text:
@article {savory2018correction, title = {Correction: Evolutionary transitions between beneficial and phytopathogenic rhodococcus challenge disease management}, journal = {eLife}, volume = {7}, year = {2018}, pages = {e36350}, author = {Savory, Elizabeth A and Fuller, Skylar L and Weisberg, Alexandra J and Thomas, William J and Gordon, Michael I and Stevens, Danielle M and Creason, Allison L and Belcher, Michael S and Serdani, Maryna and Wiseman, Michele S and others} } @article {Davise01280-18, title = {Evolution of the U.S. Biological Select Agent Rathayibacter toxicus}, journal = {mBio}, volume = {9}, year = {2018}, abstract = {Rathayibacter toxicus is a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution of R.~toxicus to explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy of Rathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequenced Rathayibacter genomes indicated that Rathayibacter forms nine species-level groups. R.~toxicus is the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover, R.~toxicus has low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates. R.~toxicus is the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of the R.~toxicus species.IMPORTANCE Rathayibacter toxicus is a toxin-producing species found in Australia and is often fatal to grazing animals. The threat of introduction of the species into the United States led to its inclusion in the Federal Select Agent Program, which makes R.~toxicus a highly regulated species. This work provides novel insights into the evolution of R.~toxicus. R.~toxicus is the only species in the genus to have acquired a CRISPR adaptive immune system to protect against bacteriophages. Results suggest that coexistence with the bacteriophage NCPPB3778 led to the massive shrinkage of the R.~toxicus genome, species divergence, and the maintenance of low genetic diversity in extant bacterial groups. This work contributes to an understanding of the evolution and ecology of an agriculturally important species of bacteria.}, doi = {10.1128/mBio.01280-18}, url = {https://mbio.asm.org/content/9/4/e01280-18}, author = {Davis, Edward W. and Tabima, Javier F. and Weisberg, Alexandra J. and Lopes, Lucas Dantas and Wiseman, Michele S. and Wiseman, Michael S. and Pupko, Tal and Belcher, Michael S. and Sechler, Aaron J. and Tancos, Matt A. and Schroeder, Brenda K. and Murray, Timothy D. and Luster, Douglas G. and Schneider, William L. and Rogers, Elizabeth E. and Andreote, Fernando D. and Gr{\"u}nwald, Niklaus J. and Putnam, Melodie L. and Chang, Jeff H.}, editor = {Vidaver, Anne K.} } @article {leboldus2017first, title = {First report of Phytophthora ramorum lineage EU1 infecting Douglas fir and grand fir in Oregon}, journal = {Plant Disease}, volume = {102}, year = {2018}, pages = {455-455}, url = {https://doi.org/10.1094/PDIS-05-17-0681-PDN}, author = {LeBoldus, JM and Sondreli, KL and Sutton, W and Reeser, P and Navarro, S and Kanaskie, A and Gr{\"u}nwald, NJ} } @article {10.3389/fgene.2018.00123, title = {Inferring Variation in Copy Number Using High Throughput Sequencing Data in R}, journal = {Frontiers in Genetics}, volume = {9}, year = {2018}, pages = {123}, abstract = {Inference of copy number variation presents a technical challenge because variant callers typically require the copy number of a genome or genomic region to be known a priori. Here we present a method to infer copy number that uses variant call format (VCF) data as input and is implemented in the R package vcfR. This method is based on the relative frequency of each allele (in both genic and non-genic regions) sequenced at heterozygous positions throughout a genome. These heterozygous positions are summarized by using arbitrarily sized windows of heterozygous positions, binning the allele frequencies, and selecting the bin with the greatest abundance of positions. This provides a non-parametric summary of the frequency that alleles were sequenced at. The method is applicable to organisms that have reference genomes that consist of full chromosomes or sub-chromosomal contigs. In contrast to other software designed to detect copy number variation, our method does not rely on an assumption of base ploidy, but instead infers it. We validated these approaches with the model system of Saccharomyces cerevisiae and applied it to the oomycete Phytophthora infestans, both known to vary in copy number. This functionality has been incorporated into the current release of the R package vcfR to provide modular and flexible methods to investigate copy number variation in genomic projects.}, issn = {1664-8021}, doi = {10.3389/fgene.2018.00123}, url = {https://www.frontiersin.org/article/10.3389/fgene.2018.00123}, author = {Knaus, Brian J. and Gr{\"u}nwald, Niklaus J.} } @article {tabima2018populations, title = {Populations of Phytophthora rubi Show Little Differentiation and High Rates of Migration Among States in the Western United States}, journal = {Molecular Plant-Microbe Interactions}, volume = {31}, year = {2018}, pages = {614{\textendash}622}, author = {Tabima, Javier F and Coffey, Michael D and Zazada, Inga A and Gr{\"u}nwald, Niklaus J} } @article {arsenault2018stable, title = {Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates}, journal = {BMC biology}, volume = {16}, year = {2018}, pages = {80}, author = {Arsenault-Labrecque, Genevi{\`e}ve and Sonah, Humira and Lebreton, Amandine and Labb{\'e}, Caroline and Marchand, Genevi{\`e}ve and Xue, Allen and Belzile, Fran{\c c}ois and Knaus, Brian J and Gr{\"u}nwald, Niklaus J and B{\'e}langer, Richard R} } @article { 10.12688/f1000research.14013.1, title = {Taxa: An R package implementing data standards and methods for taxonomic data [version 1; referees: awaiting peer review]}, journal = {F1000Research}, volume = {7}, year = {2018}, doi = {10.12688/f1000research.14013.1}, author = {Foster, ZSL and Chamberlain, S and Gr{\"u}nwald, NJ} } @article {weiland2018variation, title = {Variation in disease severity caused by Phytophthora cinnamomi, P. plurivora, and Pythium cryptoirregulare on two rhododendron cultivars}, journal = {Plant Disease}, year = {2018}, author = {Weiland, Jerry E and Scagel, Carolyn R and Gr{\"u}nwald, Niklaus J and Davis, Anne and Beck, Bryan R} } @article {shakya2018variation, title = {Variation in Genetic Diversity of Phytophthora infestans Populations in Mexico from the Center of Origin Outwards}, journal = {Plant Disease}, year = {2018}, pages = {PDIS{\textendash}11}, author = {Shakya, Shankar K and Larsen, Meredith M and Cuenca-Condoy, Mercedes Mar{\'\i}a and Lozoya-Salda{\~n}a, H{\'e}ctor and Gr{\"u}nwald, Niklaus J} } @article {shakya2018variation, title = {Variation in Genetic Diversity of Phytophthora infestans Populations in Mexico from the Center of Origin Outwards}, journal = {Plant Disease}, year = {2018}, pages = {PDIS{\textendash}11}, author = {Shakya, Shankar K and Larsen, Meredith M and Cuenca-Condoy, Mercedes Mar{\'\i}a and Lozoya-Salda{\~n}a, H{\'e}ctor and Grünwald, Niklaus J} } @article {grunwald2017best, title = {Best practices for population genetic analyses}, journal = {Phytopathology}, volume = {107}, year = {2017}, pages = {1000-1010}, abstract = {Population genetic analysis is a powerful tool to understand how pathogens emerge and adapt. However, determining the genetic structure of populations requires complex knowledge on a range of subtle skills that are often not explicitly stated in book chapters or review articles on population genetics. What is a good sampling strategy? How many isolates should I sample? How do I include positive and negative controls in my molecular assays? What marker system should I use? This review will attempt to address many of these practical questions that are often not readily answered from reading books or reviews on the topic, but emerge from discussions with colleagues and from practical experience. A further complication for microbial or pathogen populations is the frequent observation of clonality or partial clonality. Clonality invariably makes analyses of population data difficult because many assumptions underlying the theory from which analysis methods were derived are often violated. This review provides practical guidance on how to navigate through the complex web of data analyses of pathogens that may violate typical population genetics assumptions. We also provide resources and examples for analysis in the R programming environment.}, doi = {10.1094/PHYTO-12-16-0425-RVW}, url = {http://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-12-16-0425-RVW}, author = {Gr{\"u}nwald, Niklaus J and Everhart, Sydney and Knaus, Brian J and Kamvar, Zhian N} } @article {kamvar2017developing, title = {Developing educational resources for population genetics in R: an open and collaborative approach}, journal = {Molecular ecology resources}, volume = {17}, year = {2017}, pages = {120{\textendash}128}, doi = {10.1111/1755-0998.12558}, url = {https://www.google.com/url?sa=t\&rct=j\&q=\&esrc=s\&source=web\&cd=1\&ved=0ahUKEwja18eZzsXTAhVM6mMKHUuxAFsQFggqMAA\&url=http\%3A\%2F\%2Fonlinelibrary.wiley.com\%2Fdoi\%2F10.1111\%2F1755-0998.12558\%2Fabstract\&usg=AFQjCNG-77dnrhUgdVDGvCF6BhYio1Cygw\&sig2=wYRzp2_tDmgQPmdX}, author = {Kamvar, Zhian N and L{\'o}pez-Uribe, Margarita M and Coughlan, Simone and Gr{\"u}nwald, Niklaus J and Lapp, Hilmar and Manel, St{\'e}phanie} } @article {10.7554/eLife.30925, title = {Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management}, journal = {eLife}, volume = {6}, year = {2017}, month = {dec}, pages = {e30925}, abstract = {Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of \textit{Rhodococcus} and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of \textit{Rhodococcus}, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial \textit{Rhodococcus} bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses.}, keywords = {evolutionary transition, horizontal gene transfer, mutualism, plant growth promoting bacteria, Rhodococcus, virulence}, issn = {2050-084X}, doi = {10.7554/eLife.30925}, url = {https://doi.org/10.7554/eLife.30925}, author = {Savory, Elizabeth A and Fuller, Skylar L and Weisberg, Alexandra J and Thomas, William J and Gordon, Michael I and Stevens, Danielle M and Creason, Allison L and Belcher, Michael S and Serdani, Maryna and Wiseman, Michele S and Gr{\"u}nwald, Niklaus J and Putnam, Melodie L and Chang, Jeff H}, editor = {Greenberg, Jean T} } @article {MEC:MEC14000, title = {High levels of diversity and population structure in the potato late blight pathogen at the Mexico centre of origin}, journal = {Molecular Ecology}, volume = {26}, year = {2017}, pages = {1091{\textendash}1107}, keywords = {Genetic Variation, invasive pathogen, oomycete, phytophthora infestans, plant pathogen, population structure, potato, toluca valley}, issn = {1365-294X}, doi = {10.1111/mec.14000}, url = {http://dx.doi.org/10.1111/mec.14000}, author = {Wang, Jianan and Fern{\'a}ndez-Pav{\'\i}a, Sylvia P. and Larsen, Meredith M. and Garay-Serrano, Edith and Gregorio-Cipriano, Rosario and Rodr{\'\i}guez-Alvarado, Gerardo and Gr{\"u}nwald, Niklaus J. and Goss, Erica M.} } @article {10.1371/journal.pcbi.1005404, title = {Metacoder: An R package for visualization and manipulation of community taxonomic diversity data}, journal = {PLOS Computational Biology}, volume = {13}, year = {2017}, month = {02}, pages = {1-15}, abstract = {Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual.}, doi = {10.1371/journal.pcbi.1005404}, url = {http://dx.doi.org/10.1371\%2Fjournal.pcbi.1005404}, author = {Foster, Zachary S. L. and Sharpton, Thomas J. and Gr{\"u}nwald, Niklaus J.} } @article {paradis2017towards, title = {Towards an integrated ecosystem of R packages for the analysis of population genetic data}, journal = {Molecular Ecology Resources}, volume = {17}, year = {2017}, pages = {1{\textendash}4}, doi = {10.1111/1755-0998.12636}, url = {http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12636/full}, author = {Paradis, Emmanuel and Gosselin, Thierry and Gr{\"u}nwald, Niklaus J and Jombart, Thibaut and Manel, St{\'e}phanie and Lapp, Hilmar} } @article {knaus2017vcfr, title = {vcfr: a package to manipulate and visualize variant call format data in R}, journal = {Molecular Ecology Resources}, volume = {17}, year = {2017}, pages = {44{\textendash}53}, doi = {10.1111/1755-0998.12549}, url = {https://www.google.com/url?sa=t\&rct=j\&q=\&esrc=s\&source=web\&cd=1\&ved=0ahUKEwjE7b23zsXTAhUmHGMKHQf3C58QFggnMAA\&url=http\%3A\%2F\%2Fonlinelibrary.wiley.com\%2Fdoi\%2F10.1111\%2F1755-0998.12549\%2Fabstract\&usg=AFQjCNGg7alswGim7txD-iWx7H7xlzK11w\&sig2=DokjVeNKV4R54-58}, author = {Knaus, Brian J and Gr{\"u}nwald, Niklaus J} } @article {tabima2017whole, title = {Whole genome sequences of the raspberry and strawberry pathogens Phytophthora rubi and P. fragariae}, journal = {bioRxiv}, year = {2017}, pages = {115824}, doi = {10.1101/115824}, url = {https://doi.org/10.1101/115824}, author = {Tabima, Javier and Kronmiller, Brent and Press, Caroline and Tyler, Brett and Zasada, Inga and Gr{\"u}nwald, Niklaus} } @article {10.3389/fpls.2016.00284, title = {Diverse evolutionary trajectories for small RNA biogenesis genes in the oomycete genus Phytophthora}, journal = {Frontiers in Plant Science}, volume = {7}, year = {2016}, chapter = {284}, abstract = {Gene regulation by small RNA pathways is ubiquitous among eukaryotes, but little is known about small RNA pathways in the Stramenopile kingdom. Phytophthora, a genus of filamentous oomycetes, contains many devastating plant pathogens, causing multibillion-dollar damage to crops, ornamental plants, and natural environments. The genomes of several oomycetes including Phytophthora species such as the soybean pathogen P. sojae, have been sequenced, allowing evolutionary analysis of small RNA-processing enzymes. This study examined the evolutionary origins of the oomycete small RNA-related genes Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) through broad phylogenetic analyses of the key domains. Two Dicer gene homologs, DCL1 and DCL2, and one RDR homolog were cloned and analyzed from P. sojae. Gene expression analysis revealed only minor changes in transcript levels among different life stages. Oomycete DCL1 homologs clustered with animal and plant Dicer homologs in evolutionary trees, whereas oomycete DCL2 homologs clustered basally to the tree along with Drosha homologs. Phylogenetic analysis of the RDR homologs confirmed a previous study that suggested the last common eukaryote ancestor possessed three RDR homologs, which were selectively retained or lost in later lineages. Our analysis clarifies the position of some Unikont and Chromalveolate RDR lineages within the tree, including oomycete homologs. Finally, we analyzed alterations in the domain structure of oomycete Dicer and RDR homologs, specifically focusing on the proposed domain transfer of the DEAD-box helicase domain from Dicer to RDR. Implications of the oomycete domain structure are discussed, and possible roles of the two oomycete Dicer homologs are proposed.}, issn = {1664-462X}, doi = {10.3389/fpls.2016.00284}, url = {http://www.frontiersin.org/plant_biotic_interactions/10.3389/fpls.2016.00284/abstract}, author = {Bollmann, Stephanie and Fang, Yufeng and Press, Caroline and Tyler, Brett Merrick and Gr{\"u}nwald, Niklaus J} } @article { ISI:000373966100062, title = {First report of the EU1 clonal lineage of Phytophthora ramorum on tanoak in an Oregon Forest.}, journal = {PLANT DISEASE}, volume = {100}, year = {2016}, month = {MAY}, pages = {1024}, type = {News Item}, issn = {0191-2917}, doi = {10.1094/PDIS-10-15-1169-PDN}, author = {Gr{\"u}nwald, N. J. and Larsen, M. M. and Kamvar, Z. N. and Reeser, P. W. and Kanaskie, A. and Laine, J. and Wiese, R.} } @article {10.7717/peerj.2222, title = {Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria}, journal = {PeerJ}, volume = {4}, year = {2016}, pages = {e2222}, abstract = {Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution for accurate pathogen identification, but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to \textit{Agrobacterium}, \textit{Pseudomonas savastanoi}, \textit{Pantoea agglomerans}, and \textit{Rhodococcus}. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.}, keywords = {Agrobacterium, Average nucleotide identity, Genomes, Molecular diagnostics, Multilocus sequence analysis, Rhodococcus, taxonomy}, issn = {2167-8359}, doi = {10.7717/peerj.2222}, url = {https://doi.org/10.7717/peerj.2222}, author = {Davis, Edward W. and Weisberg, Alexandra J. and Tabima, Javier F. and Gr{\"u}nwald, Niklaus J. and Chang, Jeff H.} } @article {biasi2016genetic, title = {Genetic analysis of Phytophthora nicotianae populations from different hosts using microsatellite markers}, journal = {Phytopathology}, volume = {06}, year = {2016}, pages = {1006-1014}, doi = {10.1094/PHYTO-11-15-0299-R}, url = {http://dx.doi.org/10.1094/PHYTO-11-15-0299-R}, author = {Biasi, Antonio and Martin, Frank N and Cacciola, Santa O and Magnano di San Lio, Gaetano and Gr{\"u}nwald, Niklaus J and Schena, Leonardo} } @article {10.1371/journal.pone.0165690, title = {Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology}, journal = {PLOS ONE}, volume = {11}, year = {2016}, month = {11}, pages = {1-22}, abstract = {Genotyping-by-sequencing (GBS) was performed on 257 Phytophthora infestans isolates belonging to four clonal lineages to study within-lineage diversity. The four lineages used in the study were US-8 (n = 28), US-11 (n = 27), US-23 (n = 166), and US-24 (n = 36), with isolates originating from 23 of the United States and Ontario, Canada. The majority of isolates were collected between 2010 and 2014 (94\%), with the remaining isolates collected from 1994 to 2009, and 2015. Between 3,774 and 5,070 single-nucleotide polymorphisms (SNPs) were identified within each lineage and were used to investigate relationships among individuals. K-means hierarchical clustering revealed three clusters within lineage US-23, with US-23 isolates clustering more by collection year than by geographic origin. K-means hierarchical clustering did not reveal significant clustering within the smaller US-8, US-11, and US-24 data sets. Neighbor-joining (NJ) trees were also constructed for each lineage. All four NJ trees revealed evidence for pathogen dispersal and overwintering within regions, as well as long-distance pathogen transport across regions. In the US-23 NJ tree, grouping by year was more prominent than grouping by region, which indicates the importance of long-distance pathogen transport as a source of initial late blight inoculum. Our results support previous studies that found significant genetic diversity within clonal lineages of P. infestans and show that GBS offers sufficiently high resolution to detect sub-structuring within clonal populations.}, doi = {10.1371/journal.pone.0165690}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0165690}, author = {Hansen, Zachariah R. and Everts, Kathryne L. and Fry, William E. and Gevens, Amanda J. and Gr{\"u}nwald, Niklaus J. and Gugino, Beth K. and Johnson, Dennis A. and Johnson, Steven B. and Judelson, Howard S. and Knaus, Brian J. and McGrath, Margaret T. and Myers, Kevin L. and Ristaino, Jean B. and Roberts, Pamela D. and Secor, Gary A. and Smart, Christine D.