared to be confined to specific geographical localities. The partial CYTB DNA nucleotide sequences separated unequivocally the A. cantonensis isolates of Thailand, China and Hawaii as well as the congeners Angiostrongylus malaysiensis, A. costaricensis and Angiostrongylus vasorum, with A. malaysiensis grouped with A. cantonensis and A. costaricensis grouped with A. vasorum. Likewise the congeners of Metastrongylus and Onchocerca genera could also be clearly differentiated. The present study added two new definitive hosts (Bandicota savilei and Rattus losea) and three new localities (Mae Hong Son in the north, Tak in the west, and Phang Nga in the south) for A. malaysiensis in Thailand, indicating its wide occurrence in the country. Three CYTB haplotypes were found in the Thailand samples of A. malaysiensis. In addition to differentiation of congeners, CYTB gene marker could be used for determining the genetic diversity of a given population/taxon. PMID:25930187
Advances in molecular biomarkers for gastric cancer: miRNAs as emerging novel cancer markers.
Wu, Hua-Hsi; Lin, Wen-chang; Tsai, Kuo-Wang
Carcinoma of the stomach is one of the most prevalent cancer types in the world. Although the incidence of gastric cancer is declining, the outcomes of gastric cancer patients remain dismal because of the lack of effective biomarkers to detect early gastric cancer. Modern biomedical research has explored many potential gastric cancer biomarker genes by utilising serum protein antigens, oncogenic genes or gene families through improving molecular biological technologies, such as microarray, RNA-Seq and the like. Recently, the small noncoding microRNAs (miRNAs) have been suggested to be critical regulators in the oncogenesis pathways and to serve as useful clinical biomarkers. This new class of biomarkers is emerging as a novel molecule for cancer diagnosis and prognosis, including gastric cancer. By translational suppression of target genes, miRNAs play a significant role in the gastric cancer cell physiology and tumour progression. There are potential implications of previously discovered gastric cancer molecular biomarkers and their expression modulations by respective miRNAs. Therefore, many miRNAs are found to play oncogenic roles or tumour-suppressing functions in human cancers. With the surprising stability of miRNAs in tissues, serum or other body fluids, miRNAs have emerged as a new type of cancer biomarker with immeasurable clinical potential. PMID:24456939
Comparative protein profiles: potential molecular markers from spermatozoa of Acipenseriformes (Chondrostei, Pisces).
Li, Ping; Hulak, Martin; Rodina, Marek; Sulc, Miroslav; Li, Zhi-Hua; Linhart, Otomar
Sturgeon and paddlefish (Acipenseriformes), the source of roe consumed as caviar, are a unique and commercially valuable group of ancient fishes. In this study, comparative proteomics was used to analyze protein profiles of spermatozoa from five sturgeon species and one paddlefish: Siberian sturgeon (Acipenser baerii), sterlet (A. ruthenus), Russian sturgeon (A. gueldenstaedtii), starry sturgeon (A. stellatus), beluga (Huso huso), and Mississippi paddlefish (Polyodon spathula). Protein profiles of spermatozoa were determined by isoelectric focusing and two-dimensional electrophoresis (2-DE) high-resolution gels. The peptides, previously selected by 2-DE analysis as potentially species-specific, were obtained by "in-gel" tryptic digestion, followed by matrix-associated laser desorption/ionization time-of-flight/mass spectrometry (MALDI-TOF/MS). Among the 23 protein spots selected, 14 were identified as isoforms of enolase B present in all species, but with different isoelectric points or molecular mass. Exceptions were A. ruthenus and H. huso, species with a close phylogenetic relationship. Glycerol-3-phosphate dehydrogenase was detected exclusively in P. spathula. Phosphoglycerate kinase was detected only in A. ruthenus and H. huso, and 3 additional proteins (fructose bisphosphate aldolase A-2, glycogen phosphorylase type IV and glyceraldehyde-3-phosphate dehydrogenase) were found exclusively in A. gueldenstaedtii and H. huso. This study points to the application of proteomics for differential characterization and comparative studies of acipenseriform species at the molecular level. PMID:20869341
Molecular and Contextual Markers of Hepatitis C Virus and Drug Abuse
Shapshak, Paul; Somboonwit, Charurut; Drumright, Lydia N.; Frost, Simon D.W.; Commins, Deborah; Tellinghuisen, Timothy L.; Scott, William K.; Duncan, Robert; McCoy, Clyde; Page, J. Bryan; Giunta, Brian; Fernandez, Francisco; Singer, Elyse; Levine, Andrew; Minagar, Alireza; Oluwadara, Oluwadayo; Kotila, Taiwo; Chiappelli, Francesco; Sinnott, John T.
The spread of hepatitis C virus (HCV) infection involves a complex interplay of social risks, and molecular factors of both virus and host. Injection drug abuse is the most powerful risk factor for HCV infection, followed by sexual transmission and additional non-injection drug abuse factors such as co-infection with other viruses and barriers to treatment. It is clearly important to understand the wider context in which the factors related to HCV infection occur. This understanding is required for a comprehensive approach leading to the successful prevention, diagnosis, and treatment of HCV. An additional consideration is that current treatments and advanced molecular methods are generally unavailable to socially disadvantaged patients. Thus, the recognition of behavioral/social, viral, and host factors as components of an integrated approach to HCV is important to help this vulnerable group. Equally important, this approach is key to the development of personalized patient treatment – a significant goal in global healthcare. In this review, we discuss recent findings concerning the impact of drug abuse, epidemiology, social behavior, virology, immunopathology, and genetics on HCV infection and the course of disease. PMID:19650670
Validity of the bear tapeworm Diphyllobothrium ursi (Cestoda: Diphyllobothriidae) based on morphological and molecular markers.