} } @article {knaus2016genomic, title = {Genomic Analyses of Dominant US Clonal Lineages of Phytophthora infestans Reveals a Shared Common Ancestry for Clonal Lineages US11 and US18 and a Lack of Recently Shared Ancestry Among All Other US Lineages}, journal = {Phytopathology}, year = {2016}, pages = {PHYTO{\textendash}10}, doi = {10.1094/PHYTO-10-15-0279-R}, url = {http://dx.doi.org/10.1094/PHYTO-10-15-0279-R}, author = {Knaus, BJ and Tabima, JF and Davis, CE and Judelson, HS and Gr{\"u}nwald, NJ} } @article {Kasuga2016, title = {Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum}, journal = {BMC Genomics}, volume = {17}, year = {2016}, pages = {1{\textendash}17}, abstract = {Aneuploidy can result in significant phenotypic changes, which can sometimes be selectively advantageous. For example, aneuploidy confers resistance to antifungal drugs in human pathogenic fungi. Aneuploidy has also been observed in invasive fungal and oomycete plant pathogens in the field. Environments conducive to the generation of aneuploids, the underlying genetic mechanisms, and the contribution of aneuploidy to invasiveness are underexplored. We studied phenotypic diversification and associated genome changes in Phytophthora ramorum, a highly destructive oomycete pathogen with a wide host-range that causes Sudden Oak Death in western North America and Sudden Larch Death in the UK. Introduced populations of the pathogen are exclusively clonal. In California, oak (Quercus spp.) isolates obtained from trunk cankers frequently exhibit host-dependent, atypical phenotypes called non-wild type (nwt), apparently without any host-associated population differentiation. Based on a large survey of genotypes from different hosts, we previously hypothesized that the environment in oak cankers may be responsible for the observed phenotypic diversification in P. ramorum.}, issn = {1471-2164}, doi = {10.1186/s12864-016-2717-z}, url = {http://dx.doi.org/10.1186/s12864-016-2717-z}, author = {Kasuga, Takao and Bui, Mai and Bernhardt, Elizabeth and Swiecki, Tedmund and Aram, Kamyar and Cano, Liliana M. and Webber, Joan and Brasier, Clive and Press, Caroline and Gr{\"u}nwald, Niklaus J. and Rizzo, David M. and Garbelotto, Matteo} } @article {hansen2016loop, title = {Loop-Mediated Isothermal Amplification (LAMP) for Detection of the Tomato and Potato Late Blight Pathogen, Phytophthora infestans}, journal = {Journal of applied microbiology}, year = {2016}, doi = {10.1111/jam.13079}, author = {Hansen, Zachariah R and Knaus, Brian J and Tabima, Javier F and Press, Caroline M and Judelson, Howard S and Gr{\"u}nwald, Niklaus J and Smart, Christine D} } @article {foster2016metacoder, title = {MetacodeR: An R package for manipulation and heat tree visualization of community taxonomic data from metabarcoding}, journal = {bioRxiv}, year = {2016}, pages = {071019}, url = {https://doi.org/10.1101/071019}, author = {Foster, Zachary SL and Sharpton, Thomas and Gr{\"u}nwald, Niklaus J} } @article {10.7717/peerj.2279, title = {Microbe-ID: an open source toolbox for microbial genotyping and species identification}, journal = {PeerJ}, volume = {4}, year = {2016}, pages = {e2279}, abstract = {Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus \textit{Phytophthora} (phytophthora-id.org). In \textit{Phytophthora}-ID, the Sequence-ID application allows identification based on ITS or \textit{cox} spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species \textit{P. infestans} and \textit{P. ramorum}. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.}, keywords = {Genotyping, identification, Molecular diagnostics, pathogen, phytophthora, taxonomy}, issn = {2167-8359}, doi = {10.7717/peerj.2279}, url = {https://doi.org/10.7717/peerj.2279}, author = {Tabima, Javier F. and Everhart, Sydney E. and Larsen, Meredith M. and Weisberg, Alexandra J. and Kamvar, Zhian N. and Tancos, Matthew A. and Smart, Christine D. and Chang, Jeff H. and Gr{\"u}nwald, Niklaus J.} } @article {doi:10.1146/annurev-phyto-080614-115913, title = {Population Genomics of Fungal and Oomycete Pathogens}, journal = {Annual Review of Phytopathology}, volume = {54}, year = {2016}, pages = {323{\textendash}46}, abstract = {We are entering a new era in plant pathology in which whole-genome sequences of many individuals of a pathogen species are becoming readily available. Population genomics aims to discover genetic mechanisms underlying phenotypes associated with adaptive traits such as pathogenicity, virulence, fungicide resistance, and host specialization, as genome sequences or large numbers of single nucleotide polymorphisms become readily available from multiple individuals of the same species. This emerging field encompasses detailed genetic analyses of natural populations, comparative genomic analyses of closely related species, identification of genes under selection, and linkage analyses involving association studies in natural populations or segregating populations resulting from crosses. The era of pathogen population genomics will provide new opportunities and challenges, requiring new computational and analytical tools. This review focuses on conceptual and methodological issues as well as the approaches to answering questions in population genomics. The major steps start with defining relevant biological and evolutionary questions, followed by sampling, genotyping, and phenotyping, and ending in analytical methods and interpretations. We provide examples of recent applications of population genomics to fungal and oomycete plant pathogens. Expected final online publication date for the Annual Review of Phytopathology Volume 54 is August 04, 2016. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.}, doi = {10.1146/annurev-phyto-080614-115913}, url = {http://dx.doi.org/10.1146/annurev-phyto-080614-115913}, author = {Gr{\"u}nwald, Niklaus J and Bruce A. McDonald and Michael G. Milgroom} } @article {hansen2016snp, title = {SNP-Based Differentiation of Phytophthora infestans Clonal Lineages Using Locked Nucleic Acid Probes and High-Resolution Melt Analysis}, journal = {Plant Disease}, volume = {100}, year = {2016}, pages = {1297{\textendash}1306}, doi = {10.1094/PDIS-11-15-1247-RE}, url = {http://dx.doi.org/10.1094/PDIS-11-15-1247-RE}, author = {Hansen, Zachariah R and Knaus, Brian J and Tabima, Javier F and Press, Caroline M and Judelson, Howard S and Gr{\"u}nwald, Niklaus J and Smart, Christine D} } @article {Knaus041277, title = {VcfR: an R package to manipulate and visualize VCF format data}, journal = {bioRxiv}, year = {2016}, month = {2016}, abstract = {Software to call single nucleotide polymorphisms or related genetic variants has converged on the variant call format (VCF) as the output format of choice. This has created a need for tools to work with VCF files. While an increasing number of software exists to read VCF data, many only extract the genotypes without including the data associated with each genotype that describes its quality. We created the R package vcfR to address this issue. We developed a VCF file exploration tool implemented in the R language because R provides an interactive experience and an environment that is commonly used for genetic data analysis. Functions to read and write VCF files into R as well as functions to extract portions of the data and to plot summary statistics of the data are implemented. VcfR further provides the ability to visualize how various parameterizations of the data affect the results. Additional tools are included to integrate sequence (FASTA) and annotation data (GFF) for visualization of genomic regions such as chromosomes. Conversion functions translate data from the vcfR data structure to formats used by other R genetics packages. Computationally intensive functions are implemented in C++ to improve performance. Use of these tools is intended to facilitate VCF data exploration, including intuitive methods for data quality control and easy export to other R packages for further analysis. VcfR thus provides essential, novel tools currently not available in R.}, doi = {10.1111/1755-0998.12549}, url = {http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12549/full}, author = {Knaus, Brian J and Gr{\"u}nwald, Niklaus J} } @article {28343, title = {Data from: Genomic analyses of dominant US clonal lineages of Phytophthora infestans reveals recent shared ancestry for US11 and US18 and a lack of ancestry for all other lineages}, year = {2015}, publisher = {Ag Data Commons. http://dx.doi.org/10.15482/USDA.ADC/1224913}, doi = {10.15482/USDA.ADC/1224913}, url = {http://dx.doi.org/10.15482/USDA.ADC/1224913}, author = {Knaus, Brian J and Tabima, Javier F. and Judelson, Howard S. and Gr{\"u}nwald, Niklaus J.} } @article {000362386500004, title = {Diversity of Foliar Phytophthora Species on Rhododendron in Oregon Nurseries}, journal = {PLANT DISEASE}, volume = {99}, year = {2015}, month = {OCT}, pages = {1326-1332}, type = {Article}, abstract = {The genus Phytophthora contains some of the most notorious plant pathogens affecting nursery crops. Given the recent emergence of the sudden oak death pathogen Phytophthora ramorum, particularly in association with Rhododendron spp., characterization of Phytophthora communities associated with this host in nursery environments is prudent. Many taxa may present symptoms similar to P. ramorum but we do not necessarily know their identity, frequency, and importance. Here, we present a survey of Phytophthora taxa observed from seven nurseries in the U.S. state of Oregon. Incidence and diversity of Phytophthora communities differed significantly among nurseries and among seasons within nursery. The taxa P. syringae and P. plurivora were widespread and detected at most of the nurseries sampled. Nine other taxa were also detected but were found either in a single nursery or were shared among only a few nurseries. Characterization of the Phytophthora communities present in nurseries is an important step toward understanding the ecology of these organisms as well as an aid to nursery managers in determining what risks may be present when symptomatic plants are observed. This study builds on an increasing literature, which characterizes Phytophthora community structure in nurseries.}, issn = {0191-2917}, doi = {10.1094/PDIS-09-14-0964-RE}, author = {Knaus, B. J. and Fieland, V. J. and Graham, K. A. and Gr{\"u}nwald, N. J.} } @article { ISI:000360866600049, title = {First Report of Phytophthora occultans Causing Root and Collar Rot on Ceanothus, Boxwood, Rhododendron, and Other Hosts in Horticultural Nurseries in Oregon, USA}, journal = {PLANT DISEASE}, volume = {99}, year = {2015}, month = {SEP}, pages = {1282-1283}, type = {News Item}, issn = {0191-2917}, doi = {10.1094/PDIS-02-15-0156-PDN}, author = {Reeser, P. W. and Sutton, W. and Hansen, E. M. and Goheen, E. M. and Fieland, V. J. and Gr{\"u}nwald, N. J.} } @article { ISI:000360927100013, title = {Five Reasons to Consider Phytophthora infestans a Reemerging Pathogen}, journal = {PHYTOPATHOLOGY}, volume = {105}, year = {2015}, month = {JUL}, pages = {966-981}, type = {Article}, abstract = {Phytophthora infestans has been a named pathogen for well over 150 years and yet it continues to {\textquoteleft}{\textquoteleft}emerge{{\textquoteright}{\textquoteright}}, with thousands of articles published each year on it and the late blight disease that it causes. This review explores five attributes of this oomycete pathogen that maintain this constant attention. First, the historical tragedy associated with this disease (Irish potato famine) causes many people to be fascinated with the pathogen. Current technology now enables investigators to answer some questions of historical significance. Second, the devastation caused by the pathogen continues to appear in surprising new locations or with surprising new intensity. Third, populations of P. infestans worldwide are in flux, with changes that have major implications to disease management. Fourth, the genomics revolution has enabled investigators to make tremendous progress in terms of understanding the molecular biology (especially the pathogenicity) of P. infestans. Fifth, there remain many compelling unanswered questions.}, issn = {0031-949X}, doi = {10.1094/PHYTO-01-15-0005-FI}, author = {Fry, W. E. and Birch, P. R. J. and Judelson, H. S. and Gr{\"u}nwald, N. J. and Danies, G. and Everts, K. L. and Gevens, A. J. and Gugino, B. K. and Johnson, D. A. and Johnson, S. B. and McGrath, M. T. and Myers, K. L. and Ristaino, J. B. and Roberts, P. D. and Secor, G. and Smart, C. D.} } @article {saville2014fungicide, title = {Fungicide sensitivity of US genotypes of Phytophthora infestans (Mont.) de Bary to six oomycete-targeted compounds}, journal = {Plant Disease}, volume = {99}, year = {2015}, pages = {659-666}, abstract = {Phytophthora infestans causes potato late blight, an important and costly disease of potato and tomato crops. Seven clonal lineages of P. infestans identified recently in the United States were tested for baseline sensitivity to six oomycete-targeted fungicides. A subset of the dominant lineages (n = 45) collected between 2004 and 2012 was tested in vitro on media amended with a range of concentrations of either azoxystrobin, cyazofamid, cymoxanil, fluopicolide, mandipropamid, or mefenoxam. Dose-response curves and values for the effective concentration at which 50\% of growth was suppressed were calculated for each isolate. The US-8 and US-11 clonal lineages were insensitive to mefenoxam while the US-20, US-21, US-22, US-23, and US-24 clonal lineages were sensitive to mefenoxam. Insensitivity to azoxystrobin, cyazofamid, cymoxanil, fluopicolide, or mandipropamid was not detected within any lineage. Thus, current U.S. populations of P. infestans remained sensitive to mefenoxam during the displacement of the US-22 lineage by US-23 over the past 5 years.}, doi = {10.1094/PDIS-05-14-0452-RE}, url = {http://dx.doi.org/10.1094/PDIS-05-14-0452-RE}, author = {Saville, Amanda and Graham, Kimberly and Gr{\"u}nwald, Niklaus J and Myers, Kevin and Fry, William E and Ristaino, Jean Beagle} } @article { ISI:000364585600010, title = {Identification and distribution of mating-type idiomorphs in populations of Podosphaera macularis and development of chasmothecia of the fungus}, journal = {PLANT PATHOLOGY}, volume = {64}, year = {2015}, month = {OCT}, pages = {1094-1102}, type = {Article}, abstract = {Podosphaera macularis, the causal agent of hop powdery mildew, is known to produce chasmothecia (formerly cleistothecia) in eastern North America and Europe. Ascocarps have not yet been reported from the Pacific Northwestern region of North America. Reasons for the apparent absence of chasmothecia in the Pacific Northwest were unknown. This study established that P. macularis is heterothallic and ascocarp ontogeny, maturation, dehiscence and ascospore infection proceed similarly to other powdery mildew fungi. Genome sequencing of a MAT1-1 isolate revealed the structure of the MAT1 locus and presence of MAT1-1-3, demonstrating further similarities to other powdery mildew fungi. PCR assays with primers designed from conserved domains of the MAT1 idiomorphs were developed to characterize the frequency of idiomorphs in populations of P. macularis. Amongst 317 samples of P. macularis collected during 2012 and 2013 from the Pacific Northwest only the MAT1-1 idiomorph was found. In contrast, among 56 samples from the eastern United States and Europe, MAT1-1 and MAT1-2 idiomorphs were detected at equivalent frequencies. At temperatures representative of late season conditions in the Pacific Northwest, chasmothecia formed readily when a Pacific Northwest MAT1-1 isolate was paired with a MAT1-2 isolate collected from outside the region. Although these findings do not encompass all climatic, geographic or temporal barriers that could inhibit the formation of chasmothecia, the current absence of the ascigerious stage of P. macularis in the Pacific Northwest could be explained by the absence of the MAT1-2 mating type idiomorph.}, keywords = {chasmothecia, cleistothecia, hop, Humulus lupulus, Podosphaera macularis, powdery mildew}, issn = {0032-0862}, doi = {10.1111/ppa.12344}, author = {Wolfenbarger, S. N. and Twomey, M. C. and Gadoury, D. M. and Knaus, B. J. and Gr{\"u}nwald, N. J. and Gent, D. H.} } @article {PBR:PBR12287, title = {Identification of QTL controlling high levels of partial resistance to Fusarium solani f. sp. pisi in pea}, journal = {Plant Breeding}, volume = {134}, year = {2015}, pages = {446-453}, abstract = {Fusarium root rot is a common biotic restraint on pea yields, and genetic resistance is the most feasible method for improving pea production. This study was conducted to discover quantitative trait loci (QTL) controlling genetic partial resistance to Fusarium root rot caused by Fusarium solani (Mart.) Sacc. f.sp. pisi (F.R. Jones) W.C. Snyder \& H.N. Hans (Fsp). A RIL population was screened in a Fusarium root rot field disease nursery for 3{\textlnot}{\textdagger}years. Composite interval mapping was employed for QTL detection using the means of disease severity from three growing seasons. Five QTL were identified, including one QTL identified in all three years. The multiyear QTL Fsp-Ps2.1 contributed to a significant portion of the phenotypic variance (22.1{\quotesinglbase}{\"A}{\`\i}72.2\%), while a second QTL, Fsp-Ps6.1, contributed 17.3\% of the phenotypic variance. The other single growing season QTL are of additional interest as they colocate with previously reported pea{\quotesinglbase}{\"A}{\`\i}Fusarium root rot resistance QTL. QTL Fsp-Ps2.1, Fsp-Ps3.1, Fsp-4.1 and Fsp-Ps7.1 are flanked by codominant SSRs and may be useful in marker-assisted breeding of pea for high levels of partial resistance to Fsp.}, keywords = {composite interval mapping, disease resistance, Fusarium solani f. sp. pisi, MAS, pisum sativum, quantitative trait loci, RILs}, issn = {1439-0523}, doi = {10.1111/pbr.12287}, url = {http://dx.doi.org/10.1111/pbr.12287}, author = {Coyne, Clarice J. and Pilet-Nayel, Marie-Laure and McGee, Rebecca J. and Porter, Lyndon D. and Sm√Ωkal, Petr and Gr{\"u}nwald, Niklaus J.} } @article {10.3389/fgene.2015.00208, title = {Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality}, journal = {Frontiers in Genetics}, volume = {6}, year = {2015}, abstract = {To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytical tools. With the advent of high throughput sequencing technologies, obtaining genome-wide population genetic data has become easier than ever before. We previously contributed the R package poppr specifically addressing issues with analysis of clonal populations. In this paper we provide several significant extensions to poppr with a focus on large, genome-wide SNP data. Specifically, we provide several new functionalities including the new function mlg.filter to define clone boundaries allowing for inspection and definition of what is a clonal lineage, minimum spanning networks with reticulation, a sliding-window analysis of the index of association, modular bootstrapping of any genetic distance, and analyses across any level of hierarchies.}, issn = {1664-8021}, doi = {10.3389/fgene.2015.00208}, url = {http://www.frontiersin.org/plant_genetics_and_genomics/10.3389/fgene.2015.00208/abstract}, author = {Kamvar, Zhian N and Brooks, Jonah C and Gr{\"u}nwald, Niklaus J} } @article {25344, title = {Our recent experience with post-publication peer review at PubPeer}, journal = {Phytopathology NEws}, volume = {2015}, year = {2015}, pages = {43}, author = {Gr{\"u}nwald, Niklaus J} } @article {weiland2015population, title = {Population structure of Pythium irregulare, P. ultimum, and P. sylvaticum in forest nursery soils of Oregon and Washington}, journal = {Phytopathology}, volume = {105}, year = {2015}, pages = {684-694}, abstract = {Pythium species are important soilborne pathogens occurring in the forest nursery industry of the Pacific Northwest. However, little is known about their genetic diversity or population structure and it is suspected that isolates are moved among forest nurseries on seedling stock and shared field equipment. In order to address these concerns, a total of 115 isolates of three Pythium species (P. irregulare, P. sylvaticum, and P. ultimum) were examined at three forest nurseries using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. Analyses revealed distinct patterns of intraspecific variation for the three species. P. sylvaticum exhibited the most diversity, followed by P. irregulare, while substantial clonality was found in P. ultimum. For both P. irregulare and P. sylvaticum, but not P. ultimum, there was evidence for significant variation among nurseries. However, all three species also exhibited at least two distinct lineages not associated with the nursery of origin. Finally, evidence was found that certain lineages and clonal genotypes, including fungicide-resistant isolates, are shared among nurseries, indicating that pathogen movement has occurred.