Yamasaki, Hiroshi; Muto, Maki; Yamada, Minoru; Arizono, Naoki; Rausch, Robert L
The bear tapeworm Diphyllobothrium ursi is described based upon the morphology of adult tapeworms recovered from the brown bear (Ursus arctos middendorffi) and larval plerocercoids found in sockeye salmon (Oncorhynchus nerka) from Kodiak Island in Alaska in 1952. However, in 1987 D. ursi was synonymized with Diphyllobothrium dendriticum, and the taxonomic relationship between both species has not subsequently been revised. In this study mitochondrial cytochrome c oxidase subunit 1 gene (cox1) sequences of holotype and paratype D. ursi specimens that had been preserved in a formalin-acetic acid-alcohol solution since the time the species was initially described approximately 60 yr ago were analyzed. Molecular and phylogenetic analysis of the cox1 sequences revealed that D. ursi is more closely related to D. dendriticum than it is to Diphyllobothrium nihonkaiense and Diphyllobothrium latum. In addition to molecular evidence, differences in the life cycle and ecology of the larval plerocercoids between D. ursi and D. dendriticum also suggest that D. ursi is a distinct species, separate from D. dendriticum and D. nihonkaiense, and also possibly from D. latum . PMID:22663179
Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers
Background Molecular typing of pathogen populations is an important tool for the development of effective strategies for disease control. Diverse molecular markers have been used to characterize populations of Xanthomonas axonopodis pv. manihotis (Xam), the main bacterial pathogen of cassava. Recently, diversity and population dynamics of Xam in the Colombian Caribbean coast were estimated using AFLPs, where populations were found to be dynamic, diverse and with haplotypes unstable across time. Aiming to examine the current state of pathogen populations located in the Colombian Eastern Plains, we also used AFLP markers and we evaluated the usefulness of Variable Number Tandem Repeats (VNTRs) as new molecular markers for the study of Xam populations. Results The population analyses showed that AFLP and VNTR provide a detailed and congruent description of Xam populations from the Colombian Eastern Plains. These two typing strategies clearly separated strains from the Colombian Eastern Plains into distinct populations probably because of geographical distance. Although the majority of analyses were congruent between typing markers, fewer VNTRs were needed to detect a higher number of genetic populations of the pathogen as well as a higher genetic flow among sampled locations than those detected by AFLPs. Conclusions This study shows the advantages of VNTRs over AFLPs in the surveillance of pathogen populations and suggests the implementation of VNTRs in studies that involve large numbers of Xam isolates in order to obtain a more detailed overview of the pathogen to improve the strategies for disease control. PMID:24946775
New insights into family relationships within the avian superfamily Sylvioidea (Passeriformes) based on seven molecular markers
Background The circumscription of the avian superfamily Sylvioidea is a matter of long ongoing debate. While the overall inclusiveness has now been mostly agreed on and 20 families recognised, the phylogenetic relationships among the families are largely unknown. We here present a phylogenetic hypothesis for Sylvioidea based on one mitochondrial and six nuclear markers, in total ~6.3 kbp, for 79 ingroup species representing all currently recognised families and some species with uncertain affinities, making this the most comprehensive analysis of this taxon. Results The resolution, especially of the deeper nodes, is much improved compared to previous studies. However, many relationships among families remain uncertain and are in need of verification. Most families themselves are very well supported based on the total data set and also by indels. Our data do not support the inclusion of Hylia in Cettiidae, but do not strongly reject a close relationship with Cettiidae either. The genera Scotocerca and Erythrocercus are closely related to Cettiidae, but separated by relatively long internodes. The families Paridae, Remizidae and Stenostiridae clustered among the outgroup taxa and not within Sylvioidea. Conclusions Although the phylogenetic position of Hylia is uncertain, we tentatively support the recognition of the family Hyliidae Bannerman, 1923 for this genus and Pholidornis. We propose new family names for the genera Scotocerca and Erythrocercus, Scotocercidae and Erythrocercidae, respectively, rather than including these in Cettiidae, and we formally propose the name Macrosphenidae, which has been in informal use for some time. We recommend that Paridae, Remizidae and Stenostiridae are not included in Sylvioidea. We also briefly discuss the problems of providing a morphological diagnosis when proposing a new family-group name (or genus-group name) based on a clade. PMID:22920688
Identification of Barramundi (Lates calcarifer) DC-SCRIPT, a Specific Molecular Marker for Dendritic Cells in Fish
Zoccola, Emmanuelle; Delamare-Deboutteville, Jérôme; Barnes, Andrew C.