}, doi = {10.1094/PHYTO-05-14-0147-R}, url = {http://dx.doi.org/10.1094/PHYTO-05-14-0147-R}, author = {Weiland, Jerry and Garrido, Patricia and Kamvar, Zhian N and Espindola, Andres S and Marek, Stephen and Gr{\"u}nwald, Niklaus J and Garzon, Carla D} } @article {25344, title = {Significant improvements are coming to APS Journals}, journal = {Phytopathology NEws}, volume = {2015}, year = {2015}, pages = {44}, author = {Gr{\"u}nwald, Niklaus J and Subbarao, K. V. and Glazebrook, J and Gleason, M and Roberts, P} } @article {25291, title = {Soilborne diseases of nursery crops}, year = {2015}, month = {06/2015}, pages = {33-36}, type = {Popular press}, author = {Weiland, Jerry E and Scagel, C and Gr{\"u}nwald, Niklaus J and Fieland, Valerie J and Foster, Zachary and Santamaria, Luisa and Uribe, Gilbert} } @article {24909, title = {Spatial and temporal analysis of populations of the sudden oak death pathogen in Oregon forests}, journal = {Phytopathology}, year = {2015}, month = {2015/06/12}, pages = {PHYTO-12-14-0350-FI}, abstract = {Sudden oak death caused by the oomycete Phytophthora ramorum was first discovered in California toward the end of the 20th century and subsequently emerged on tanoak forests in Oregon before its first detection in 2001 by aerial surveys. The Oregon Department of Forestry has since monitored the epidemic and sampled symptomatic tanoak trees from 2001 to the present. Populations sampled over this period were genotyped using microsatellites and studied to infer the population genetic history. To date, only the NA1 clonal lineage is established in this region, although three lineages exist on the North American west coast. The original introduction into the Joe Hall area eventually spread to several regions: mostly north but also east and southwest. A new introduction into Hunter Creek appears to correspond to a second introduction not clustering with the early introduction. Our data are best explained by both introductions originating from nursery populations in California or Oregon and resulting from two distinct introduction events. Continued vigilance and eradication of nursery populations of P. ramorum are important to avoid further emergence and potential introduction of other clonal lineages.}, isbn = {0031-949X}, doi = {10.1094/PHYTO-12-14-0350-FI}, url = {http://dx.doi.org/10.1094/PHYTO-12-14-0350-FI}, author = {Kamvar, Z. N. and Larsen, M. M. and Kanaskie, A. M. and Hansen, E. M. and Gr{\"u}nwald, N. J.} } @article { ISI:000353344000008, title = {The Top 10 oomycete pathogens in molecular plant pathology}, journal = {MOLECULAR PLANT PATHOLOGY}, volume = {16}, year = {2015}, pages = {413-434}, type = {Review}, abstract = {Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.}, keywords = {diversity, genomics, microbiology, oomycetes plant pathology}, doi = {10.1111/mpp.12190}, author = {Kamoun, Sophien and Furzer, Oliver and Jones, Jonathan D. G. and Judelson, Howard S. and Ali, Gul Shad and Dalio, Ronaldo J. D. and Roy, Sanjoy Guha and Schena, Leonardo and Zambounis, Antonios and Panabi{\`e}res, Franck and Cahill, David and Ruocco, Michelina and Figueiredo, Andreia and Chen, Xiao-Ren and Hulvey, Jon and Stam, Remco and Lamour, Kurt and Gijzen, Mark and Tyler, Brett M. and Gr{\"u}nwald, Niklaus J. and Mukhtar, M. Shahid and Tom{\'e}, Daniel F. A. and Toer, Mahmut and Van den Ackerveken, Guido and McDowell, John and Daayf, Fouad and Fry, William E. and Lindqvist-Kreuze, Hannele and Meijer, Harold J. G. and Petre, Benjamin and Ristaino, Jean and Yoshida, Kentaro and Birch, Paul R. J. and Govers, Francine} } @article {17612, title = {An ephemeral sexual population of Phytophthora infestans in the Northeastern United States and Canada.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014}, pages = {e116354}, abstract = {
Phytophthora infestans, the causal agent of late blight disease, has been reported in North America since the mid-nineteenth century. In the United States the lack of or very limited sexual reproduction has resulted in largely clonal populations of P. infestans. In 2010 and 2011, but not in 2012 or 2013, 20 rare and diverse genotypes of P. infestans were detected in a region that centered around central New York State. The ratio of A1 to A2 mating types among these genotypes was close to the 50:50 ratio expected for sexual recombination. These genotypes were diverse at the glucose-6-phosphate isomerase locus, differed in their microsatellite profiles, showed different banding patterns in a restriction fragment length polymorphism assay using a moderately repetitive and highly polymorphic probe (RG57), were polymorphic for four different nuclear genes and differed in their sensitivity to the systemic fungicide mefenoxam. The null hypothesis of linkage equilibrium was not rejected, which suggests the population could be sexual. These new genotypes were monomorphic in their mitochondrial haplotype that was the same as US-22. Through parentage exclusion testing using microsatellite data and sequences of four nuclear genes, recent dominant lineages US-8, US-11, US-23, and US-24 were excluded as possible parents for these genotypes. Further analyses indicated that US-22 could not be eliminated as a possible parent for 14 of the 20 genotypes. We conclude that US-22 could be a parent of some, but not all, of the new genotypes found in 2010 and 2011. There were at least two other parents for this population and the genotypic characteristics of the other parents were identified.}, keywords = {Canada, DNA, Mitochondrial, Genetic Markers, Genotype, Haplotypes, Microsatellite Repeats, phytophthora infestans, Population Density, Reproduction, United States}, issn = {1932-6203}, doi = {10.1371/journal.pone.0116354}, author = {Danies, Giovanna and Myers, Kevin and Mideros, Mar{\'\i}a F and Restrepo, Silvia and Martin, Frank N and Cooke, David E L and Smart, Christine D and Ristaino, Jean B and Seaman, Abby J and Gugino, Beth K and Gr{\"u}nwald, Niklaus J and Fry, William E} } @article {16815, title = {Evolution of an Experimental Population of Phytophthora capsici in the Field.}, journal = {Phytopathology}, volume = {104}, year = {2014}, month = {2014 Oct}, pages = {1107-17}, chapter = {1107-1117}, abstract = {
Populations of the vegetable pathogen Phytophthora capsici are often highly diverse, with limited gene flow between fields. To investigate the structure of a newly established, experimental population, an uninfested research field was inoculated with two single-zoospore isolates of P. capsici in September 2008. From 2009 through 2012, \≈50 isolates of P. capsici were collected from the field each year and genotyped using five microsatellite loci. The same two isolates were also crossed in the lab. High levels of diversity were detected in the research field, with 26 to 37 unique multilocus genotypes detected each year. Through 2012, genotypic diversity did not decline and no evidence of genetic drift was observed. However, during the 2011 and 2012 growing seasons, four new alleles not present in either parental isolate were observed in the field. Selfing (but not apomixis) was observed at low frequency among in vitro progeny. In addition, evidence for loss of heterozygosity was observed in half of the in vitro progeny. These results suggest that recombination, mutation, and loss of heterozygosity can affect the genetic structure observed in P. capsici populations.}, keywords = {Alleles, Biological Evolution, Gene Flow, Genetic Variation, Genotype, Microsatellite Repeats, phytophthora, Plant Diseases}, issn = {0031-949X}, doi = {10.1094/PHYTO-12-13-0346-R}, author = {Dunn, Amara R and Bruening, Stephen R and Gr{\"u}nwald, Niklaus J and Smart, Christine D} } @article {knaus2014, title = {Excel file with PCR-RFLP patterns for identification of nursery Phytophthora spp.}, year = {2014}, month = {09}, url = {http://dx.doi.org/10.6084/m9.figshare.1153948}, author = {Knaus, Brian J and Fieland, Valerie J and Graham, Kim A and Gr{\"u}nwald, Niklaus J} } @article {Goss02062014, title = {The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes}, journal = {Proceedings of the National Academy of Sciences}, volume = {111}, year = {2014}, pages = {8791-8796 }, abstract = {Phytophthora infestans is a destructive plant pathogen best known for causing the disease that triggered the Irish potato famine and remains the most costly potato pathogen to manage worldwide. Identification of P. infestan{\textquoteright}s elusive center of origin is critical to understanding the mechanisms of repeated global emergence of this pathogen. There are two competing theories, placing the origin in either South America or in central Mexico, both of which are centers of diversity of Solanum host plants. To test these competing hypotheses, we conducted detailed phylogeographic and approximate Bayesian computation analyses, which are suitable approaches to unraveling complex demographic histories. Our analyses used microsatellite markers and sequences of four nuclear genes sampled from populations in the Andes, Mexico, and elsewhere. To infer the ancestral state, we included the closest known relatives Phytophthora phaseoli, Phytophthora mirabilis, and Phytophthora ipomoeae, as well as the interspecific hybrid Phytophthora andina. We did not find support for an Andean origin of P. infestans; rather, the sequence data suggest a Mexican origin. Our findings support the hypothesis that populations found in the Andes are descendants of the Mexican populations and reconcile previous findings of ancestral variation in the Andes. Although centers of origin are well documented as centers of evolution and diversity for numerous crop plants, the number of plant pathogens with a known geographic origin are limited. This work has important implications for our understanding of the coevolution of hosts and pathogens, as well as the harnessing of plant disease resistance to manage late blight.}, doi = {10.1073/pnas.1401884111}, url = {http://www.pnas.org/content/early/2014/05/29/1401884111.abstract}, author = {Goss, Erica M. and Tabima, Javier F. and Cooke, David E. L. and Restrepo, Silvia and Fry, William E. and Forbes, Gregory A. and Fieland, Valerie J. and Cardenas, Martha and Niklaus J. Gr{\"u}nwald} } @article {16857, title = {Knowing your Phytophthora}, number = {9}, year = {2014}, month = {09/2014}, pages = {33-35}, type = {Popular Press}, author = {Gr{\"u}nwald, Niklaus J} } @article {eyre2014lineage, title = {Lineage, temperature, and host species have interacting effects on lesion development in Phytophthora ramorum}, journal = {Plant Disease}, volume = {98}, year = {2014}, pages = { 1717-1727}, abstract = {There are four recognized clonal lineages of the pathogen Phytophthora ramorum. The two major lineages present in North America are NA1 and NA2. With a few exceptions, NA1 is found in natural forest ecosystems and nurseries, and NA2 is generally restricted to nurseries. Isolates from the NA1 and NA2 lineages were used to infect rhododendron, camellia, and California bay laurel in detached leaf assays to study the effects of lineage, temperature, and host on pathogenicity and host susceptibility. Isolates within both lineages were highly variable in their ability to form lesions on each host. There was also a tendency toward reduced lesion size in successive trials, suggesting degeneration of isolates over time. Temperature had a significant effect on lesion size, with a response that varied depending on the host and isolate. Phenotypic differences between lineages appear to be heavily influenced by the representation of isolates used, host, and temperature. The importance of temperature, host, and lineage are discussed with respect to disease management, as well as future range expansions and migrations of the pathogen.}, doi = {10.1094/PDIS-02-14-0151-RE}, url = {http://dx.doi.org/10.1094/PDIS-02-14-0151-RE}, author = {Eyre, Catherine A and Hayden, Katherine J and Kozanitas, Melina and Gr{\"u}nwald, Niklaus J and Garbelotto, Matteo} } @article { ISI:000348827600016, title = {Pathogenicity, Fungicide Resistance, and Genetic Variability of Phytophthora rubi Isolates from Raspberry (Rubus idaeus) in the Western United States}, journal = {PLANT DISEASE}, volume = {98}, year = {2014}, month = {DEC}, pages = {1702-1708}, type = {Article}, abstract = {Root rot of raspberry (Rubus idaeus), thought to be primarily caused by Phytophthora rubi, is an economically important disease in the western United States. The objectives of this study were to determine which Phytophthora species are involved in root rot, examine the efficacy of different isolation methods (cane, root, and root/soil baiting with young raspberry plants), and determine if pathogenicity, fungicide resistance, and/or genetic variation exists among P rubi isolates collected from raspberry fields in Washington, Oregon, and California. Of 275 samples, direct isolation from cane material resulted in a greater number of P rubi isolates (39\%), whereas root/soil baiting yielded the least (11\%). Sequencing of the internal transcribed spacer region of 210 of the total 597 collected Phytophthora isolates showed that all but one isolate (identified as P. bisheria) were P rubi. Results of the pathogenicity and fungicide resistance to mefenoxam comparing 14 total isolates from Washington, Oregon, and California showed that isolates were similarly virulent against red raspberry and the EC50 frequency distributions showed no significant difference. These results, combined with amplified fragment length polymorphism results show that P rubi isolates from Washington, Oregon, and California represent one large mixed population. This work provides novel insights into the isolation and biology of P rubi in western U.S. raspberry production systems.}, issn = {0191-2917}, doi = {10.1094/PDIS-11-13-1130-RE}, author = {Stewart, Jane E. and Kroese, Duncan and Tabima, Javier F. and Larsen, Meredith M. and Fieland, Valerie J. and Press, Caroline M. and Zasada, Inga A. and Gr{\"u}nwald, Niklaus J.} } @article {16816, title = {Phytophthora community structure analyses in Oregon nurseries inform systems approaches to disease management.}, journal = {Phytopathology}, volume = {104}, year = {2014}, month = {2014 Oct}, pages = {1052-62}, abstract = {
Nursery plants are important vectors for plant pathogens. Understanding what pathogens occur in nurseries in different production stages can be useful to the development of integrated systems approaches. Four horticultural nurseries in Oregon were sampled every 2 months for 4 years to determine the identity and community structure of Phytophthora spp. associated with different sources and stages in the nursery production cycle. Plants, potting media, used containers, water, greenhouse soil, and container yard substrates were systematically sampled from propagation to the field. From 674 Phytophthora isolates recovered, 28 different species or taxa were identified. The most commonly isolated species from plants were Phytophthora plurivora (33\%), P. cinnamomi (26\%), P. syringae (19\%), and P. citrophthora (11\%). From soil and gravel substrates, P. plurivora accounted for 25\% of the isolates, with P. taxon Pgchlamydo, P. cryptogea, and P. cinnamomi accounting for 18, 17, and 15\%, respectively. Five species (P. plurivora, P. syringae, P. taxon Pgchlamydo, P. gonapodyides, and P. cryptogea) were found in all nurseries. The greatest diversity of taxa occurred in irrigation water reservoirs (20 taxa), with the majority of isolates belonging to internal transcribed spacer clade 6, typically including aquatic opportunists. Nurseries differed in composition of Phytophthora communities across years, seasons, and source within the nursery. These findings suggest likely contamination hazards and target critical control points for management of Phytophthora disease using a systems approach.}, keywords = {Genetic Variation, phytophthora, Plant Diseases, Plant Leaves, Plant Roots, Plant Stems, Plants, Soil Microbiology, Water Microbiology}, issn = {0031-949X}, doi = {10.1094/PHYTO-01-14-0014-R}, author = {Parke, Jennifer L and Knaus, Brian J and Fieland, Valerie J and Lewis, Carrie and Gr{\"u}nwald, Niklaus J} } @inbook {16915, title = {Phytophthora ramorum}, booktitle = {Genomics of Plant-Associated Fungi and Oomycetes: Dicot Pathogens,}, year = {2014}, pages = {159-174}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, chapter = {8}, address = {Berlin Heidelberg}, doi = {0.1007/978-3-662-44056-8_8}, author = {Everhart, S. E. and Tabima, Javier F. and Gr{\"u}nwald, Niklaus J.} } @article {16918, title = {The plant destroyer genus Phytophthora in the 21st century}, journal = {Rev. Plant Pathol.}, volume = {6}, year = {2014}, month = {2014}, chapter = {387-412}, abstract = {The 21st century has already seen a major paradigm shift in our understanding of the biology, evolution, and genetics of the genus Phytophthora as well as the tools and approaches used to develop novel approaches for disease management. The combination of novel tools and approaches provided by the convergence of genome sequencing, computing power and novel genomic/biotechnological tools paints a promising picture of the future of Phytophthora disease management. At the same time Phytophthora pathogens continue to emerge at an accelerated rate due to increased global travel and trade. This article provides a brief review of the impact, biology and the current genome-enabled era that will characterize progress in the 21st century.}, author = {Guha-Roy, S and Gr{\"u}nwald, Niklaus J} } @article {10.7717/peerj.281, title = {Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction}, journal = {PeerJ}, volume = {2}, year = {2014}, month = {3}, pages = {e281}, abstract = {Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package *poppr* providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, *poppr* can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including *GenAlEx* formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo{\textquoteright}s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in *poppr* are also valuable to analysis of any populations. A manual with documentation and examples is provided. *Poppr* is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under resources at: http://grunwaldlab.cgrb.oregonstate.edu/.}, keywords = {Bootstrap, Bruvo{\textquoteright}s distance, Clonality, Clone correction, genotypic diversity, Hierarchy, Index of association, Minimum spanning networks, Permutation, population genetics}, issn = {2167-8359}, doi = {10.7717/peerj.281}, url = {http://dx.doi.org/10.7717/peerj.281}, author = {Kamvar, Zhian N. and Tabima, Javier F. and Niklaus J. Gr{\"u}nwald} } @article {10.1371/journal.pone.0085368, title = {Population History and Pathways of Spread of the Plant Pathogen Phytophthora plurivora}, journal = {PLoS ONE}, volume = {9}, year = {2014}, month = {01}, pages = {e85368}, abstract = {
Human activity has been shown to considerably affect the spread of dangerous pests and pathogens worldwide. Therefore, strict regulations of international trade exist for particularly harmful pathogenic organisms.
Phytophthora plant pathogens contain many hundreds of effectors potentially involved in infection of host plants. Comparative genomic analyses have shown that these effectors evolve rapidly and have been subject to recent expansions. We examined the recent sequence evolution of RXLR-class effector gene families in the sudden oak death pathogen, P. ramorum. We found that P. ramorum RXLR effectors have taken multiple evolutionary paths, including loss or gain of repeated domains, recombination or gene conversion among paralogs, and selection on point mutations. Sequencing of homologs from two subfamilies in P. ramorum{\textquoteright}s closest known relatives revealed repeated gene duplication and divergence since speciation with P. lateralis. One family showed strong signatures of recombination while the other family has evolved primarily by point mutation. Comparison of a small number of the hundreds of RXLR-class effectors across three clonal lineages of P. ramorum shows striking divergence in alleles among lineages, suggesting the potential for functional differences between lineages. Our results suggest future avenues for examination of rapidly evolving effectors in P. ramorum, including investigation of the functional and coevolutionary significance of the patterns of sequence evolution that we observed.}, doi = {10.1371/journal.pone.0079347}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0079347}, author = {Goss, Erica M. and Press, Caroline M. and Niklaus J. Gr{\"u}nwald} } @article {rooney2013first, title = {First report of camphor tree (Cinnamomum camphora) as a host of Phytophthora ramorum}, journal = {Plant Disease}, volume = {97}, year = {2013}, chapter = {1377-1377 }, abstract = {Cinnamomum camphora (Lauraceae) is an evergreen shade tree grown in many parts of the United States, including California. From 2007 to 2011, an arborist working in a residential neighborhood in Mill Valley (Marin Co.) noticed several camphor trees with branch dieback and decline. Affected trees had patchy, irregular cankers on the branches and shoot blight. Cankers were black and most had horizontal fissures. Cankers were most abundant in the inside and lower portions of the canopies. In 2011, samples sent to Bartlett Tree Laboratory tested positive for Phytophthora sp. using the Agdia ELISA Phytophthora kit (Agdia, Elkhart, IN). In February 2009 and April 2011, camphor leaf samples were collected by Sacramento Co. inspectors during an annual nursery inspection for Phytophthora ramorum and submitted to CDFA. The normally bright green leaves were reddish with small necrotic spots surrounded by green halos. Camphor samples from Marin Co. were also collected and sent to CDFA in September 2011. An organism with coralloid coenocytic hyphae, chlamydospores, and ellipsoidal semi-papillate sporangia grew on CMA-PARP (4) from both Marin and Sacramento Co. samples. Morphologically, it matched the description of P. ramorum (3). rDNA sequences of the internal transcribed spacer (ITS) region of the Marin (GenBank KC473521) and Sacramento (KC473522) isolates, amplified using primers ITS1 and ITS4 (4), were 100\% identical to P. ramorum by a BLAST query (AY038058). Microsatellite loci placed the Marin isolate in the NA1 clonal lineage, while the Sacramento isolate belonged to the NA2 lineage (2). Pathogenicity of both isolates was tested on 5 trees grown in 18.93-liter pots. Three leaves on each tree were inoculated with 6-mm agar plugs taken from the margin of 7-day-old cultures grown on V8 juice agar (V8). Leaves were wounded with a sterile pushpin and two colonized plugs of each isolate were covered with a freezer tube cap filled with sterile dH2O and attached to the leaves with a pin-curl clip (4). Three branches of the same plants were wounded and inoculated with a 3-mm colonized agar plug for each isolate and secured with Parafilm. An equal number of leaves and stems were treated with uncolonized V8 plugs as controls. Plants were sprayed with dH2O, covered in large plastic bags, and placed in a growth chamber at 18{\textdegree}C. After 4 days, the bags, caps, and plugs were removed from the leaves. Black lesions were seen 7 days after inoculation on most leaves and 10 to 14 days on inoculated branches. After 32 days, P. ramorum was isolated from leaf lesions and canker margins onto CMA-PARP. No Phytophthora spp. grew from the controls. The experiment was repeated once with similar results. Overall, leaf and stem lesions were larger with the NA2 lineage isolate than the NA1 lineage isolate, which is consistent with previous research (1). Leaf abscission was seen in 30\% of the leaves inoculated with the NA2 lineage isolate but none of the NA1 or control leaves. To our knowledge, this is the first report of P. ramorum on camphor in nursery and landscape settings. Mill Valley is known for its mild temperatures and abundant summer fog. Optimal weather conditions likely led to the spread of P. ramorum from infected neighboring forest hosts to camphor in Mill Valley, rather than from an introduction of infected nursery plants. References: (1) E. Elliott et al. For. Pathol. 41:7, 2011. (2) E. M. Goss et al. Phytopathology 101:166, 2011. (3) S. Werres et al. Mycol. Res. 105:1155, 2001. (4) L. E. Yakabe et al. Plant Dis. 93:883, 2009.}, author = {Rooney-Latham, S. and Honeycutt, E. and Ochoa, J. and Niklaus J. Gr{\"u}nwald and Blomquist, C. L.} } @article {137, title = {Fungal Planet description sheets: 154{\textendash}213}, journal = {Persoonia}, volume = {31}, year = {2013}, pages = {188{\textendash}296}, abstract = {
Novel species of microfungi described in the present study include the following from South Africa: Camarosporium aloes, Phaeococcomyces aloes and Phoma aloes from Aloe, C. psoraleae, Diaporthe psoraleae and D. psoraleae-pinnatae from Psoralea, Colletotrichum euphorbiae from Euphorbia, Coniothyrium prosopidis and Peyronellaea prosopidis from Prosopis, Diaporthe cassines from Cassine, D. diospyricola from Diospyros, Diaporthe maytenicola from Maytenus, Harknessia proteae from Protea, Neofusicoccum ursorum and N. cryptoaustrale from Eucalyptus, Ochrocladosporium adansoniae from Adansonia, Pilidium pseudoconcavum from Greyia radlkoferi, Stagonospora pseudopaludosa from Phragmites and Toxicocladosporium ficiniae from Ficinia. Several species were also described from Thailand, namely: Chaetopsina pini and C. pinicola from Pinus spp., Myrmecridium thailandicum from reed litter, Passalora pseudotithoniae from Tithonia, Pallidocercospora ventilago from Ventilago, Pyricularia bothriochloae from Bothriochloa and Sphaerulina rhododendricola from Rhododendron. Novelties from Spain include Cladophialophora multiseptata, Knufia tsunedae and Pleuroascus rectipilus from soil and Cyphellophora catalaunica from river sediments. Species from the USA include Bipolaris drechsleri from Microstegium, Calonectria blephiliae from Blephilia, Kellermania macrospora (epitype) and K. pseudoyuccigena from Yucca. Three new species are described from Mexico, namely Neophaeosphaeria agaves and K. agaves from Agave and Phytophthora ipomoeae from Ipomoea. Other African species include Calonectria mossambicensis from Eucalyptus (Mozambique), Harzia cameroonensis from an unknown creeper (Cameroon), Mastigosporella anisophylleae from Anisophyllea (Zam- bia) and Teratosphaeria terminaliae from Terminalia (Zimbabwe). Species from Europe include Auxarthron longi- sporum from forest soil (Portugal), Discosia pseudoartocreas from Tilia (Austria), Paraconiothyrium polonense and P. lycopodinum from Lycopodium (Poland) and Stachybotrys oleronensis from Iris (France). Two species of Chryso- sporium are described from Antarctica, namely C. magnasporum and C. oceanitesii. Finally, Licea xanthospora is described from Australia, Hypochnicium huinayensis from Chile and Custingophora blanchettei from Uruguay. Novel genera of Ascomycetes include Neomycosphaerella from Pseudopentameris macrantha (South Africa), and Paramycosphaerella from Brachystegia sp. (Zimbabwe). Novel hyphomycete genera include Pseudocatenomycopsis from Rothmannia (Zambia), Neopseudocercospora from Terminalia (Zambia) and Neodeightoniella from Phrag- mites (South Africa), while Dimorphiopsis from Brachystegia (Zambia) represents a novel coelomycetous genus. Furthermore, Alanphillipsia is introduced as a new genus in the Botryosphaeriaceae with four species, A. aloes, A. aloeigena and A. aloetica from Aloe spp. and A. euphorbiae from Euphorbia sp. (South Africa). A new combina- tion is also proposed for Brachysporium torulosum (Deightoniella black tip of banana) as Corynespora torulosa. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.}, author = {Crous, PW and Wingfield, MJ and Guarro, J and Cheewangkoon, R and van der Bank, M and Swart, WJ and Stchigel, AM and Cano-Lira, JF and Roux, J and Madrid, H and Damm, U and Wood, AR and Shuttleworth, LA and Hodges, CS and Munster, M and de Jes{\'u}s Y{\'a}{\~n}ez-Morales, M and Z{\'u}{\~n}iga- Estrada, L and Cruywagen, EW and de Hoog, GS and Silvera, C and Najafzadeh, J and Davison, EM and Davison, PJN and Barrett, MD and Barrett, RL and Manamgoda, DS and Minnis, AM and Kleczewski, NM and Flory, SL and Castlebury, LA and Clay, K and Hyde, KD and Ma{\'u}sse-Sitoe, SND and Shuaifei Chen, S and Lechat, C and Hairaud, M and Lesage-Meessen, L and Pawlowska, J and Wilk, M and Sliwinska-Wyrzychowska, A and Metrak, M and Wrzosek, M and Pavlic-Zupanc, D and Maleme, HM and Slippers, B and Mac Cormack, WP and Archuby, DI and Niklaus J. Gr{\"u}nwald and Teller{\'\i}a, MT and Duenas, M and Mart{\'\i}n, MP and Marincowitz, S and de Beer, ZW and Perez, CA and Gen{\'e}, J and Marin-Felix, Y and Groenewald, JZ} } @article {16757, title = {Hierarchical Analysis of Diversity, Selfing, and Genetic Differentiation in Populations of the Oomycete Aphanomyces euteiches}, year = {2013}, doi = {doi:10.6084/m9.figshare.877104}, url = {http://figshare.com/articles/Hierarchical\_Analysis\_of\_Diversity\_Selfing\_and\_Genetic\_Differentiation\_in\_Populations\_of\_the\_Oomycete\_Aphanomyces\_euteiches\_/877104}, author = {Niklaus J. Gr{\"u}nwald and Hoheisel, Gwen-Alyn} } @article { ISI:000317302300001, title = {Identification of Phytophthora species baited and isolated from forest soil and streams in northwestern Yunnan province, China}, journal = {Forest Pathology}, volume = {43}, year = {2013}, month = {APR}, pages = {87-103}, type = {Review}, abstract = {
Phytophthora species were surveyed by collecting soil samples and placing bait leaves in selected streams during JuneOctober in the years 2005, 2006 and 2010 at three sites in oak forests in Diqing Tibetan Autonomous Prefecture of NW Yunnan province, China. Seventy-three isolates of Phytophthora spp. were recovered from 135 baited leaf samples and 81 soil samples. Eight Phytophthora species were identified by observation of morphological features and ITS1-5.8S-ITS2 rDNA sequence analysis. The eight taxa included two well-known species P.gonapodyides and P.cryptogea, two recently described species P.gregata and P.plurivora, two named but as yet undescribed taxa, P.taxon PgChlamydo and P.taxon Salixsoil, and two previously unrecognized species, Phytophthora sp.1 and P. sp.2. The most numerous species, P.taxon PgChlamydo, and the second most abundant species, P.taxon Salixsoil, were recovered at all three sites. Phytophthora cryptogea was detected only once at site Nixi. Phytophthora gregata and P. sp.2 were isolated from a stream only at site Bitahai, while the other three species were each found at two sites. Phylogenetic analysis revealed that the isolates belonged to three ITS clades, one species including six isolates in clade 2, six species including 66 isolates in clade 6 and one species in clade 8. There was a relatively rich species and genetic diversity of Phytophthora detected in the investigated regions where the forest biotic and abiotic factors affecting the growth and evolution of Phytophthora populations were diverse.}, issn = {1437-4781}, doi = {10.1111/efp.12015}, author = {Huai, W-x and Tian, G. and Hansen, E. M. and Zhao, W-x and Goheen, E. M. and Niklaus J. Gr{\"u}nwald and Cheng, C.} } @article {16713, title = {Phytophthora database 2.0: update and future direction.}, journal = {Phytopathology}, volume = {103}, year = {2013}, month = {2013 Dec}, pages = {1204-8}, abstract = {
The online community resource Phytophthora database (PD) was developed to support accurate and rapid identification of Phytophthora and to help characterize and catalog the diversity and evolutionary relationships within the genus. Since its release in 2008, the sequence database has grown to cover 1 to 12 loci for \≈2,600 isolates (representing 138 described and provisional species). Sequences of multiple mitochondrial loci were added to complement nuclear loci-based phylogenetic analyses and diagnostic tool development. Key characteristics of most newly described and provisional species have been summarized. Other additions to improve the PD functionality include: (i) geographic information system tools that enable users to visualize the geographic origins of chosen isolates on a global-scale map, (ii) a tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies, (iii) a comprehensive review of molecular diagnostics tools and relevant references, (iv) sequence alignments used to develop polymerase chain reaction-based diagnostics tools to support their utilization and new diagnostic tool development, and (v) an online community forum for sharing and preserving experience and knowledge accumulated in the global Phytophthora community. Here we present how these improvements can support users and discuss the PD\&$\#$39;s future direction.}, keywords = {Computational Biology, Databases, Genetic, DNA, Mitochondrial, Genotype, Geography, Internet, Microsatellite Repeats, phylogeny, phytophthora, sequence alignment, Sequence Analysis, DNA, Species Specificity}, issn = {0031-949X}, doi = {10.1094/PHYTO-01-13-0023-R}, author = {Park, Bongsoo and Martin, Frank and Geiser, David M and Kim, Hye-Seon and Mansfield, Michele A and Nikolaeva, Ekaterina and Park, Sook-Young and Coffey, Michael D and Russo, Joseph and Kim, Seong H and Balci, Yilmaz and Abad, Gloria and Burgess, Treena and Gr{\"u}nwald, Niklaus J and Cheong, Kyeongchae and Choi, Jaeyoung and Lee, Yong-Hwan and Kang, Seogchan} } @article {10.1371/journal.pone.0077181, title = {Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs}, journal = {PLoS ONE}, volume = {8}, year = {2013}, month = {10}, pages = {e77181}, abstract = {
In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems.