Antigen presentation is a critical step bridging innate immune recognition and specific immune memory. In mammals, the process is orchestrated by dendritic cells (DCs) in the lymphatic system, which initiate clonal proliferation of antigen-specific lymphocytes. However, fish lack a classical lymphatic system and there are currently no cellular markers for DCs in fish, thus antigen-presentation in fish is poorly understood. Recently, antigen-presenting cells similar in structure and function to mammalian DCs were identified in various fish, including rainbow trout (Oncorhynchus mykiss) and zebrafish (Danio rerio). The present study aimed to identify a potential molecular marker for DCs in fish and therefore targeted DC-SCRIPT, a well-conserved zinc finger protein that is preferentially expressed in all sub-types of human DCs. Putative dendritic cells were obtained in culture by maturation of spleen and pronephros-derived monocytes. DC-SCRIPT was identified in barramundi by homology using RACE PCR and genome walking. Specific expression of DC-SCRIPT was detected in barramundi cells by Stellaris mRNA FISH, in combination with MHCII expression when exposed to bacterial derived peptidoglycan, suggesting the presence of DCs in L. calcarifer. Moreover, morphological identification was achieved by light microscopy of cytospins prepared from these cultures. The cultured cells were morphologically similar to mammalian and trout DCs. Migration assays determined that these cells have the ability to move towards pathogens and pathogen associated molecular patterns, with a preference for peptidoglycans over lipopolysaccharides. The cells were also strongly phagocytic, engulfing bacteria and rapidly breaking them down. Barramundi DCs induced significant proliferation of responder populations of T-lymphocytes, supporting their role as antigen presenting cells. DC-SCRIPT expression in head kidney was higher 6 and 24 h following intraperitoneal challenge with peptidoglycan and lipopolysaccharide and declined after 3 days relative to PBS-injected controls. Relative expression was also lower in the spleen at 3 days post challenge but increased again at 7 days. As DC-SCRIPT is a constitutively expressed nuclear receptor, independent of immune activation, this may indicate initial migration of immature DCs from head kidney and spleen to the injection site, followed by return to the spleen for maturation and antigen presentation. DC-SCRIPT may be a valuable tool in the investigation of antigen presentation in fish and facilitate optimisation of vaccines and adjuvants for aquaculture. PMID:26173015
Molecular diversity of Enteromorpha from the coast of Yantai: a dual-marker assessment
NASA Astrophysics Data System (ADS)
Liu, Haiyan; Liu, Zhengyi; Wang, Yinchu; Zhao, Yushan; Qin, Song
We collected nine Enteromorpha specimens from the coast of Yantai and evaluated their diversity based on analyses of their ITS (internal transcribed spacer) and 5S rDNA NTS (non-transcribed spacer) sequences. The ITS sequences showed slight nucleotide divergences between Enteromorpha linza and Enteromorpha prolifera. In contrast, multiple highly variable regions were found in the ITS region of Enteromorpha flexuosa. In general, there were more variable sites in the NTS region than in the ITS region in the three species. The variations in 5S rDNA NTS sequences indicated that the molecular diversity of Enteromorpha from the coast of Yantai is very high. However, a phylogenetic tree constructed using 5S rDNA NTS sequence data indicated that genetic differences were not directly related to geographical distribution.
Toxic chemicals-induced genotoxicity detected by random amplified polymorphic DNA (RAPD) in bean (Phaseolus vulgaris L.) seedlings.
Cenkci, Süleyman; Yildiz, Mustafa; Ci?erci, Ibrahim Hakki; Konuk, Muhsin; Bozda?, Ahmet
Assessment of genotoxins-induced DNA damage and mutations at molecular level is important in eco-genotoxicology. In this research, RAPD was used to detect DNA damage in the roots and leaves of bean (Phaseolus vulgaris L.) seedlings exposed to toxic chemicals of Hg, B, Cr and Zn (HgCl(2), H(3)BO(3), K(2)Cr(2)O(7) and ZnSO(4)7H(2)O) at concentrations of 150 and 350 ppm for 7 d. Inhibition of shoot and root growth and increase of Hg, B, Cr and Zn element contents in the roots and leaves were observed with an increase in the concentration. For the RAPD analyses, 12 RAPD primers of 60-70% GC content were found to produce unique polymorphic band profiles and subsequently were used to produce a total of 120 bands of 263-3125 bp in the roots and leaves of untreated and treated seedlings. Polymorphisms became evident as disappearance and/or appearance of DNA bands in 150 and 350 ppm treatments compared with untreated control treatments. The DNA changes in RAPD profiles were more in the roots than in the leaves. The highest polymorphism was observed in boric acid treatments among the toxic chemicals. In a dendrogram constructed based on genetic similarity coefficients, the treatments were grouped into three main clusters: (a) root-B-150 ppm treatment grouped alone, (b) root-350 ppm-Hg, B, Cr and Zn treatments clustered together, and (c) the others including untreated control treatments merged together. We concluded that DNA alterations detected by RAPD analysis offered a useful biomarker assay for the evaluation of genotoxic effects of Hg, B, Cr and Zn pollutions on plants. PMID:19477479
Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers
Background The amphiploid species Brassica napus (oilseed rape, Canola) is a globally important oil crop yielding food, biofuels and industrial compounds such as lubricants and surfactants. Identification of the likely ancestors of each of the two genomes (designated A and C) found in B. napus would facilitate incorporation of novel alleles from the wider Brassica genepool in oilseed rape crop genetic improvement programmes. Knowledge of the closest extant relatives of the genotypes involved in the initial formation of B. napus would also allow further investigation of the genetic factors required for the formation of a stable amphiploid and permit the more efficient creation of fully fertile re-synthesised B. napus. We have used a combination of chloroplast and nuclear genetic markers to investigate the closest extant relatives of the original maternal progenitors of B. napus. This was based on a comprehensive sampling of the relevant genepools, including 83 accessions of A genome B. rapa L. (both wild and cultivated types), 94 accessions of B. napus and 181 accessions of C genome wild and cultivated B. oleracea L. and related species. Results Three chloroplast haplotypes occurred in B. napus. The most prevalent haplotype (found in 79% of accessions) was not present within the C genome accessions but was found at low frequencies in B. rapa. Chloroplast haplotypes characteristic of B. napus were found in a small number of wild and weedy B. rapa populations, and also in two accessions of cultivated B. rapa 'brocoletto'. Whilst introgression of the B. napus chloroplast type in the wild and weedy B. rapa populations has been proposed by other studies, the presence of this haplotype within the two brocoletto accessions is unexplained. Conclusions The distribution of chloroplast haplotypes eliminate any of the C genome species as being the maternal ancestor of the majority of the B. napus accessions. The presence of multiple chloroplast haplotypes in B. napus and B. rapa accessions was not correlated with nuclear genetic diversity as determined by AFLPs, indicating that such accessions do not represent recent hybrids. Whilst some chloroplast diversity observed within B. napus can be explained by introgression from inter-specific crosses made during crop improvement programmes, there is evidence that the original hybridisation event resulting in to B. napus occurred on more than one occasion, and involved different maternal genotypes. PMID:20350303
Molecular markers to assess short-term disease local recurrence in nasopharyngeal carcinoma
An important challenge in nasopharyngeal carcinoma (NPC) research is to develop effective predictors of tumor recurrence following treatment to determine whether immediate adjuvant therapy is necessary. We retrospectively analyzed archived specimens collected from 45 patients with paired samples of primary NPC (pNPC) and recurrent NPC (rNPC). Clinical samples were collected from the Cancer Center Databases of the First People's Hospital of Foshan and Shantou Central Hospital (affiliates of Sun Yat-Sen University) between 2001 and 2012. Expression levels of phosphor-Stat3 (p-Stat3), signalosome complex subunit 5 (Jab1/Csn5), Akt1, C/EBP homologous protein (CHOP), Ki-67, and apoptosis were determined by immunohistochemistry in pNPC and rNPC samples from the same patients. Differences in these markers between the short-term interval to recurrence (ITR) group (ITR <18 months) and long-term ITR group (ITR ?18 months) were further analyzed. In Cox's regression analysis, the ITR was significantly associated as an independent-negative prognostic factor for overall survival (hazard ratio, 0.211; 95% confidence interval, 0.053–0.841; P=0.027). p-Stat3 was increased in the short-term ITR group (ITR <18 months) and tended to be lower in the long-term ITR group (ITR ?18 months). In the short-term ITR group, nuclear Akt expression was significantly increased in paired rNPC (P=0.028). In the long-term ITR group, the expression of nuclear Jab1/Csn5 (P=0.047) and assessment of apoptosis measured with TdT-mediated dUTP nick end-labeling (TUNEL) (P=0.003) was significantly increased in paired rNPC. The results suggest that differences between short- and long-term ITR may predict outcome in rNPC. Furthermore, the overexpression of Jab1/Csn5 and Akt may contribute to the carcinogenesis of rNPC, and Akt seems to promote the progression of short-term ITR. Intra-individual changes of Jab1/Csn5, Akt, and TUNEL may help to identify short-term ITR. PMID:25607111
Sequestration of organic nitrogen in a paddy soil chronosequence as assessed by amino sugars molecular markers
NASA Astrophysics Data System (ADS)
Roth, Philipp; Lehndorff, E.; Cao, Z.; Amelung, W.
Available nitrogen is a limiting factor in paddy rice systems due to ammonia volatilization, denitrification and stabilization in organic complexes. Soil organic nitrogen (SON) might therefore constitute a critical component of the nitrogen cycle in rice systems. The objective of this study was to elucidate the role of microorganisms for the sequestration of paddy N in organic forms. For this purpose we analyzed amino sugars as markers for the residues of bacteria and fungi in a chronosequence of soils that were used for paddy rice production for a period of 0 to 2000 years in the Hangzhou bay area in Southeast China. Within the soil profile, amino sugar concentrations were generally highest in the puddled Ap horizon and decreased with increasing depth along with organic carbon concentrations regardless of the time of rice cultivation. Nevertheless, a sharp increase of total amino sugar concentration from 0.1 g kg-1 to 0.3 g kg-1 was observed in the Ah horizon when comparing tidal wetland to salt marsh that had been impoldered 30 years ago, indicating an increasing importance of microbial residues in SON stabilization following the conversion of the semiaquatic marsh to a terrestrial system. With increased time of paddy rice cropping, amino sugar concentrations continued to increase up to a maximum of 2.1 g kg-1 after 300 years of paddy cultivation but declined again to 1 g kg-1 in soils with 700-2000 years history of cultivation despite increasing organic matter accumulation. Changes in the composition of the amino sugars were also most pronounced at initial stages of paddy rice management. The proportions of glucosamine (abundant in fungal chitin) decreased during the first 50 years of cultivation relative to mainly galactosamine (abundant in bacterial gums) and muramic acid (abundant in bacterial peptidoglycan), that remained at constantly low levels. At later stages of paddy rice cultivation, the ratios of glucosamine to galactosamine and to muramic acid re-increased. We conclude that microorganisms significantly contribute to the sequestration of paddy N in organic forms during the first 300 years of cropping, within an increasing contribution of bacteria as cropping time proceeds. At even longer periods of paddy rice cultivation, there appears to be a backshift to lower concentrations of microbial residues with higher proportions of fungal N remaining.
Molecular mapping of the Pl(16) downy mildew resistance gene from HA-R4 to facilitate marker-assisted selection in sunflower.