The recently emerged plant pathogen Phytophthora ramorum is responsible for causing the sudden oak death epidemic. This review documents the emergence of P. ramorum based on evolutionary and population genetic analyses. Currently infection by P. ramorum occurs only in Europe and North America and three clonal lineages are distinguished: EU1, NA1 and NA2. Ancient divergence of these lineages supports a scenario in which P. ramorum originated from reproductively isolated populations and underwent at least four global migration events. This recent work sheds new light on mechanisms of emergence of exotic pathogens and provides crucial insights into migration pathways.}, keywords = {central mexico, clonal lineages, genome sequences, interspecific hybridization, microsatellite markers, natural hybrid, oregon tanoak forests, plant pathology, port-orford-cedar, toluca valley}, isbn = {0966-842X}, doi = {10.1016/j.tim.2011.12.006}, author = {Niklaus J. Gr{\"u}nwald and Garbelotto, M. and Goss, E. M. and Heungens, K. and Prospero, S.} } @article {385, title = {Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen.}, journal = {PLoS Pathog}, volume = {8}, year = {2012}, month = {2012}, pages = {e1002940}, abstract = {
Pest and pathogen losses jeopardise global food security and ever since the 19(th) century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to document the emergence of a lineage, termed 13_A2, in the European P. infestans population, and its rapid displacement of other lineages to exceed 75\% of the pathogen population across Great Britain in less than three years. We show that isolates of the 13_A2 lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a 13_A2 isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the 13_A2 isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly, 13_A2 isolates carry intact and in planta induced Avrblb1, Avrblb2 and Avrvnt1 effector genes that trigger resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings point towards a strategy for deploying genetic resistance to mitigate the impact of the 13_A2 lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics.}, keywords = {Crops, Agricultural, DNA Copy Number Variations, Gene Expression Profiling, Genes, Plant, Genome, Fungal, Host-Pathogen Interactions, Immunity, Innate, phytophthora infestans, Plant Diseases, Plant Proteins, Polymorphism, Genetic, Sequence Analysis, DNA, solanum tuberosum}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1002940}, author = {Cooke, David E L and Cano, Liliana M and Raffaele, Sylvain and Bain, Ruairidh A and Cooke, Louise R and Etherington, Graham J and Deahl, Kenneth L and Farrer, Rhys A and Gilroy, Eleanor M and Goss, Erica M and Gr{\"u}nwald, Niklaus J and Hein, Ingo and MacLean, Daniel and McNicol, James W and Randall, Eva and Oliva, Ricardo F and Pel, Mathieu A and Shaw, David S and Squires, Julie N and Taylor, Moray C and Vleeshouwers, Vivianne G A A and Birch, Paul R J and Lees, Alison K and Kamoun, Sophien} } @article {117, title = {Genome sequences of Phytophthora enable translational plant disease management and accelerate research}, journal = {Canadian Journal of Plant Pathology-Revue Canadienne De Phytopathologie}, volume = {34}, number = {1}, year = {2012}, note = {936CETimes Cited:0Cited References Count:55}, pages = {13-19}, abstract = {
Whole and partial genome sequences are becoming available at an ever-increasing pace. For many plant pathogen systems, we are moving into the era of genome resequencing. The first Phytophthora genomes, P. ramorum and P. sojae, became available in 2004, followed shortly by P. infestans in 2006. Availability of whole genome sequences has provided rapid and immediate advances in several areas also resulting in many practical applications and critical new insights. Availability of comparative genome data facilitated discovery of new classes of effectors, such as the RxLR-dEER and crinkler effector families. Genome data also enabled development of molecular markers for population genomic approaches that provided critical new insights into the evolutionary history of species and clades of Phytophthora. Several select examples of advances resulting from comparative genomic approaches in a concerted effort of the Oomycete research community are reviewed.}, keywords = {avirulence, clonal lineages, downy mildew, effector, emerging pathogens, european populations, exotic pathogens, genome analysis, microsatellite markers, north-american, pathogen phytophthora, phytophthora, ramorum detection, sojae-effector avr1b, sudden oak death, translational analysis}, isbn = {0706-0661}, doi = {10.1080/07060661.2012.664568}, url = {http://dx.doi.org/10.1080/07060661.2012.664568}, author = {Niklaus J. Gr{\"u}nwald} } @article {113, title = {Novel insights into the emergence of pathogens: the case of chestnut blight}, journal = {Molecular Ecology}, volume = {21}, number = {16}, year = {2012}, note = {980MNTimes Cited:0Cited References Count:21}, month = {Aug}, pages = {3896-3897}, abstract = {
Exotic, invasive pathogens have emerged repeatedly and continue to emerge to threaten the worlds forests. Ecosystem structure and function can be permanently changed when keystone tree species such as the American chestnut (Castanea dentata) are eliminated from a whole range by disease. The fungal ascomycete pathogen Cryphonectria parasitica is responsible for causing chestnut blight. Once the pathogen was introduced into the Eastern US, where chestnuts were predominant, chestnuts were all but eliminated. This pathogen is currently causing extensive damage in Europe. A study in this issue of Molecular Ecology sheds new light on the pattern and process of emergence of this devastating plant pathogen (Dutech 2012). The authors used microsatellite markers to investigate the evolutionary history of C.similar to parasitica populations introduced into North America and Europe. To infer sources of migrants and the migration events, the authors included putative source populations endemic to China and Japan, inferred potentially unsampled populations and conducted a multivariate population genetic and complex ABC analysis. Cryphonectria parasitica emerges as an example of an introduced pathogen with limited genotypic diversity and some admixture in the invaded ranges, yet repeated invasions into different areas of Europe and the United States. This work sheds new light on the emergence of C.similar to parasitica providing compelling evidence that this pathogen emerged by repeated migration and occasional admixture.}, keywords = {chytridiomycosis, cryphonectria-parasitica, diversity, ecology, evolution, exotic pathogen, fungus, genetics, host, invasion biology, keystone species, phytophthora-ramorum, plant pathogen, sudden oak death}, isbn = {0962-1083}, doi = {10.1111/j.1365-294X.2012.05597.x}, author = {Niklaus J. Gr{\"u}nwald} } @article {114, title = {Phytophthora obscura sp nov., a new species of the novel Phytophthora subclade 8d}, journal = {Plant Pathology}, volume = {61}, number = {3}, year = {2012}, note = {939GJTimes Cited:1Cited References Count:43}, month = {Jun}, pages = {610-622}, abstract = {
A new Phytophthora species was detected (i) in the USA, infecting foliage of Kalmia latifolia, (ii) in substrate underneath Pieris, and (iii) in Germany in soil samples underneath Aesculus hippocastanum showing disease symptoms. The new species Phytophthora obscura sp. nov. is formally named based on phylogenetic analysis, host range, Kochs postulates and morphology. Phytophthora obscura is homothallic with paragynous antheridia and semipapillate sporangia. It is genetically closely related to P.similar to syringae and P. austrocedrae and together these three species define a new Phytophthora subclade 8d, with significant support for all genetic loci analysed including seven nuclear genes and the mitochondrial gene coxII. The morphological and ecological characteristics are very similar to P.similar to syringae, and it is likely that P.similar to obscura was not described earlier because it was identified as P.similar to syringae. Artificial inoculations indicated that horse chestnut, kalmia, pieris and rhododendron might be hosts, and Kochs postulates were confirmed for kalmia from which it was isolated. This pathogen was named after its elusive nature since it has to date rarely been detected in the US and Germany.}, keywords = {aesculus hippocastanum, california, clonal lineages, kalmia latifolia, oomycete, oregon, pathogen, phylogenetic-relationships, pieris, pseudosyringae, ramorum blight, rhododendron, sudden oak death, taxonomy, trees}, isbn = {0032-0862}, doi = {10.1111/j.1365-3059.2011.02538.x}, author = {Niklaus J. Gr{\"u}nwald and Werres, S. and Goss, E. M. and Taylor, C. R. and Fieland, V. J.} } @article {118, title = {Potato Yield with Regard to Late Blight (Phytophthora Infestans Mont. De Bary) Epiphytotics}, journal = {Revista Fitotecnia Mexicana}, volume = {35}, number = {1}, year = {2012}, note = {918WLTimes Cited:0Cited References Count:25}, month = {Jan-Mar}, pages = {69-78}, abstract = {
In order to study the quantitative relationship between tuber yield of two potato (Solanum tuberosum L.) cultivars (Alpha\&$\#$39;, susceptible, and \&$\#$39;Zafiro\&$\#$39;, moderately resistant to late blight), and severity of the pathogen in Toluca, Mexico, managed by weekly foliar sprays of 0.575 kg i.a ha(-1), 1.15 kg i.a ha(-1), and without application of the fungicide Clorothalonil. There were statistical differences between cultivars and among treatments within each cultivar (P \< 0.05). The relationship between yield and disease severity was described by linear regression models. Yield by commercial standards (classes 1, 2 and 3) depended on the accumulated severity 80 d after planting in cv. \&$\#$39;Zafiro\&$\#$39;, and at 58 d in \&$\#$39;Alpha\&$\#$39; for class 1 and for total yield, at 65 d for class 2, and at 94 d for class 3. The determination coefficient varied between 54 and 78 \% in the selected models for \&$\#$39;Alpha\&$\#$39;, while in \&$\#$39;Zafiro\&$\#$39; the range was from 54 to 75 \%. Yield loss was less in \&$\#$39;Zafiro\&$\#$39;, for its epiphytotics were less intense until start of tuberization. It is concluded that it is necessary to consider tuber iniciation as the critical point. The previous period is the most important to reduce losses. Hence, handling should focus on the delay of the epiphytotic iniciation (Yo) and intensity in this period (r(k)).}, keywords = {crops, cultivars, disease, losses, management, model, quantification, resistance, solanum tuberosum cultivars {\textquoteright}alpha{\textquoteright} and {\textquoteright}zafiro{\textquoteright}, toluca, toluca valley}, isbn = {0187-7380}, url = {http://www.revistafitotecniamexicana.org/documentos/35-1/8a.pdf}, author = {Montes, G. R. and Saldana, H. L. and Aguilera, G. M. and Pavia, S. F. and Niklaus J. Gr{\"u}nwald} } @book {griesbachsafe, title = {Safe Procurement and Production Manual}, year = {2012}, author = {Griesbach, John A and Parke, Jennifer L and Chastagner, Gary A and Niklaus J. Gr{\"u}nwald and Aguirre, John} } @article {112, title = {A Systems Approach for Management of Pests and Pathogens of Nursery Crops}, journal = {Plant Disease}, volume = {96}, number = {9}, year = {2012}, note = {991COTimes Cited:0Cited References Count:28}, month = {Sep}, pages = {1236-1244}, keywords = {north-america, phytophthora-ramorum, sudden oak death}, isbn = {0191-2917}, doi = {10.1094/PDIS-11-11-0986-FE}, url = {http://dx.doi.org/10.1094/PDIS-11-11-0986-FE}, author = {Parke, J. L. and Niklaus J. Gr{\"u}nwald} } @article {127, title = {Evolution and Population Genetics of Exotic and Re-Emerging Pathogens: Novel Tools and Approaches}, journal = {Annual Review of Phytopathology}, volume = {49}, year = {2011}, note = {Bwt50Times Cited:6Cited References Count:105Annual Review of Phytopathology}, pages = {249-267}, abstract = {
Given human population growth and accelerated global trade, the rate of emergence of exotic plant pathogens is bound to increase. Understanding the processes that lead to the emergence of new pathogens can help manage emerging epidemics. Novel tools for analyzing population genetic variation can be used to infer the evolutionary history of populations or species, allowing for the unprecedented reconstruction of the demographic history of pathogens. Specifically, recent advances in the application of coalescent, maximum likelihood (ML), and Bayesian methods to population genetic data combined with increasing availability of affordable sequencing and parallel computing have created the opportunity to apply these methods to a broad range of questions regarding the evolution of emerging pathogens. These approaches are particularly powerful when used to test multiple competing hypotheses. We provide several examples illustrating how coalescent analysis provides critical insights into understanding migration pathways as well as processes of divergence, speciation, and recombination.}, keywords = {bayesian inference, clonal lineages, coalescent, coalescent approach, genealogy, invasive pathogen, maximum likelihood, maximum-likelihood-estimation, migration rates, monte-carlo approach, multilocus genotype data, mycosphaerella-graminicola, phytophthora-ramorum, population structure, recombination rates, sudden oak death}, isbn = {0066-4286}, doi = {10.1146/annurev-phyto-072910-095246}, author = {Niklaus J. Gr{\"u}nwald and Goss, E. M.} } @article {121, title = {Genetic and Pathogenic Relatedness of Pseudoperonospora cubensis and P. humuli}, journal = {Phytopathology}, volume = {101}, number = {7}, year = {2011}, note = {783WSTimes Cited:1Cited References Count:65}, month = {Jul}, pages = {805-818}, abstract = {
The most economically important plant pathogens in the genus Pseudoperonospora (family Peronosporaceae) are Pseudoperonospora cubensis and P humuli, causal agents of downy mildew on cucurbits and hop, respectively. Recently, P. humuli was reduced to a taxonomic synonym of P. cubensis based on internal transcribed spacer (ITS) sequence data and morphological characteristics. Nomenclature has many practical implications for pathogen identification and regulatory considerations; therefore, further clarification of the genetic and pathogenic relatedness of these organisms is needed. Phylogenetic analyses were conducted considering two nuclear and three mitochondrial loci for 21 isolates of P cubensis and 14 isolates of P humuli, and all published ITS sequences of the pathogens in GenBank. There was a consistent separation of the majority of the P hunudi isolates and the P cubensis isolates in nuclear, mitochondrial, and ITS phylogenetic analyses, with the exception of isolates of P. humuli from Hainalus japonicas from Korea. The P cubensis isolates appeared to contain the P humuli cluster, which may indicate that P. humuli descended from P cubensis. Host-specificity experiments were conducted with two reportedly universally susceptible hosts of P cubensis and two hop cultivars highly susceptible to P cubensis consistently infected the hop cultivars at very low rates, and sporangiophores invariably emerged from necrotic or chlorotic hypersensitive-like lesions. Only a single sporangiophore of P humuli was observed on a cucurbit plant during the course of the studies. Together, molecular data and host specificity indicate that there are biologically relevant characteristics that differentiate P. cubensis and P humuli that may be obfuscated if P humuli were reduced to a taxonomic synonym of P. cubensis. Thus, we recommend retaining the two species names P. cubensis and P humuli until the species boundaries can be resolved unambiguously.}, keywords = {hop downy mildew, infection, inference, mixed models, molecular phylogeny, peronospora, phylogenetic-relationships, phytophthora-ramorum, sequence-analysis, sudden oak death}, isbn = {0031-949X}, doi = {10.1094/PHYTO-10-10-0270}, url = {http://dx.doi.org/10.1094/PHYTO-10-10-0270}, author = {Mitchell, M. N. and Ocamb, C. M. and Niklaus J. Gr{\"u}nwald and Mancino, L. E. and Gent, D. H.} } @article {125, title = {Genetic diversity of Phytophthora infestans in the Northern Andean region}, journal = {BMC Genetics}, volume = {12}, year = {2011}, note = {730GZTimes Cited:2Cited References Count:51}, month = {Feb 9}, abstract = {
Background: Phytophthora infestans (Mont.) de Bary, the causal agent of potato late blight, is responsible for tremendous crop losses worldwide. Countries in the northern part of the Andes dedicate a large proportion of the highlands to the production of potato, and more recently, solanaceous fruits such as cape gooseberry (Physalis peruviana) and tree tomato (Solanum betaceum), all of which are hosts of this oomycete. In the Andean region, P. infestans populations have been well characterized in Ecuador and Peru, but are poorly understood in Colombia and Venezuela. To understand the P. infestans population structure in the Northern part of the Andes, four nuclear regions (ITS, Ras, beta-tubulin and Avr3a) and one mitochondrial (Cox1) region were analyzed in isolates of P. infestans sampled from different hosts in Colombia and Venezuela.Results: Low genetic diversity was found within this sample of P. infestans isolates from crops within several regions of Colombia and Venezuela, revealing the presence of clonal populations of the pathogen in this region. We detected low frequency heterozygotes, and their distribution patterns might be a consequence of a high migration rate among populations with poor effective gene flow. Consistent genetic differentiation exists among isolates from different regions.Conclusions: The results here suggest that in the Northern Andean region P. infestans is a clonal population with some within-clone variation. P. infestans populations in Venezuela reflect historic isolation that is being reinforced by a recent self-sufficiency of potato seeds. In summary, the P. infestans population is mainly shaped by migration and probably by the appearance of variants of key effectors such as Avr3a.}, keywords = {central mexico, cultivated potato, DNA polymorphism, effector avr3a, late blight, maximum-likelihood, phylogenetic analysis, population-structure, solanaceous hosts, statistical-method}, isbn = {1471-2156}, doi = {10.1186/1471-2156-12-23}, url = {https://bmcgenet.biomedcentral.com/articles/10.1186/1471-2156-12-23}, author = {Cardenas, M. and Grajales, A. and Sierra, R. and Rojas, A. and Gonzalez-Almario, A. and Vargas, A. and Marin, M. and Fermin, G. and Lagos, L. E. and Niklaus J. Gr{\"u}nwald and Bernal, A. and Salazar, C. and Restrepo, S.} } @article {119, title = {Identification of new polymorphic microsatellite markers in the NA1 and NA2 lineages of Phytophthora ramorum}, journal = {Mycologia}, volume = {103}, number = {6}, year = {2011}, note = {852WJTimes Cited:1Cited References Count:17}, month = {Nov-Dec}, pages = {1245-1249}, abstract = {
Phytophthora ramorum is a recently introduced pathogen in Europe and North America consisting of three clonal lineages. Due to the limited intralineage genetic variation, only a few polymorphic markers are available for use in studies involving the epidemiology and evolution of P. ramorum. A total of 159 primer pairs for candidate polymorphic SSR loci were tested with universal labeling. Four polymorphic microsatellite loci were identified within the NA1 lineage and one within the NA2 lineage, demonstrating the power and flexibility of the screening technique. The markers may significantly increase the number of genotypes that can be identified and as such can help better characterize the North American lineages of P. ramorum.}, keywords = {california, clonal lineages, genetic diversity, microsatellite markers, migration, north-america, nursery, oak death pathogen, oomycetes, sudden oak death, universal labeling}, isbn = {0027-5514}, doi = {10.3852/10-420}, author = {Vercauteren, A. and Larsen, M. and Goss, E. M. and Niklaus J. Gr{\"u}nwald and Maes, M. and Heungens, K.} } @article {126, title = {Phenotypic differences among three clonal lineages of Phytophthora ramorum}, journal = {Forest Pathology}, volume = {41}, number = {1}, year = {2011}, note = {715MITimes Cited:4Cited References Count:35}, month = {Feb}, pages = {7-14}, abstract = {
P\>There are three major clonal lineages of Phytophthora ramorum present in North America and Europe named NA1, NA2, and EU1. Twenty-three isolates representing all three lineages were evaluated for phenotype including (i) aggressiveness on detached Rhododendron leaves and (ii) growth rate at minimum, optimum, and maximum temperatures. Closely related species P. foliorum and P. hibernalis were included in phenotypic tests since these species are encountered in nursery surveys for P. ramorum. Isolates from the NA2 and EU1 lineages were the most aggressive and isolates from the NA1 group were the least aggressive. The NA1 lineage of P. ramorum was the most variable in aggressiveness and growth rate. The variability in the NA1 lineage was due to the presence of non-wild type (nwt) isolates. There was no significant difference in growth rate among NA1 wild type (wt), NA2, and EU1 lineages at any temperature tested. The difference between wt and nwt P. ramorum isolates is discussed.}, keywords = {australia, cinnamomi, european populations, infection, mating-type, north-american, pathogen, rhododendron, sudden oak death, susceptibility}, isbn = {1437-4781}, doi = {10.1111/j.1439-0329.2009.00627.x}, author = {Elliott, M. and Sumampong, G. and Varga, A. and Shamoun, S. F. and James, D. and Masri, S. and Niklaus J. Gr{\"u}nwald} } @article {128, title = {Phytophthora ramorum in Canada: Evidence for Migration Within North America and from Europe}, journal = {Phytopathology}, volume = {101}, number = {1}, year = {2011}, note = {698BTTimes Cited:15Cited References Count:29}, month = {Jan}, pages = {166-171}, abstract = {
Phytophthora ramorum, the cause of sudden oak death on oak and ramorum blight on woody ornamentals, has been reported in ornamental nurseries on the West Coast of North America from British Columbia to California. Long-distance migration of P ramorum has occurred via the nursery trade, and shipments of host plants are known to have crossed the U.S.-Canadian border. We investigated the genotypic diversity of P ramorum in Canadian nurseries and compared the Canadian population with U.S. and European nursery isolates for evidence of migration among populations. All three of the P. ramorum clonal lineages were found in Canada but, unexpectedly, the most common was the NA2 lineage. The NA1 clonal lineage, which has been the most common lineage in U.S. nurseries, was found relatively infrequently in Canada, and these isolates may have been the result of migration from the United States to Canada. The EU1 lineage was observed almost every year and shared multilocus genotypes with isolates from Europe and the United States. Estimation of migration rates between Europe and North America indicated that migration was higher from Europe to North America than vice versa, and that unidirectional migration from Europe to North America was more likely than bidirectional migration.}, keywords = {california, clonal lineages, genotypic diversity, identify 3 lineages, in-vitro, management, oregon, pathogen, populations, sudden oak death}, isbn = {0031-949X}, doi = {10.1094/PHYTO-05-10-0133}, url = {http://dx.doi.org/10.1094/PHYTO-05-10-0133}, author = {Goss, E. M. and Larsen, M. and Vercauteren, A. and Werres, S. and Heungens, K. and Niklaus J. Gr{\"u}nwald} } @article {16859, title = {Phytophthora ramorum: Plant pathologists track where it came from and how it has managed to spread}, year = {2011}, month = {09/2014}, pages = {42-45}, type = {Popular Press}, author = {Gr{\"u}nwald, Niklaus J} } @article {124, title = {Phytophthora-ID.org: A Sequence-Based Phytophthora Identification Tool}, journal = {Plant Disease}, volume = {95}, number = {3}, year = {2011}, note = {725BTTimes Cited:6Cited References Count:35}, month = {Mar}, pages = {337-342}, abstract = {
Contemporary species identification relies strongly on sequence-based identification, yet resources for identification of many fungal and oomycete pathogens are rare. We developed two web-based, searchable databases for rapid identification of Phytophthora spp. based on sequencing of the internal transcribed spacer (ITS) or the cytochrome oxidase (cox) I and 2 spacer region, followed by BLAST searching the databases. Both databases are highly selective. For ITS, only sequences associated with published Phytophthora spp. descriptions or classic Phytophthora phylogenetics references are included. For the cox spacer region, only data obtained by resequencing select isolates reported in published work were included. Novel taxa tentatively named are selectively included in the database and labeled as Phytophthora taxon \"X\"; as in, for example, P. taxon \"asparagi\". The database was validated with 700 Phytophthora isolates collected from nursery environments during 2006 to 2009. This resource, found at www.Phytophthora-ID.org, is a robust and validated tool for molecular identification of Phytophthora spp. and is regularly being updated.}, keywords = {blight, california, database, gene, mitochondrial genome, pathogen, phylogenetic-relationships, plant, ramorum, sudden oak death}, isbn = {0191-2917}, doi = {10.1094/PDIS-08-10-0609}, url = {http://dx.doi.org/10.1094/PDIS-08-10-0609}, author = {Niklaus J. Gr{\"u}nwald and Martin, F. N. and Larsen, M. M. and Sullivan, C. M. and Press, C. M. and Coffey, M. D. and Hansen, E. M. and Parke, J. L.} } @article {120, title = {The Plant Pathogen Phytophthora andina Emerged via Hybridization of an Unknown Phytophthora Species and the Irish Potato Famine Pathogen, P. infestans}, journal = {PLoS ONE}, volume = {6}, number = {9}, year = {2011}, note = {824BITimes Cited:4Cited References Count:73}, month = {Sep 16}, abstract = {
Emerging plant pathogens have largely been a consequence of the movement of pathogens to new geographic regions. Another documented mechanism for the emergence of plant pathogens is hybridization between individuals of different species or subspecies, which may allow rapid evolution and adaptation to new hosts or environments. Hybrid plant pathogens have traditionally been difficult to detect or confirm, but the increasing ease of cloning and sequencing PCR products now makes the identification of species that consistently have genes or alleles with phylogenetically divergent origins relatively straightforward. We investigated the genetic origin of Phytophthora andina, an increasingly common pathogen of Andean crops Solanum betaceum, S. muricatum, S. quitoense, and several wild Solanum spp. It has been hypothesized that P. andina is a hybrid between the potato late blight pathogen P. infestans and another Phytophthora species. We tested this hypothesis by cloning four nuclear loci to obtain haplotypes and using these loci to infer the phylogenetic relationships of P. andina to P. infestans and other related species. Sequencing of cloned PCR products in every case revealed two distinct haplotypes for each locus in P. andina, such that each isolate had one allele derived from a P. infestans parent and a second divergent allele derived from an unknown species that is closely related but distinct from P. infestans, P. mirabilis, and P. ipomoeae. To the best of our knowledge, the unknown parent has not yet been collected. We also observed sequence polymorphism among P. andina isolates at three of the four loci, many of which segregate between previously described P. andina clonal lineages. These results provide strong support that P. andina emerged via hybridization between P. infestans and another unknown Phytophthora species also belonging to Phytophthora clade 1c.}, keywords = {central mexico, genome sequences, haplotype reconstruction, host-specificity, interspecific hybridization, molecular phylogeny, natural hybrid, phylogenetic tree selection, population genetic-analysis, toluca valley}, isbn = {1932-6203}, doi = {10.1371/journal.pone.0024543}, url = {https://doi.org/10.1371/journal.pone.0024543}, author = {Goss, E. M. and Cardenas, M. E. and Myers, K. and Forbes, G. A. and Fry, W. E. and Restrepo, S. and Niklaus J. Gr{\"u}nwald} } @article {135, title = {Clonal expansion of the Belgian Phytophthora ramorum populations based on new microsatellite markers}, journal = {Molecular Ecology}, volume = {19}, number = {1}, year = {2010}, note = {535XRTimes Cited:15Cited References Count:67}, month = {Jan}, pages = {92-107}, abstract = {
Co-existence of both mating types A1 and A2 within the EU1 lineage of Phytophthora ramorum has only been observed in Belgium, which begs the question whether sexual reproduction is occurring. A collection of 411 Belgian P. ramorum isolates was established during a 7-year survey. Our main objectives were genetic characterization of this population to test for sexual reproduction, determination of population structure, evolution and spread, and evaluation of the effectiveness and impact of control measures. Novel, polymorphic simple sequence repeat (SSR) markers were developed after screening 149 candidate loci. Eighty isolates of P. ramorum, broadly representing the Belgian population, were analyzed using four previously described and three newly identified polymorphic microsatellite loci as well as amplified fragment length polymorphisms. SSR analysis was most informative and was used to screen the entire Belgian population. Thirty multilocus genotypes were identified, but 68\% of the isolates belonged to the main genotype EU1MG1. Although accumulated mutation events were detected, the overall level of genetic diversity within the Belgian isolates of P. ramorum appears to be limited, indicating a relatively recent clonal expansion. Based on our SSR analysis there is no evidence of sexual recombination in the Belgian population of P. ramorum. Metalaxyl use decreased the genetic diversity of P. ramorum until 2005, when the majority of the isolates had become resistant. Most genotypes were site-specific and despite systematic removal of symptomatic and neighbouring plants, some genotypes were detected over a period of several years at a single site, sometimes discontinuously, indicating (latent) survival of the pathogen at those sites.}, keywords = {1st report, fungicide resistance, genotypic diversity, infestans, mating-type, metalaxyl resistance, nurseries, oomycetes, ornamental plants, pathogen, population genetics, practical experience, sudden oak death, universal labelling}, isbn = {0962-1083}, doi = {10.1111/j.1365-294X.2009.04443.x}, author = {Vercauteren, A. and De Dobbelaere, I. and Niklaus J. Gr{\"u}nwald and Bonants, P. and Van Bockstaele, E. and Maes, M. and Heungens, K.} } @article {134, title = {Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009-31 January 2010}, journal = {Molecular Ecology Resources}, volume = {10}, number = {3}, year = {2010}, note = {579WITimes Cited:4Cited References Count:0}, month = {May}, pages = {576-579}, abstract = {
This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross-tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mulleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus.}, isbn = {1755-098X}, author = {Anderson, C. M. and Aparicio, G. J. and Atangana, A. R. and Beaulieu, J. and Bruford, M. W. and Cain, F. and Campos, T. and Cariani, A. and Carvalho, M. A. and Chen, N. and Chen, P. P. and Clamens, A. L. and Clark, A. M. and Coeur D{\textquoteright}Acier, A. and Connolly, P. and Cordero-Rivera, A. and Coughlan, J. P. and Cross, T. S. and David, B. and De Bruyn, C. and De Meyer, M. and De Ridder, C. and Delatte, H. and Dettori, M. T. and Downer, S. J. and Dubreuil, C. and Evans, K. J. and Fan, B. and Ferrara, G. and Gagne, A. and Gaillard, M. and Gigliarelli, L. and Giovinazzi, J. and Gomez, D. R. and Niklaus J. Gr{\"u}nwald and Hansson, B. and Huotari, T. and Jank, L. and Jousselin, E. and Jungmann, L. and Kaczmarek, M. E. and Khasa, D. P. and Kneebone, J. and Korpelainen, H. and Kostamo, K. and Lanfaloni, L. and Lin, H. R. and Liu, X. C. and Lucentini, L. and Maes, G. E. and Mahaffee, W. F. and Meng, Z. N. and Micali, S. and Milano, I. and Mok, H. F. and Morin, L. and Neill, T. M. and Newton, C. H. and Ostrow, D. G. and Palomba, A. and Panara, F. and Puletti, M. E. and Quarta, R. and Quilici, S. and Ramos, A. K. B. and Rigaud, T. and Risterucci, A. M. and Salomon, M. P. and Sanchez-Guillen, R. A. and Sarver, S. K. and Sequeira, A. S. and Sforca, D. A. and Simiand, C. and Smith, B. and Sousa, A. C. B. and Souza, A. P. and Stepien, C. C. and Stuckert, A. J. and Sulikowski, J. and Tayeh, A. and Tinti, F. and Tsang, P. C. W. and Van Houdt, J. K. J. and Vendramin, E. and Verde, I. and Virgilio, M. and Wang, H. L. and Wang, L. and Wattier, R. A. and Wellenreuther, M. and Xie, C. X. and Zane, L. and Zhang, X. J. and Zhang, Y. and Zhuang, Z. M. and Zucchi, M. I. and Mol Ecology Resources Primer Dev} } @article {130, title = {The Promise and Pitfalls of Sequence-Based Identification of Plant-Pathogenic Fungi and Oomycetes}, journal = {Phytopathology}, volume = {100}, number = {8}, year = {2010}, note = {628RXTimes Cited:11Cited References Count:51}, month = {Aug}, pages = {732-737}, abstract = {
Sequences of selected marker loci have been widely used for the identification of specific pathogens and the development of sequence-based diagnostic methods. Although such approaches offer several advantages over traditional culture-based methods for pathogen diagnosis and identification, they have their own pitfalls. These include erroneous and incomplete data in reference databases, poor or oversimplified interpretation of search results, and problems associated with defining species boundaries. In this letter, we outline the potential benefits and drawbacks of using sequence data for identification and taxonomic deductions of plant-pathogenic fungi and oomycetes, using Phytophthora as a primary example. We also discuss potential remedies for these pitfalls and address why coordinated community efforts are essential to make such remedies more efficient and robust.}, keywords = {culture collection, database, diagnosis, DNA barcode, DNA-sequences, fusarium, genbank, life, molecular phylogeny, phylogeny, phytophthora, recognition, solani species complex, taxonomy, tree}, isbn = {0031-949X}, author = {Kang, S. and Mansfield, M. A. and Park, B. and Geiser, D. M. and Ivors, K. L. and Coffey, M. D. and Niklaus J. Gr{\"u}nwald and Martin, F. N. and Levesque, C. A. and Blair, J. E.} } @article {129, title = {Quantitative resistance to late blight from Solanum berthaultii cosegregates with RPi-ber: insights in stability through isolates and environment}, journal = {Theoretical and Applied Genetics}, volume = {121}, number = {8}, year = {2010}, note = {671KCTimes Cited:5Cited References Count:84}, month = {Nov}, pages = {1553-1567}, abstract = {
Genetic resistance is a valuable tool in the fight against late blight of potatoes but little is known about the stability and specificity of quantitative resistance including the effect of defeated major resistance genes. In the present study we investigated the effect of different isolates of Phytophthora infestans on the mode of action of R (Pi-ber) , an R-gene originating from Solanum berthaultii. The experiments were conducted on progenies derived from two reciprocal inter-specific backcrosses of Solanum tuberosum and S. berthaultii. The plant-pathogen interaction was tested in diverse environments including field, greenhouse and growth chamber conditions. The R (Pi-ber) gene provided complete resistance against a US8 isolate of P. infestans in all trials. When isolates compatible with R (Pi-ber) were used for inoculation, a smaller, but significant resistance effect was consistently detected in the same map position as the R-gene. This indicates that this R-gene provides a residual resistance effect, and/or that additional resistance loci are located in this genomic region of chromosome X. Additional quantitative resistance loci (QRL) were identified in the analyzed progenies. While some of the QRL (such as those near TG130 on chromosome III) were effective against several isolates of the pathogen, others were isolate specific. With a single exception, the S. berthaultii alleles were associated with a decrease in disease severity. Resistance loci reported in the present study co-locate with previously reported R-genes and QRL to P. infestans and other pathogens.}, keywords = {chromosome-ix, disease resistance, field-resistance, phytophthora-infestans, potato late blight, powdery mildew resistance, qtl analysis, race-specific resistance, trait loci, virus-y}, isbn = {0040-5752}, author = {Rauscher, G. and Simko, I. and Mayton, H. and Bonierbale, M. and Smart, C. D. and Niklaus J. Gr{\"u}nwald and Greenland, A. and Fry, W. E.} } @article {145, title = {Ancient isolation and independent evolution of the three clonal lineages of the exotic sudden oak death pathogen Phytophthora ramorum}, journal = {Molecular Ecology}, volume = {18}, number = {6}, year = {2009}, note = {414HDTimes Cited:29Cited References Count:82}, month = {Mar}, pages = {1161-1174}, abstract = {
The genus Phytophthora includes some of the most destructive plant pathogens affecting agricultural and native ecosystems and is responsible for a number of recent emerging and re-emerging infectious diseases of plants. Sudden oak death, caused by the exotic pathogen P. ramorum, has caused extensive mortality of oaks and tanoaks in Northern California, and has brought economic losses to US and European nurseries as well due to its infection of common ornamental plants. In its known range, P. ramorum occurs as three distinct clonal lineages. We inferred the evolutionary history of P. ramorum from nuclear sequence data using coalescent-based approaches. We found that the three lineages have been diverging for at least 11\% of their history, an evolutionarily significant amount of time estimated to be on the order of 165 000 to 500 000 years. There was also strong evidence for historical recombination between the lineages, indicating that the ancestors of the P. ramorum lineages were members of a sexually reproducing population. Due to this recombination, the ages of the lineages varied within and between loci, but coalescent analyses suggested that the European lineage may be older than the North American lineages. The divergence of the three clonal lineages of P. ramorum supports a scenario in which the three lineages originated from different geographic locations that were sufficiently isolated from each other to allow independent evolution prior to introduction to North America and Europe. It is thus probable that the emergence of P. ramorum in North America and Europe was the result of three independent migration events.}, keywords = {central mexico, coalescent, DNA-sequences, emerging disease, emerging infectious-diseases, genome sequences, irish potato famine, microsatellite markers, oomycete, plant disease, population genetic-analysis, recombination, resistance gene, rxlr-class effector, sojae-effector avr1b, statistical tests}, isbn = {0962-1083}, author = {Goss, E. M. and Carbone, I. and Niklaus J. Gr{\"u}nwald} } @inbook {16747, title = {Evolution and Genetics of the Invasive Sudden Oak Death pathogen Phytophthora ramorum}, booktitle = {Oomycete Genetics and Genomics: Diversity, Interactions, and Research Tools}, year = {2009}, pages = {179-196}, publisher = { John Wiley \& Sons}, organization = { John Wiley \& Sons}, chapter = {9}, address = {Hoboken, NJ}, issn = {978-0-470-25567-4}, url = {http://elibrary.com.ng/UploadFiles/file0_10095.pdf}, author = {Niklaus J. Gr{\"u}nwald and Goss, Erica M} } @article {136, title = {Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans}, journal = {Nature}, volume = {461}, number = {7262}, year = {2009}, note = {494QBTimes Cited:192Cited References Count:24}, month = {Sep 17}, pages = {393-398}, abstract = {
Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world\&$\#$39;s population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74\% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.}, keywords = {avirulence, avr3a, cell-death, effector proteins, genes, infection, plant, resistance, rxlr effectors}, isbn = {0028-0836}, author = {Haas, B. J. and Kamoun, S. and Zody, M. C. and Jiang, R. H. Y. and Handsaker, R. E. and Cano, L. M. and Grabherr, M. and Kodira, C. D. and Raffaele, S. and Torto-Alalibo, T. and Bozkurt, T. O. and Ah-Fong, A. M. V. and Alvarado, L. and Anderson, V. L. and Armstrong, M. R. and Avrova, A. and Baxter, L. and Beynon, J. and Boevink, P. C. and Bollmann, S. R. and Bos, J. I. B. and Bulone, V. and Cai, G. H. and Cakir, C. and Carrington, J. C. and Chawner, M. and Conti, L. and Costanzo, S. and Ewan, R. and Fahlgren, N. and Fischbach, M. A. and Fugelstad, J. and Gilroy, E. M. and Gnerre, S. and Green, P. J. and Grenville-Briggs, L. J. and Griffith, J. and Niklaus J. Gr{\"u}nwald and Horn, K. and Horner, N. R. and Hu, C. H. and Huitema, E. and Jeong, D. H. and Jones, A. M. E. and Jones, J. D. G. and Jones, R. W. and Karlsson, E. K. and Kunjeti, S. G. and Lamour, K. and Liu, Z. Y. and Ma, L. J. and MacLean, D. and Chibucos, M. C. and McDonald, H. and McWalters, J. and Meijer, H. J. G. and Morgan, W. and Morris, P. F. and Munro, C. A. and O{\textquoteright}Neill, K. and Ospina-Giraldo, M. and Pinzon, A. and Pritchard, L. and Ramsahoye, B. and Ren, Q. H. and Restrepo, S. and Roy, S. and Sadanandom, A. and Savidor, A. and Schornack, S. and Schwartz, D. C. and Schumann, U. D. and Schwessinger, B. and Seyer, L. and Sharpe, T. and Silvar, C. and Song, J. and Studholme, D. J. and Sykes, S. and Thines, M. and van de Vondervoort, P. J. I. and Phuntumart, V. and Wawra, S. and Weide, R. and Win, J. and Young, C. and Zhou, S. G. and Fry, W. E. and Meyers, B. C. and van West, P. and Ristaino, J. and Govers, F. and Birch, P. R. J. and Whisson, S. C. and Judelson, H. S. and Nusbaum, C.} } @article {144, title = {Migration Patterns of the Emerging Plant Pathogen Phytophthora ramorum on the West Coast of the United States of America}, journal = {Phytopathology}, volume = {99}, number = {6}, year = {2009}, note = {447SWTimes Cited:21Cited References Count:73}, month = {Jun}, pages = {739-749}, abstract = {