Liu, Zhao; Gulya, Thomas J; Seiler, Gerald J; Vick, Brady A; Jan, Chao-Chien
The major genes controlling sunflower downy mildew resistance have been designated as Pl genes. Ten of the more than 20 Pl genes reported have been mapped. In this study, we report the molecular mapping of gene Pl(16) in a sunflower downy mildew differential line, HA-R4. It was mapped on the lower end of linkage group (LG) 1 of the sunflower reference map, with 12 markers covering a distance of 78.9 cM. One dominant simple sequence repeat (SSR) marker, ORS1008, co-segregated with Pl(16), and another co-dominant expressed sequence tag (EST)-SSR marker, HT636, was located 0.3 cM proximal to the Pl(16) gene. The HT636 marker was also closely linked to the Pl(13) gene in another sunflower differential line, HA-R5. Thus the Pl(16) and Pl(13) genes were mapped to a similar position on LG 1 that is different from the previously reported Pl(14) gene. When the co-segregating and tightly linked markers for the Pl(16) gene were applied to other germplasms or hybrids, a unique band pattern for the ORS1008 marker was detected in HA-R4 and HA-R5 and their F(1) hybrids. This is the first report to provide two tightly linked markers for both the Pl(16) and Pl(13) genes, which will facilitate marker-assisted selection in sunflower resistance breeding, and provide a basis for the cloning of these genes. PMID:22350177
Processes Underpinning Development and Maintenance of Diversity in Rice in West Africa: Evidence from Combining Morphological and Molecular Markers
Maat, Harro; Richards, Paul; Struik, Paul C.
We assessed the interplay of artificial and natural selection in rice adaptation in low-input farming systems in West Africa. Using 20 morphological traits and 176 molecular markers, 182 farmer varieties of rice (Oryza spp.) from 6 West African countries were characterized. Principal component analysis showed that the four botanical groups (Oryza sativa ssp. indica, O. sativa ssp. japonica, O. glaberrima, and interspecific farmer hybrids) exhibited different patterns of morphological diversity. Regarding O. glaberrima, morphological and molecular data were in greater conformity than for the other botanical groups. A clear difference in morphological features was observed between O. glaberrima rices from the Togo hills and those from the Upper Guinea Coast, and among O. glaberrima rices from the Upper Guinea Coast. For the other three groups such clear patterns were not observed. We argue that this is because genetic diversity is shaped by different environmental and socio-cultural selection pressures. For O. glaberrima, recent socio-cultural selection pressures seemed to restrict genetic diversity while this was not observed for the other botanical groups. We also show that O. glaberrima still plays an important role in the selection practices of farmers and resulting variety development pathways. This is particularly apparent in the case of interspecific farmer hybrids where a relationship was found between pericarp colour, panicle attitude and genetic diversity. Farmer varieties are the product of long and complex trajectories of selection governed by local human agency. In effect, rice varieties have emerged that are adapted to West African farming conditions through genotype × environment × society interactions. The diversity farmers maintain in their rice varieties is understood to be part of a risk-spreading strategy that also facilitates successful and often serendipitous variety innovations. We advocate, therefore, that farmers and farmer varieties should be more effectively involved in crop development. PMID:24465809
Technology Transfer Automated Retrieval System (TEKTRAN)
For bean rust, as with most host/hypervariable pathogen interactions, co-evolution of numerous resistance genes and pathotypes has transpired. Nine named and four undefined rust resistance genes have been tagged with RAPD or SCAR markers. The markers can be used for indirect selection and to facili...
Molecular classification of prostate cancer progression: foundation for marker-driven treatment of prostate cancer.
Logothetis, Christopher J; Gallick, Gary E; Maity, Sankar N; Kim, Jeri; Aparicio, Ana; Efstathiou, Eleni; Lin, Sue-Hwa
Recently, many therapeutic agents for prostate cancer have been approved that target the androgen receptor and/or the prostate tumor microenvironment. Each of these therapies has modestly increased patient survival. A better understanding of when in the course of prostate cancer progression specific therapies should be applied, and of what biomarkers would indicate when resistance arises, would almost certainly improve survival due to these therapies. Thus, applying the armamentarium of therapeutic agents in the right sequences in the right combination at the right time is a major goal in prostate cancer treatment. For this to occur, an understanding of prostate cancer evolution during progression is required. In this review, we discuss the current understanding of prostate cancer progression, but challenge the prevailing view by proposing a new model of prostate cancer progression, with the goal of improving biologic classification and treatment strategies. We use this model to discuss how integrating clinical and basic understanding of prostate cancer will lead to better implementation of molecularly targeted therapeutics and improve patient survival. PMID:23811619
Molecular Classification of Prostate Cancer Progression: Foundation for Marker driven-Treatment of Prostate Cancer
Logothetis, Christopher J; Gallick, Gary E.; Maity, Sankar N.; Kim, Jeri; Aparicio, Ana; Efstathiou, Eleni; Lin, Sue-Hwa
Recently, many therapeutic agents for prostate cancer (PCa) have been approved that target the androgen receptor and/or the prostate tumor microenvironment. Each of these therapies has modestly increased patient survival. However, if a better understanding as to when in the course of PCa progression specific therapies should be applied, and what biomarkers would indicate when resistance arises, survival due to these therapies would almost certainly improve. Thus, applying the armamentarium of therapeutic agents in the right sequences in the right combination at the right time is a major goal in prostate cancer treatment. For this to occur, an understanding of prostate cancer evolution during progression is required. In this review, we discuss the current understanding of PCa progression, but challenge the prevailing view by proposing a new model of PCa progression, with the goal of improving biologic classification and treatment strategies. We use this model to discuss how integrating clinical and basic understanding of PCa will lead to better implementation of molecularly-targeted therapeutics and improve patient survival. PMID:23811619
Molecular characterization of Platonia insignis Mart. ("bacurizeiro") using inter simple sequence repeat (ISSR) markers.