Phytophthora ramorum (oomycetes) is the causal agent of sudden oak death and ramorum blight on trees, shrubs, and woody ornamentals in the forests of coastal California and southwestern Oregon and in nurseries of California, Oregon, and Washington. In this study, we investigated the genetic structure of P. ramorum on the West Coast of the United States, focusing particularly on population differentiation potentially indicative of gene flow. In total, 576 isolates recovered from 2001 to 2005 were genotyped at 10 microsatellite loci. Our analyses of genetic diversity and inferences of reproductive mode confirm previous results for the Oregon and California populations, with the strong majority of the genotypes belonging to the NA1 clonal lineage and showing no evidence for sexual reproduction. The high incidence of genotypes shared among populations and the lack of genetic structure among populations show that important large-scale, interpopulation genetic exchanges have occurred. This emphasizes the importance of human activity in shaping the current structure of the P. ramorum population on the West Coast of the United States.}, keywords = {california, european populations, evolutionary, genotypic diversity, in-vitro, infestans populations, microsatellite markers, north-american, oregon, simple sequence repeats, sudden oak death}, isbn = {0031-949X}, author = {Prospero, S. and Niklaus J. Gr{\"u}nwald and Winton, L. M. and Hansen, E. M.} } @article {138, title = {PCR-RFLP markers identify three lineages of the North American and European populations of Phytophthora ramorum}, journal = {Forest Pathology}, volume = {39}, number = {4}, year = {2009}, note = {479JFTimes Cited:4Cited References Count:34}, month = {Aug}, pages = {266-278}, abstract = {
P\>Phytophthora ramorum, the cause of sudden oak death and ramorum blight, has three major clonal lineages and two mating types. Molecular tests currently available for detecting P. ramorum do not distinguish between clonal lineages and mating type is determined by cultural methods on a limited number of samples. In some molecular diagnostic tests, cross-reaction with other closely related species such as P. hibernalis, P. foliorum or P. lateralis can occur. Regions in the mitochondrial gene Cox1 are different among P. ramorum lineages and mitochondrial genotyping of the North American and European populations seems to be sufficient to differentiate between mating types, because the EU1 lineage is mostly A1 and both NA1 and NA2 lineages are A2. In our study, we were able to identify P. ramorum isolates according to lineage using polymerase chain reaction-restriction fragment-length polymorphism (PCR-RFLP) of the Cox1 gene, first by using ApoI to separate P. ramorum from other species and EU1 from North American populations, and then AvaI to distinguish between NA1 and NA2 genotypes. However, P. foliorum had the same restriction profile as P. ramorum NA1 isolates.}, keywords = {california, genome sequences, infestans, mating-type, molecular-detection, nurseries, pathogen, sudden oak death, viburnum}, isbn = {1437-4781}, author = {Elliott, M. and Sumampong, G. and Varga, A. and Shamoun, S. F. and James, D. and Masri, S. and Briere, S. C. and Niklaus J. Gr{\"u}nwald} } @inbook {16749, title = {Phytophthora sojae: diversity among and within populations}, booktitle = {Oomycete Genetics and Genomics: Diversity, Interactions, and Research Tools}, year = {2009}, publisher = {John Wiley \& Sons}, organization = {John Wiley \& Sons}, address = {Hoboken, NJ}, issn = {978-0-470-25567-4}, url = {http://elibrary.com.ng/UploadFiles/file0_10095.pdf}, author = {Dorrance, A. E. and Niklaus J. Gr{\"u}nwald} } @article {137, title = {Population Genetic Analysis Infers Migration Pathways of Phytophthora ramorum in US Nurseries}, journal = {PLoS Pathogens}, volume = {5}, number = {9}, year = {2009}, note = {506VOTimes Cited:22Cited References Count:65}, month = {Sep}, abstract = {
Recently introduced, exotic plant pathogens may exhibit low genetic diversity and be limited to clonal reproduction. However, rapidly mutating molecular markers such as microsatellites can reveal genetic variation within these populations and be used to model putative migration patterns. Phytophthora ramorum is the exotic pathogen, discovered in the late 1990s, that is responsible for sudden oak death in California forests and ramorum blight of common ornamentals. The nursery trade has moved this pathogen from source populations on the West Coast to locations across the United States, thus risking introduction to other native forests. We examined the genetic diversity of P. ramorum in United States nurseries by microsatellite genotyping 279 isolates collected from 19 states between 2004 and 2007. Of the three known P. ramorum clonal lineages, the most common and genetically diverse lineage in the sample was NA1. Two eastward migration pathways were revealed in the clustering of NA1 isolates into two groups, one containing isolates from Connecticut, Oregon, and Washington and the other isolates from California and the remaining states. This finding is consistent with trace forward analyses conducted by the US Department of Agriculture\&$\#$39;s Animal and Plant Health Inspection Service. At the same time, genetic diversities in several states equaled those observed in California, Oregon, and Washington and two-thirds of multilocus genotypes exhibited limited geographic distributions, indicating that mutation was common during or subsequent to migration. Together, these data suggest that migration, rapid mutation, and genetic drift all play a role in structuring the genetic diversity of P. ramorum in US nurseries. This work demonstrates that fast-evolving genetic markers can be used to examine the evolutionary processes acting on recently introduced pathogens and to infer their putative migration patterns, thus showing promise for the application of forensics to plant pathogens.}, keywords = {3 clonal lineages, california, diversity, microbial forensics, multilocus genotype data, north-american, pathogen, south-africa, sudden oak death, united-states}, isbn = {1553-7366}, author = {Goss, E. M. and Larsen, M. and Chastagner, G. A. and Givens, D. R. and Niklaus J. Gr{\"u}nwald} } @inbook {16748, title = {Population Genetics and population diversity of Phytophthora infestans}, booktitle = {Oomycete Genetics and Genomics: Diversity, Interactions, and Research Tools}, year = {2009}, publisher = {John Wiley \& Sons}, organization = {John Wiley \& Sons}, address = {Hoboken, NJ}, issn = {978-0-470-25567-4}, url = {http://elibrary.com.ng/UploadFiles/file0_10095.pdf}, author = {Fry, W. E. and Niklaus J. Gr{\"u}nwald and Cooke, David E L and McLeod, A. and Forbes, G. A. and Cao, K.} } @article {139, title = {Standardizing the Nomenclature for Clonal Lineages of the Sudden Oak Death Pathogen, Phytophthora ramorum}, journal = {Phytopathology}, volume = {99}, number = {7}, year = {2009}, note = {457XETimes Cited:26Cited References Count:39}, month = {Jul}, pages = {792-795}, abstract = {
Phytophthora ramorum, the causal agent of sudden oak death and ramorum blight, is known to exist as three distinct clonal lineages which can only be distinguished by performing molecular marker-based analyses. However, in the recent literature there exists no consensus on naming of these lineages. Here we propose a system for naming clonal lineages of P. ramorum based on a consensus established by the P. ramorum research community. Clonal lineages are named with a two letter identifier for the continent on which they were first found (e. g., NA = North America; EU = Europe) followed by a number indicating order of appearance. Clonal lineages known to date are designated NA1 (mating type: A2; distribution: North America; environment: forest and nurseries), NA2 (A2; North America; nurseries), and EU1 (predominantly A1, rarely A2; Europe and North America; nurseries and gardens). It is expected that novel lineages or new variants within the existing three clonal lineages could in time emerge.}, keywords = {california, central mexico, DNA polymorphisms, european populations, exotic pathogen, forensics, genotypic diversity, in-vitro, infestans, molecular ecology, north-american, phylogeography, population genetics, toluca valley, united-states}, isbn = {0031-949X}, author = {Niklaus J. Gr{\"u}nwald and Goss, E. M. and Ivors, K. and Garbelotto, M. and Martin, F. N. and Prospero, S. and Hansen, E. and Bonants, P. J. M. and Hamelin, R. C. and Chastagner, G. and Werres, S. and Rizzo, D. M. and Abad, G. and Beales, P. and Bilodeau, G. J. and Blomquist, C. L. and Brasier, C. and Briere, S. C. and Chandelier, A. and Davidson, J. M. and Denman, S. and Elliott, M. and Frankel, S. J. and Goheen, E. M. and de Gruyter, H. and Heungens, K. and James, D. and Kanaskie, A. and McWilliams, M. G. and in {\textquoteright}t Veld, W. M. and Moralejo, E. and Osterbauer, N. K. and Palm, M. E. and Parke, J. L. and Sierra, A. M. P. and Shamoun, S. F. and Shishkoff, N. and P.W. Tooley and Vettraino, A. M. and Webber, J. and Widmer, T. L.} } @article {153, title = {Environment and slow epidemics favor oosporulation of Phytophthora infestans Mont. De Bary, on potato leaves in the Toluca Valley, Mexico}, journal = {American Journal of Potato Research}, volume = {85}, number = {2}, year = {2008}, note = {294FJTimes Cited:1Cited References Count:28}, month = {Apr}, pages = {101-109}, abstract = {
The Toluca Valley, located in the central highlands of Mexico, has optimal climatic conditions for the development of Phytophthora infestans as well as for sexual reproduction due to the presence of two mating types (1:1, ratio). Therefore, it is a suitable place to study late blight epidemics on cultivated potatoes. In order to quantify oospore formation on foliage during the progress of late blight epidemics and to establish the implications of (a) genetic resistance of the host, (b) disease management (fungicide application), and (c) environmental conditions, a study was conducted in the summer of 2002 and 2003 on two potato cultivars during the progress of the epidemic under rainfed and natural infection conditions in the Toluca Valley. The cultivars were exposed to 0.0, 0.5, and 1.0x doses of the protectant fungicide chlorothalonil (1.0x=1.15 kg a. i. ha(-1)). Oosporulation started 56 and 46 days after planting (2002 and 2003, respectively) with a maximum peak at 72 days in the two growing cycles. The total number of oospores in both years on cultivar Zafiro, resistant to P. infestans, was higher than on susceptible cv. Alpha (101 vs. 67). However, there were no statistically significant differences (P=0.40), which suggests that the resistance level of the host did not have a direct influence on oospore formation. The epidemics obtained from each of the treatments were characterized through multivariate analysis. Initial severity (Yo), as a percentage of damage from total foliage, time of total epidemic duration (T-t ), and average of apparent infection rate (b(-1)) were the variables that best explained the epidemics. These epidemics were organized into four groups. The group with an average rate of apparent infection of 0.010-0.015 units day(-1) and a duration of more than 50 days allowed higher oospore formation, regardless of host genotype. The nine days accumulated rainfall prior to the formation of oospores had a significant positive correlation (r \>= 0.7) with the absolute number of oospores per leaflet. It is concluded that oosporulation depended more on environmental factors (rain) and on the induction of slow epidemics (disease management), than on the genetic makeup of the host.}, keywords = {cultivars, epidemics, field conditions, germination, in-vitro, late blight, late-blight management, oospore formation, resistance, solanum tuberosum, survival, viability}, isbn = {1099-209X}, author = {Romero-Montes, G. and Lozoya-Saldana, H. and Mora-Aguilera, G. and Fernandez-Pavia, S. P. and Niklaus J. Gr{\"u}nwald} } @article {156, title = {First report of the European lineage of Phytophthora ramorum on viburnum and Osmanthus spp. in a California Nursery}, journal = {Plant Disease}, volume = {92}, number = {2}, year = {2008}, note = {253GPTimes Cited:15Cited References Count:4}, month = {Feb}, pages = {314-314}, abstract = {
Phytophthora ramorum S. Werres \& A.W.A.M. de Cock is the causal agent of sudden oak death in California and Oregon forests and ramorum blight on a broad range of host species in wildlands and nurseries. It is thought to be an introduced pathogen and only three clonal lineages are known (3). The North American lineage (lineage NA1, mating type A2) is responsible for infections in California and Oregon forests. The European lineage (lineage EU1, predominantly A1) is responsible for infections in Europe, but has also been found in nurseries in Oregon and Washington. A third lineage (NA2) has only been isolated in a few instances from nurseries in Washington and California. In June 2006, P. ramorum was isolated from diseased Viburnum tinus, Osmanthus heterophyllus, and O. fragrans cultivars from a Humboldt County retail nursery in northern California. We genotyped isolates and placed them into clonal lineages using microsatellite markers developed for P. ramorum (3,4). Genomic DNA was extracted from mycelia with the FastDNA SPIN kit (Q-Biogene, Morgan, Irvine, CA). Primers used were PrMS6, Pr9C3, PrMS39, PrMS43a, PrMS43b, and PrMS45 (3) and 18, 64, and 82 (4). We sized fluorescently labeled amplicons using capillary electrophoresis (3100 Avant Genetic Analyzer, Applied Biosystems, Foster City, CA). Isolate genotypes were compared with control isolates of known clonal lineage, including BBA9/95 (EU1), Pr102 (NA1), and WSDA3765 (NA2). Three of four isolates belonged to genotype EU1. The fourth isolate, obtained from O. fragrans, belonged to genotype NA1. We repeated genotyping on independent genomic DNA extractions and obtained identical results. Two EU1 isolates and the single NA1 isolate were tested for mating type (1) and found to be of A1, A1, and A2 mating type, respectively. The coexistence of A1 and A2 mating types in the same retail nursery suggests the potential for sexual reproduction, as is the case in P. infestans where clonal and sexual populations exist (2), although to date, sexual reproduction in nature has not been documented in P. ramorum. The California retail nursery infestation highlights the risks associated with the unintentional transport of host nursery stock infested with P. ramorum.
References: (1) C. M. Brasier and S. Kirk. Mycol. Res. 108:823, 2004. (2) N. J. Gr{\"u}nwald and W. G. Flier. Ann. Rev. Phytopathol. 43:171, 2005. (3) K. Ivors et al. Mol. Ecol. 15:1493, 2006. (4) S. Prospero et al. Mol. Ecol. 16:2958, 2007.}, isbn = {0191-2917}, author = {Niklaus J. Gr{\"u}nwald and Goss, E. M. and Larsen, M. M. and Press, C. M. and McDonald, V. T. and Blomquist, C. L. and Thomas, S. L.} } @article {152, title = {Marker stability throughout 400 days of in vitro hyphal growth in the filamentous ascomycete, Sclerotinia sclerotiorum}, journal = {Fungal Genetics and Biology}, volume = {45}, number = {5}, year = {2008}, note = {290WNTimes Cited:3Cited References Count:18}, month = {May}, pages = {613-617}, abstract = {
The stability of routinely used, population genetic markers through approximately I year of continuous laboratory growth was investigated in the common, plant pathogentic ascomycete Selerotinia sclerotiorum. Given reports of accelerated mutation rates at higher temperatures, both a permissive temperature, 22 degrees C, and a temperature at the high end of tolerance, 30 degrees C, were employed. Because mycelial growth rate was tracked among mitotic lineages established for each strain, a subsidiary objective was addressed, testing the stability of a 30 degrees C-competent phenotype. Twelve laboratory strains of S. sclerotiorum, including the genome sequence isolate, 1980, were propagated serially for up to 400 days at 22 degrees C. Five of these strains were also propagated at 30 degrees C. No mutations were observed in mycelial compatibility groupings (MCGs), DNA fingerprints, alleles at 7 microsatellite loci, or alleles at 56 AFLP loci. All of these markers show variation in field populations, which are likely much larger and influenced by different and more stochastic environmental processes. In S. sclerotiorum, population genetic markers were stable over time through serial transfer and growth of laboratory strains at both 22 degrees C and 30 degrees C. The strain isolated after extended drought and capable of infecting plants at 28 degrees C demonstrated the stability of its high temperature-competent phenotype, in addition to its stable growth rate at 22 degrees C. This observation has implications for modeling pathogen tolerance or adaptation under conditions of environmental stochasticity, including climate warming. (c) 2007 Elsevier Inc. All rights reserved.}, keywords = {aflp, experimental evolution, microsatellite, mutation, pathogen, populations, rates, rflp, vegetative incompatibility}, isbn = {1087-1845}, author = {Kohn, L. M. and Schaffer, M. R. and Anderson, J. B. and Niklaus J. Gr{\"u}nwald} } @article {154, title = {Pathogenicity of North American and European populations of Phytophthora ramorum and other Phytophthora spp. on Pacific northwest host plants}, journal = {Canadian Journal of Plant Pathology-Revue Canadienne De Phytopathologie}, volume = {30}, number = {2}, year = {2008}, note = {350KFTimes Cited:0Cited References Count:0}, month = {Apr-Jun}, pages = {373-373}, isbn = {0706-0661}, author = {Elliott, M. and Sumampong, G. and Varga, A. and Shamoun, S. F. and James, D. and Masri, S. and Briere, S. C. and Niklaus J. Gr{\"u}nwald} } @article {150, title = {Phytophthora database: a forensic database supporting the identification and monitoring of Phytophthora}, journal = {Plant Disease}, volume = {92}, number = {6}, year = {2008}, note = {302ZCTimes Cited:21Cited References Count:36}, month = {Jun}, pages = {966-972}, abstract = {
Phytophthora spp. represent a serious threat to agricultural and ecological systems. Many novel Phytophthora spp. have been reported in recent years, which is indicative of our limited understanding of the ecology and diversity of Phytophthora spp. in nature. Systematic cataloging of genotypic and phenotypic information on isolates of previously described species serves as a baseline for identification, classification, and risk assessment of new Phytophthora isolates. The Phytophthora Database (PD) was established to catalog such data in a web-accessible and searchable format. To support the identification of new Phytophthora isolates via comparison of their sequences at one or more loci with the corresponding sequences derived from the isolates archived in the PD, we generated and deposited sequence data from more than 1,500 isolates representing the known diversity in the genus. Data search and analysis tools in the PD include BLAST, Phyloviewer (a program for building phylogenetic trees using sequences of selected isolates), and Virtual Gel (a program for generating expected restriction patterns for given sequences). The PD also provides a customized means of storing and sharing data via the web. The PD serves as a model that easily can be adopted to develop databases for other important pathogen groups.}, keywords = {california, culture collection, disease management, forest trees, genome sequences, invasive pathogens, leaf-blight, molecular diagnosis, pathogen, ramorum, rot, sequence alignment, sp-nov., species causing root}, isbn = {0191-2917}, author = {Park, J. and Park, B. and Veeraraghavan, N. and Jung, K. and Lee, Y. H. and Blair, J. E. and Geiser, D. M. and Isard, S. and Mansfield, M. A. and Nikolaeva, E. and Park, S. Y. and Russo, J. and Kim, S. H. and Greene, M. and Ivors, K. L. and Balci, Y. and Peiman, M. and Erwin, D. C. and Coffey, M. D. and Rossman, A. and Farr, D. and Cline, E. and Niklaus J. Gr{\"u}nwald and Luster, D. G. and Schrandt, J. and Martin, F. and Ribeiro, O. K. and Makalowska, I. and Kang, S.} } @article {146, title = {Phytophthora ramorum: a pathogen with a remarkably wide host range causing sudden oak death on oaks and ramorum blight on woody ornamentals}, journal = {Molecular Plant Pathology}, volume = {9}, number = {6}, year = {2008}, note = {361PFTimes Cited:33Cited References Count:70}, month = {Nov}, pages = {729-740}, abstract = {
Phytophthora ramorum is an oomycete plant pathogen classified in the kingdom Stramenopila. P. ramorum is the causal agent of sudden oak death on coast live oak and tanoak as well as ramorum blight on woody ornamental and forest understorey plants. It causes stem cankers on trees, and leaf blight or stem dieback on ornamentals and understorey forest species. This pathogen is managed in the USA and Europe by eradication where feasible, by containment elsewhere and by quarantine in many parts of the world. Genomic resources provide information on genes of interest to disease management and have improved tremendously since sequencing the genome in 2004. This review provides a current overview of the pathogenicity, population genetics, evolution and genomics of P. ramorum.Taxonomy:Phytophthora ramorum (Werres, De Cock \& Man in\&$\#$39;t Veld): kingdom Stramenopila; phylum Oomycota; class Peronosporomycetidae; order Pythiales; family Pythiaceae; genus Phytophthora.Host range:The host range is very large and the list of known hosts continues to expand at the time of writing. Coast live oak and tanoak are ecologically, economically and culturally important forest hosts in the USA. Rhododendron, Viburnum, Pieris, Syringa and Camellia are key ornamental hosts on which P. ramorum has been found repeatedly, some of which have been involved in moving the pathogen via nursery shipments.Disease symptoms:P. ramorum causes two different diseases with differing symptoms: sudden oak death (bleeding lesions, stem cankers) on oaks and ramorum blight (twig dieback and/or foliar lesions) on tree and woody ornamental hosts.Useful websites: http://nature.berkeley.edu/comtf/, http://rapra.csl.gov.uk/, http://www.aphis.usda.gov/plant_health/plant_pest_info/pram/index.shtml, http://genome.jgi-psf.org/Phyra1_1/Phyra1_1.home.html, http://pamgo.vbi.vt.edu/, http://pmgn.vbi.vt.edu/, http://vmd.vbi.vt.edu./, http://web.science.oregonstate.edu/bpp/labs/grunwald/resources.htm, http://www.defra.gov.uk/planth/pramorum.htm, http://www.invasive.org/browse/subject.cfm?sub=4603, http://www.forestry.gov.uk/forestry/WCAS-4Z5JLL}, keywords = {1st report, california, coast live oak, forest, in-vitro, infestans, mitochondrial genome sequences, north-american, p-kernoviae, susceptibility}, isbn = {1464-6722}, author = {Niklaus J. Gr{\"u}nwald and Goss, E. M. and Press, C. M.} } @article {151, title = {Registration of W6 26740, W6 26743, and W6 26745 Green Pea Germplasm Resistant to Fusarium Root Rot}, journal = {Journal of Plant Registrations}, volume = {2}, number = {2}, year = {2008}, note = {483ABTimes Cited:0Cited References Count:6}, month = {May}, pages = {137-139}, abstract = {