Souza, I G B; Souza, V A B; Lima, P S C
Platonia insignis Mart. (Clusiaceae) is widespread throughout the Amazon and adjacent areas. The fruits (known locally as "bacuri") have significant commercial potential, but the species is under threat from agro-industrial expansion. The genetic variability within 72 genotypes of P. insignis belonging to ten populations collected in the Brazilian states of Maranhăo and Piauí, and maintained in the germplasm collection of Embrapa Meio-Norte, has been determined, and the organization of genetic diversity within populations, between populations and among geographic groups verified. Eighteen selected inter simple sequence repeat primers allowed amplification of 236 loci of which 221 (93.64%) were polymorphic, indicating a high level of genetic diversity. At the population level, the Shannon and Nei diversity indices ranged from 0.082 to 0.323 and from 0.120 to 0.480, respectively. The global coefficient of genetic differentiation (G(ST)) was 0.4730 indicating that differentiation between populations was significant, a finding that was confirmed by analysis of molecular variance (?(ST) = 0.28). UPGMA cluster analysis revealed that the genotypes could be stratified into groups that were well defined and consistent with those identified in the dendrogram constructed using pair wise ?(ST) values. The high genetic diversity established in this study may facilitate the management and conservation of the germplasm of P. insignis. PMID:23275206
Postallogeneic monitoring with molecular markers detected by pretransplant next-generation or Sanger sequencing predicts clinical relapse in patients with myelodysplastic/myeloproliferative neoplasms.
Fu, Yuewen; Schroeder, Thomas; Zabelina, Tatjana; Badbaran, Anita; Bacher, Ulrike; Kobbe, Guido; Ayuk, Francis; Wolschke, Christine; Schnittger, Susanne; Kohlmann, Alexander; Haferlach, Torsten; Kröger, Nicolaus
Relapse is the major cause of treatment failure after allogeneic stem-cell transplantation (AHSCT) for patients with myelodysplastic syndrome/myeloproliferative syndrome neoplasms (MDS/MPN). We evaluated the impact of molecular mutations on outcome and the value of molecular monitoring post-transplantation. We screened 45 patients with chronic myelomonocytic leukemia (n = 39 patients, including seven with transformed-acute myeloid leukemia), MDS/MPN unclassifiable (n = 5), and atypical BCR-ABL1-negative CML (n = 1) for mutations in ASXL1, CBL, NRAS, and TET2 genes by molecular genetics including a sensitive next-generation sequencing (NGS) technique. In 36 patients, sufficient DNA was available for molecular analyses. In particular, TET2 and CBL mutations were screened applying amplicon deep sequencing. In 89% of cases, at least one mutation could be detected: ASXL1: n = 18 (50%); CBL: n = 7 (19%); TET2: n = 15 (42%); and NRAS: n = 11 (32%). Survival after AHSCT at 5 yr was 46% (95% CI 28-64%) and was not influenced by any mutation. After a median of 6 months after AHSCT in 33% of the patients, one of the molecular markers was still detectable, resulting in a higher incidence of relapse than in patients with undetectable mutations (50% vs. 15%, P = 0.04). In conclusion, pretransplant molecular mutation analysis can help to detect biomarkers in patients with MPN/MDS, which may be subsequently used as minimal residual disease markers after AHSCT. PMID:24164563
Molecular Markers in Sex Hormone Pathway Genes Associated with the Efficacy of Androgen-Deprivation Therapy for Prostate Cancer
Yu, Chia-Cheng; Huang, Shu-Pin; Lee, Yung-Chin; Huang, Chao-Yuan; Liu, Chia-Chu; Hour, Tzyh-Chyuan; Huang, Chun-Nung; You, Bang-Jau; Chang, Ta-Yuan; Huang, Chun-Hsiung; Bao, Bo-Ying
Although most advanced prostate cancer patients respond to androgen-deprivation therapy (ADT), the efficacy is widely variable. We investigated whether the host genetic variations in sex hormone pathway genes are associated with the efficacy of ADT. A cohort of 645 patients with advanced prostate cancer treated with ADT was genotyped for 18 polymorphisms across 12 key genes involved in androgen and estrogen metabolism. We found that after adjusting for known risk factors in multivariate Cox regression models, AKR1C3 rs12529 and AR-CAG repeat length remained significantly associated with prostate cancer-specific mortality (PCSM) after ADT (P?0.041). Furthermore, individuals carrying two unfavorable genotypes at these loci presented a 13.7-fold increased risk of PCSM compared with individuals carrying zero (P<0.001). Our results identify two candidate molecular markers in key genes of androgen and estrogen pathways associated with PCSM after ADT, establishing the role of pharmacogenomics in this therapy. PMID:23359804
Identification of Ty1-copia retrotransposons in three ectomycorrhizal basidiomycetes: evolutionary relationships and use as molecular markers.
Díez, Jesús; Béguiristain, Thierry; Le Tacon, François; Casacuberta, Josep M; Tagu, Denis
We amplified by PCR and sequenced 46 partial Ty1- copia reverse transcriptase (RT) sequences from the ectomycorrhizal basidiomycetes Pisolithus and Laccaria bicolor and the host tree Eucalyptus globulus. Phylogenetic analyses indicated that these sequences represent a new class of Ty1- copia RT, characteristic of basidiomycetes but related to plant Ty1- copia retrotransposons. To generate fingerprints of L. bicolor strains, outward facing PCR primers annealing to RTs were designed. This method, which is a modification of the inter-retrotransposon amplified polymorphism (IRAP) analysis, enables the detection of polymorphisms or changes within the insertion sites of Ty1- copia elements in the genome. Using this method, we investigated whether the transposition of Ty1- copia elements was related to the somaclonal variation observed in L. bicolor S238, an inoculant strain used in French Douglas-fir plantations. Data indicated that no differences in the IRAP fingerprints were detected in phenotypic variants of L. bicolor S238. We reported here for the first time the presence of Ty1- copia retrotransposon sequences in basidiomycetes, which resulted in suitable targets for developing new molecular markers. PMID:12684843
Predictive molecular markers of response to epidermal growth factor receptor(EGFR) family-targeted therapies.
Barton, Sarah; Starling, Naureen; Swanton, Charles
Constitutive activation of the EGFR/RAS/PI3K cell-signaling pathway that may occur through molecular aberrations in core pathway components occurs in many solid tumours, including colorectal cancer(CRC), non-small-cell lung cancer(NSCLC) and breast cancer. Predictive biomarkers of response to therapeutics targeting this pathway are necessary to select patients more likely to respond, and importantly, to avoid treating patients likely to suffer a worse outcome with therapy compared to standard of care. Determination of EGFR by immunohistochemistry(IHC) is not strongly predictive of response to EGFR-targeted therapy in CRC and NSCLC. EGFR gene mutations in the tyrosine kinase(TK) binding domain are predictive of response to EGFR tyrosine kinase inhibitors(TKIs) in NSCLC, and the acquisition of a point mutation in a gene encoding an amino acid in an adjacent area, T790M, is predictive of resistance. However, novel irreversible EGFR inhibitors such as BIBW-2992 and HKI-272 may retain activity in tumours with T790M mutations. It is well established in CRC that mutations in KRAS are predictive of resistance to EGFR pathway inhibition, and may predict for a poorer outcome with therapy. Other potentially useful biomarkers of resistance to EGFR-targeted therapy in the process of clinical validation include mutations in BRAF, PTEN loss and PI3KCA mutations, nuclear factor-kappa beta(NF-??) pathway activity, and expression of alternative EGFR ligands. Functional genomics elucidation of drug resistance pathways using RNA interference (RNAi) techniques may provide novel therapeutic approaches in disease resistant to EGFR pathway targeting and accelerate predictive biomarker development. PMID:20718710
Evaluation of the RAPD profiles from different body parts of Euglossa pleosticta Dressler male bees (Hymenoptera: Apidae, Euglossina).
Pascual, Amália N T; Suzuki, Karen M; Almeida, Fernanda S; Sodré, Leda M K; Sofia, Silvia H
In the current literature, information is scarce on which part of the adult insect body is suitable for isolation of genomic DNA for genetic analysis based on DNA-markers. In this study, we evaluated RAPD profiles generated from total genomic DNA isolated from distinct body parts (head, legs, thorax + wings and abdomen) of 12 males of Euglossa pleosticta Dressler. From the total of bands analyzed, 9.0% did not show reproducibility. Percent variations of bands in each body segment were: 1.1% (head); 0.4% (legs); 0.8% (thorax/wings) and 6.7% (abdomen). The much higher variation (chi2(one sample) = 10.27; df = 1; P < 0.01) in the RAPD profiles obtained by using DNA isolated from abdomen of the euglossine males suggests that this body part of adult insects should be avoided in DNA extraction procedures. Conversely, the low variation among the RAPD profiles obtained from amplifications of genomic DNA extracted from head, legs and thorax/wings indicates that all these body parts of male bees are equally useful and secure for using in isolation and amplification procedures of total genomic DNA. PMID:17273713
Occurrence and suitability of pharmaceuticals and personal care products as molecular markers for raw wastewater contamination in surface water and groundwater.
Tran, Ngoc Han; Li, Jinhua; Hu, Jiangyong; Ong, Say Leong
This study aimed to provide the first and comprehensive data on the occurrence of 17 target pharmaceuticals and personal care products (PPCPs) in urban water environment in Singapore. Meanwhile, this study also verified the suitability of these PPCPs as specific markers of raw wastewater contamination in receiving water bodies in highly urbanized areas where both surface water and groundwater are not impacted by the discharge of treated wastewater effluents. Analytical results of wastewater showed that among 17 target PPCPs examined, only 5 PPCPs were detected in 100 % of raw wastewater samples, including acetaminophen (ACT), carbamazepine (CBZ), caffeine (CF), diethyltoluamide (DEET), and salicylic acid (SA). Similarly, these PPCPs were found in most surface water and groundwater. Interestingly, the three PPCPs (ACT, CBZ, and SA) were only detected in surface water and groundwater in the sampling sites close to relatively older sewer systems, while they were absent in background samples that were collected from the catchment with no known wastewater sources. This suggests that ACT, CBZ, and SA can be used as specific molecular markers of raw wastewater in surface water and groundwater. This study also confirmed that CF and DEET were not really associated with wastewater sources, thus cannot serve well as specific molecular markers of wastewater contamination in receiving water bodies. To the best knowledge of the authors, the use of ACT and SA as specific molecular markers of raw wastewater contamination in urban surface waters and groundwater was first reported. Further studies on the use of ACT, CBZ, and SA along with other chemical/microbial markers are recommended to identify and differentiate contamination sources of surface waters/groundwater. PMID:24352549
Functional markers based molecular characterization and cloning of resistance gene analogs encoding NBS-LRR disease resistance proteins in finger millet (Eleusine coracana).
Panwar, Preety; Jha, Anand Kumar; Pandey, P K; Gupta, Arun K; Kumar, Anil
Magnaporthe grisea, the blast fungus is one of the main pathological threats to finger millet crop worldwide. A systematic search for the blast resistance gene analogs was carried out, using functional molecular markers. Three-fourths of the recognition-dependent disease resistance genes (R-genes) identified in plants encodes nucleotide binding site (NBS) leucine-rich repeat (LRR) proteins. NBS-LRR homologs have only been isolated on a limited scale from Eleusine coracana. Genomic DNA sequences sharing homology with NBS region of resistance gene analogs were isolated and characterized from resistant genotypes of finger millet using PCR based approach with primers designed from conserved regions of NBS domain. Attempts were made to identify molecular markers linked to the resistance gene and to differentiate the resistant bulk from the susceptible bulk. A total of 9 NBS-LRR and 11 EST-SSR markers generated 75.6 and 73.5% polymorphism respectively amongst 73 finger millet genotypes. NBS-5, NBS-9, NBS-3 and EST-SSR-04 markers showed a clear polymorphism which differentiated resistant genotypes from susceptible genotypes. By comparing the banding pattern of different resistant and susceptible genotypes, five DNA amplifications of NBS and EST-SSR primers (NBS-05(504,) NBS-09(711), NBS-07(688), NBS-03(509) and EST-SSR-04(241)) were identified as markers for the blast resistance in resistant genotypes. Principal coordinate plot and UPGMA analysis formed similar groups of the genotypes and placed most of the resistant genotypes together showing a high level of genetic relatedness and the susceptible genotypes were placed in different groups on the basis of differential disease score. Our results provided a clue for the cloning of finger millet blast resistance gene analogs which not only facilitate the process of plant breeding but also molecular characterization of blast resistance gene analogs from Eleusine coracana. PMID:21116864
Combining charcoal sediment and molecular markers to infer a Holocene fire history in the Maya lowlands of Petén, Guatemala
NASA Astrophysics Data System (ADS)
Kirchgeorg, Torben; Schüpbach, Simon; Colombaroli, Daniele; Beffa, Giorgia; Radaelli, Marta; Kehrwald, Natalie; Barbante, Carlo
Holocene vegetation changes in the Maya Lowlands during the Holocene are a result of changing climate conditions, solely anthropogenic activities, or interactions of both factors. As a consequence, it is difficult to assess how tropical ecosystems will cope with projected changes in precipitation and land-use intensification over the next decades. We investigated the role of fire during the Holocene by combining different proxies. We distinguished between three different morphotypes (grass, wood and leaves) in macroscopic charcoal. We also determined the molecular fire proxies levoglucosan, mannosan and galactosan. Combining these different fire proxies allows a more robust understanding of the complex history of fire regimes at different spatial scales during the Holocene. Comparing the two biomass burning proxies may help increase our understanding about advantages and limitations of molecular markers as proxies for past fire reconstruction in lake sediments. In order to infer changes in past biomass burning, we analysed a lake sediment core from Lake Petén Itzá, Guatemala (17°00'N, 89°50'W, 110 m above sea level), and compared our results with millennial-scale vegetation and climate change data available in this area. Some differences were observed between the two records and we assumed that while macroscopic charcoal represents a local fire signal, the molecular fire proxies records seem to be influenced by regional to supra-regional fire or low temperature fires. During the Holocene we detected three periods of high fire activity: 9500-6000 cal yr BP, 3800 cal yr BP and 2700 cal yr BP. We attributed the first maximum (9500-6000 cal yr BP) to only climate conditions, which corresponds with observations from previous studies in this region. The fast decrease in the relative abundance of woody charcoal to grass charcoal at the 3800 cal yr BP fire maximum may result from human activity, but we cannot exclude that this shift was related to climate conditions during this period. The last maximum (2700 cal yr BP) we attribute to the agricultural activity of the Maya at Lake Petén Itzá.
Identification and sequence characterisation of molecular markers polymorphic between male kiwifruit ( Actinidia chinensis var. deliciosa (A. Chev.) A. Chev.) accessions exhibiting different flowering time
Marina Novo; Silvia Romo; Manuel Rey; María Jesús Prado; María Victoria González
Fruit set in kiwifruit is strongly dependent on pollination, which is limited by the lack of efficient male pollen donors,\\u000a among other factors. We searched for molecular markers that could be polymorphic in relation to flowering time in order to\\u000a classify male kiwifruit plants to discard those that are not likely to perform as efficient pollen donors. Random amplified\\u000a polymorphic
Identification and confirmation of molecular markers and orange flesh color associated with major QTL for high beta-carotene content in muskmelon
Napier, Alexandra Bamberger
IDENTIFICATION AND CONFIRMATION OF MOLECULAR MARKERS AND ORANGE FLESH COLOR ASSOCIATED WITH MAJOR QTL FOR HIGH BETA-CAROTENE CONTENT IN MUSKMELON A Thesis by ALEXANDRA BAMBERGER NAPIER Submitted to the Office of Graduate... COLOR ASSOCIATED WITH MAJOR QTL FOR HIGH BETA-CAROTENE CONTENT IN MUSKMELON A Thesis by ALEXANDRA BAMBERGER NAPIER Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment...
Molecular Characterization of c-Abl\\/c-Src Kinase Inhibitors Targeted against Murine Tumour Progenitor Cells that Express Stem Cell Markers
Thomas Kruewel; Silvia Schenone; Marco Radi; Giovanni Maga; Astrid Rohrbeck; Maurizio Botta; Juergen Borlak; Maria A. Deli
BackgroundThe non-receptor tyrosine kinases c-Abl and c-Src are overexpressed in various solid human tumours. Inhibition of their hyperactivity represents a molecular rationale in the combat of cancerous diseases. Here we examined the effects of a new family of pyrazolo [3,4-d] pyrimidines on a panel of 11 different murine lung tumour progenitor cell lines, that express stem cell markers, as well