Three F(8)-derived breeding lines W6 26740 (RIL 846_34; GP-96, PI 652444), W6 26743 (RIL 846_40; GP-97, PI 652445), and W6 26745 (RIL 847_36; GP-98, PI 652446) of green pea (Pisum sativum L.), selected from a recombinant inbred line population developed by the USDA-ARS in 2002, are unique in combining high levels of resistance to Fusarium root rot [caused by Fusarium solani (Mart.) Sacc. f. sp. pisi (F.R. Jones) W.C. Snyder \& H.N. Hans.] with acceptable agronomic traits. They will be useful as a resource for developing root rot resistant green pea cultivars. The parentage of W6 26740, W6 26743, and W6 26745 is a cross between \&$\#$39;Dark Skin Perfection\&$\#$39;/90-2131 made in 1994 at Pullman, WA. Dark Skin Perfection is a freezing and canning cultivar characterized by straight, blunt, green, double pods; it was used by pea breeders in the 1950s as a source of resistance to Fusarium wilt race 1 [caused by F. oxysporum Schlecht. f. sp. pisi (van Hall) Snyd. \& Hans]. 90-2131 is a germplasm release characterized by white flowers, green cotyledons, a clear seed coat, a black hilum and dimpled seed. This line has partial resistance to Aphanomyces root rot (caused by Aphanomyces euteiches Drechs.), Fusarium root rot, and Fusarium wilt races 1, 5, and 6. W6 26740, W6 26743 and W6 26746 are expected to serve as parental lines in the development of cultivars with improved disease resistance primarily to Fusarium root rot.}, isbn = {1936-5209}, author = {Coyne, C. J. and Porter, L. D. and Inglis, D. A. and Niklaus J. Gr{\"u}nwald and McPhee, K. E. and Muehlbauer, F. J.} } @article {155, title = {Susceptibility in Viburnum to Phytophthora ramorum}, journal = {Plant Disease}, volume = {92}, number = {2}, year = {2008}, note = {253GPTimes Cited:10Cited References Count:22}, month = {Feb}, pages = {210-214}, abstract = {
Phytophthora ramorum, the causal agent of sudden oak death on oak and tanoak and Ramorum blight or Ramorum shoot dieback on ornamentals, is a recently emerged pathogen. Viburnum is a genus of commonly grown ornamental shrubs known to be susceptible to P. ramorum. The entire genus has been placed on the P. ramorum host list. The range of susceptibility of genotypes in the genus is currently not understood. We evaluated whether or not cultivars in the genus Viburnum differ in susceptibility to P. ramorum in controlled, detached leaf inoculations using two isolates belonging to the two clonal lineages found in Oregon. The genus Viburnum shows remarkable differences in susceptibility to infection by P. ramorum. Viburnum genotypes differed significantly in susceptibility to P. ramorum in detached leaf inoculations. V. x burkwoodii was consistently the most susceptible host genotype, followed by V. plicatum \&$\#$39;Mariesii\&$\#$39; and V. lentago. Most cultivars evaluated for resistance to P. ramorum were not susceptible or developed only small lesions as determined with a detached leaf assay. Our work only provides information on leaf based resistance, and inferences on epidemic development in whole canopies and under field conditions cannot currently be made.}, keywords = {in-vitro, inoculation, nurseries, oregon, pathogen, rhododendron, sudden oak death}, isbn = {0191-2917}, author = {Niklaus J. Gr{\"u}nwald and Kitner, M. and McDonald, V. and Goss, E. M.} } @article {16858, title = {Tracing the path of pathogens}, year = {2008}, month = {12/2008}, pages = {43-51}, type = {Popular Press}, url = {http://www.oan.org/associations/4440/files/digger/Digger2008-12Pathogens.pdf}, author = {Parke, Jennifer and Lewis, Carrie and Gr{\"u}nwald, Niklaus J} } @article {157, title = {Development of codominant simple sequence repeat, single nucleotide polymorphism and sequence characterized amplified region markers for the pea root rot pathogen, Aphanomyces euteiches}, journal = {Journal of Microbiological Methods}, volume = {71}, number = {1}, year = {2007}, note = {224DLTimes Cited:2Cited References Count:6}, month = {Oct}, pages = {82-86}, abstract = {
Three kinds of genetic markers including simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs) and sequence characterized amplified regions (SCARs) were developed from Aphanomyces euteiches. Of 69 loci tested, seven SSR, two SNP and two SCAR markers were codominantly polymorphic. These codominant markers and dominant markers described herein will facilitate population genetic and evolutionary studies of this important plant pathogen. (C) 2007 Published by Elsevier B.V.}, keywords = {aphanomyces euteiches, oomycete, pisum sativum l., sequence characterized amplified region (scar), simple sequence repeat (ssr), single nucleotide polymorphism (snp)}, isbn = {0167-7012}, author = {Akamatsu, H. O. and Niklaus J. Gr{\"u}nwald and Chilvers, M. I. and Porter, L. D. and Peever, T. L.} } @article {162, title = {First report of haplotype I-b of Phytophthora infestans in Central Mexico.}, journal = {Plant Disease}, volume = {91}, number = {7}, year = {2007}, note = {181DLTimes Cited:0Cited References Count:4}, month = {Jul}, pages = {909-909}, keywords = {population-structure, toluca valley}, isbn = {0191-2917}, author = {Garay-Serrano, E. and Fernandez-Pavia, S. P. and Rodriguez-Alvarado, G. and Flier, W. G. and Lozoya-Saldana, H. and Rojas-Martinez, R. and Goss, E. M. and Niklaus J. Gr{\"u}nwald} } @article {158, title = {Late blight resistance of five Mexican potato cultivars in the eastern Sierra of the state of Mexico}, journal = {American Journal of Potato Research}, volume = {84}, number = {5}, year = {2007}, note = {242YCTimes Cited:1Cited References Count:50}, month = {Sep-Oct}, pages = {385-392}, abstract = {
cultivated potato areas as well as potential regions for commercial production and seed production. Prevailing weather conditions during the summer in these regions are also favorable for potato late blight disease (Phytophthora infestans (Mont) De Bary). The objectives of this work were to evaluate five resistant cultivars versus a susceptible control (\&$\#$39;Alpha\&$\#$39;) in the eastern sierra of the State of Mexico in order to assess resistance against the disease.Environmental conditions for potato late blight were favorable all five years of the study, and at the end of each growing cycle, Alpha had 100\% of late blight severity. Cultivars Montserrat, Michoacan, Nortena and Sangema (Rosita) showed acceptable disease resistance. Disease severity on the resistant varieties varied from 2\% to 20\%. There was a delay of two to eight weeks in the appearance of the first symptoms in relation to Alpha cultivar. These delays were four to five times greater than the ones observed at the Toluca Valley in previous experiments. Yield varied from 94 to 1,475 g per plant and was related to resistance to late blight. This work corroborates potato late blight resistance observed by INIFAP and CEEM scientists at the Toluca Valley. The expression of resistance is considered to be of great help in controlling the disease with a lower number of fungicide applications and better profit. In addition, using these varieties and therefore reducing the number of fungicide sprays also reduces direct damage to people and the environment.}, keywords = {diseases, durable resistance, field-resistance, fungicide, general resistance, horizontal resistance, host-resistance, integration, intraracial variation, phytophthora infestans, phytophthora-infestans populations, polygenic resistance, r-genes, race non-specific resistance, race-specific, resistance, solanum tubarosum, vertical resistance}, isbn = {1099-209X}, author = {Cadena-Hinojosa, M. A. and Diaz-Valasis, M. and Guzman-Plazola, R. A. and Fernandez-Pavia, S. P. and Niklaus J. Gr{\"u}nwald} } @article {163, title = {New populations of Sclerotinia sclerotiorum from lettuce in California and peas and lentils in Washington}, journal = {Phytopathology}, volume = {97}, number = {4}, year = {2007}, note = {150MFTimes Cited:17Cited References Count:61}, month = {Apr}, pages = {470-483}, abstract = {
Four populations of Sclerotinia sclerotiorum in North America were inferred previously, based on analyses of both rapidly evolving markers (DNA fingerprint and mycelial compatiblity), and multilocus DNA sequence spanning the range between fast and slow evolution. Each population was defined as an interbreeding unit of conspecific individuals sharing a common recent ancestor and arising in a unique evolutionary event. The present study applies this standard to extend characterization of S. sclerotiorum populations to the Western United States. Isolates of S. sclerotiorum (N = 294) were determined to represent three genetically differentiated populations: California (CA, lettuce), Washington (WA, pea/lentil), and Ontario (ON, lettuce). CA was the most diverse population yet sampled in North America. Clonality was detected in ON and WA. No DNA fingerprints were common among the populations. The index of association (I-A), based on fingerprint, was closer to zero (0) for CA than it was for the other populations. High diversity and lack of association of markers in California are consistent either with genetic exchange and recombination, or with large population size and high standing genetic variation. Intra- and interlocus conflict among three DNA sequence loci was consistent with recombination. The coalescent IGS genealogy confirmed subdivision and showed CA to be older than WA or ON. The Nearest Neighbor statistic on combined data confirmed subdivision among all present and previously defined populations. All isolates had both MAT1-1 and MAT1-2, consistent with uniform homothallism.}, keywords = {aspergillus-fumigatus, clonal lineages, coccidioides-immitis, drop incidence, field populations, gene genealogies, mating type, mcg, mdiv, migration, mitochondrial-DNA, multilocus haplotype, mushroom agaricus-bisporus, pathogenic fungus, phylogeny, pinus-radiata, population genetics, vegetative compatibility}, isbn = {0031-949X}, author = {Malvarez, G. and Carbone, I. and Niklaus J. Gr{\"u}nwald and Subbarao, K. V. and Schafer, M. and Kohn, L. M.} } @article {159, title = {Population dynamics of the sudden oak death pathogen Phytophthora ramorum in Oregon from 2001 to 2004}, journal = {Molecular Ecology}, volume = {16}, number = {14}, year = {2007}, note = {186CRTimes Cited:47Cited References Count:60}, month = {Jul}, pages = {2958-2973}, abstract = {
Phytophthora ramorum (Oomycetes) is an emerging plant pathogen in forests in southwestern Oregon (Curry County). Moreover, since 2003 it has been repeatedly isolated from plants in Oregon nurseries. In this study, we analysed the genetic diversity of the P. ramorum population in Oregon from 2001 to 2004 by using microsatellites. A total of 323 isolates (272 from the infested forest; 51 from nurseries) were screened at 10 loci. The overall P. ramorum population in Oregon is characterized by low genetic diversity and has all the hallmarks of an introduced organism. All isolates within the A2 mating type belonged to the same clonal lineage and no recombinant genotypes were found. The forest population (24 genotypes) was dominated by a single multilocus genotype which persisted over years, indicating that eradication efforts in the forest have not completely eliminated inoculum sources. In contrast, genotypic evidence suggests that eradication was effective in nurseries. In 2003 and 2004, a total of 11 genotypes were found in the nurseries (one belonged to the European lineage of P. ramorum) but no genotype was recovered in both sampling years. Significant differentiation and low gene flow were detected between nursery and forest populations. Only two nursery genotypes were also found in the forest, and then at low frequency. Thus, the nursery infestation is not caused by the genotypes observed in Curry County, but likely resulted through introduction of novel genotypes from nurseries out-of-state. This highlights the continued importance of sanitation and quarantine in nurseries to prevent further introduction and spread of P. ramorum.}, keywords = {california, differentiation, epidemiology, eradication, forest, genetic distance, genetic diversity, heterozygosity, infestans, microsatellite markers, microsatellites, north-america, nurseries, oomycetes, sp nov., trees}, isbn = {0962-1083}, author = {Prospero, S. and Hansen, E. M. and Niklaus J. Gr{\"u}nwald and Winton, L. M.} } @article {173, title = {Characterization of Phytophthora infestans (Mont.) De Bary. II. Subpopulations obtained from wild Solanum species}, journal = {Agrociencia}, volume = {40}, number = {3}, year = {2006}, note = {046DNTimes Cited:1Cited References Count:26}, month = {May-Jun}, pages = {325-333}, abstract = {
In the summer of 2000, isolates from natural infections of P. infestans (P.i.) were obtained from six wild species of Solanum planted ex-profeso under rainfed conditions in the Toluca Valley of Mexico to determine possible host-pathogen specificity and for characterization regarding mating type (MT; A1, A2), sensitivity to metalaxyl, and the presence of allozymes of glucose-6-phosphate-isomerase (Gpi) and peptidase (Pep). Solanum phureja and S. acaule presented diverse degrees of severity of the disease among individuals of each population. The rest of the species was uniformly resistant to the pathogen. Of 24 isolates from S. phureja, 13 multilocus genotypes were detected, the most frequent of which was the A2 100/100 Gpi and 100/100 Pep (22\%) and an A1:A2 ratio of 0.6:1. Nine multilocus genotypes were found in the population of P.i. obtained from S. acaule. The most common one was also A2, 100/100 Gpi and 100/100 Pep (22\% of such population too), with a NIT proportion of 1:1. In S. bulbocastanum, no particular genotype was more common, and the only MT was A1, nor was there a more frequent genotype found in S. caripense, where the proportion of MT AI:A2 was 0.25:1. The only genotype recovered from S. muticatum was A1 86/11, 92/100 (Gpi, Pep), corresponding to US1. The two isolates from S. andreanum were A1. 86/100 Gpi and 100/100 Pep. Solanum phureja and S. acaule had the greatest frequency of isolates highly resistant to metalaxyl, and to a lesser degree of resistance those of S. caripense and S. muricatum. The isolates from S. bulbocastanum and S. andreanum, two species resistant to P.i., were A1 and susceptible to metalaxyl. All of the homothallic isolates were highly resistant to metalaxyl, and host-pathogen specificity, was observed only in S. muricatum.}, keywords = {identification, isozymes, mating type, mating-type, metalaxyl resistance, mexico, migration, population-structure, potato, toluca valley}, isbn = {1405-3195}, author = {Lozoya-Saldana, H. and Perales-Rosas, D. and Fernandez-Pavia, S. P. and Niklaus J. Gr{\"u}nwald} } @article {165, title = {Hierarchical analysis of diversity, selfing, and genetic differentiation in populations of the oomycete Aphanomyces euteiches}, journal = {Phytopathology}, volume = {96}, number = {10}, year = {2006}, note = {089AJTimes Cited:14Cited References Count:70}, month = {Oct}, pages = {1134-1141}, abstract = {
Relatively little is known about the population biology of the legume pathogen Aphanomyces euteiches. A. euteiches is a soilborne pathogen causing Aphanomyces root rot of several legumes, including alfalfa, bean, lentil, and pea. Our objectives were to assess the degree of diversity, selfing, and population differentiation in A. euteiches. We contrasted populations within and among two geographically separated fields with a history of pea production. Molecular genotyping relied on amplified fragment length polymorphism analysis. Samples of A. euteiches recovered from two fields in northeast Oregon and western Washington confirmed previous reports of moderately high genetic diversity in populations of A. euteiches at the regional scale, but revealed higher-than-expected genotypic diversity within individual soil samples. Populations of A. euteiches were significantly differentiated at the soil sample, field, and regional level. The population structure appears to be patterned by regular selfing via oospores, a mixed reproductive system including both asexual and sexual reproduction, with occasional migration of novel genotypes or outcrossing.}, keywords = {chestnut blight fungus, cryphonectria-parasitica, genotypic diversity, multilocus structure, natural-populations, partial resistance, phytophthora-infestans, quantitative trait loci, recombination, single-zoospore, united-states}, isbn = {0031-949X}, author = {Niklaus J. Gr{\"u}nwald and Hoheisel, G. A.} } @article {168, title = {Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis}, journal = {Science}, volume = {313}, number = {5791}, year = {2006}, note = {081JITimes Cited:322Cited References Count:30}, month = {Sep 1}, pages = {1261-1266}, abstract = {
Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oomycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species\&$\#$39; genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oomycete avirulence genes.}, keywords = {arabidopsis, avirulence, downy mildew, effector proteins, expression, genes, locus, resistance, sojae, virulence}, isbn = {0036-8075}, author = {Tyler, B. M. and Tripathy, S. and Zhang, X. M. and Dehal, P. and Jiang, R. H. Y. and Aerts, A. and Arredondo, F. D. and Baxter, L. and Bensasson, D. and Beynon, J. L. and Chapman, J. and Damasceno, C. M. B. and Dorrance, A. E. and Dou, D. L. and Dickerman, A. W. and Dubchak, I. L. and Garbelotto, M. and Gijzen, M. and Gordon, S. G. and Govers, F. and Niklaus J. Gr{\"u}nwald and Huang, W. and Ivors, K. L. and Jones, R. W. and Kamoun, S. and Krampis, K. and Lamour, K. H. and Lee, M. K. and McDonald, W. H. and Medina, M. and Meijer, H. J. G. and Nordberg, E. K. and Maclean, D. J. and Ospina-Giraldo, M. D. and Morris, P. F. and Phuntumart, V. and Putnam, N. H. and Rash, S. and Rose, J. K. C. and Sakihama, Y. and Salamov, A. A. and Savidor, A. and Scheuring, C. F. and Smith, B. M. and Sobral, B. W. S. and Terry, A. and Torto-Alalibo, T. A. and Win, J. and Xu, Z. Y. and Zhang, H. B. and Grigoriev, I. V. and Rokhsar, D. S. and Boore, J. L.} } @article {175, title = {Phytophthora infestans (Mont.) de Bary. I. Host-pathogen specificity and resistance components}, journal = {Agrociencia}, volume = {40}, number = {2}, year = {2006}, note = {025GATimes Cited:2Cited References Count:24}, month = {Mar-Apr}, pages = {205-217}, abstract = {
The molecular identity of Phytophthora infestans strains infecting potatoes in the Toluca Valley has been documented. Nevertheless, the relationship of the P infestans genotypes to the host\&$\#$39;s genetic resistance is unclear. In order to identify potential host-pathogen specificity, isolates of the oomycete obtained from five potato varieties with differing levels of disease resistance were compared regarding mating type (MT), isozyme genotype for glucose-6-phosphate isomerase (Gpi) and peptidase (Pep), and sensitivity to metalaxyl. Also, host resistance components and specificity on the host-pathogen interaction were assessed twice in detached leaves in the laboratory and once in attached leaves in the greenhouse for three of the varieties. No mating type predominated relative to host genetic resistance (frequency of A1:A2; Alpha, susceptible: 1:1.6; Rosita, resistant: 1:0.75; Nortena, resistant: 1:0.9; Monserrat, resistant: 1:2; Michoacan, resist-ant: 1:0.20). Eighteen MT-isozyme combinations were identified from 97 isolates. All of them have been previously reported. The most common multilocus genotypes (MT, Gpi, and Pep) were A1, 86/100, 100/100 (37\% of the whole population) and A2, 86/100, 100/100 (14\%). Both genotypes represented 66\% of the P. infestans population obtained from cvs. Michoacan and Monserrat. The level of metalaxyl sensitivity was lower relative to the levels reported in previous studies. A relationship between frequency of pathogen genotypes and level of host genetic resistance was not observed. The isolate from Rosita was the most aggressive. It resulted in the largest lesion area in the laboratory and in the greenhouse,, and showed the highest sporulation in the greenhouse. The isolate from Alpha, which showed the highest sporulation in the laboratory, was second in sporulation under greenhouse conditions. Aggressiveness was higher in isolates obtained from resistant varieties and only limited host-pathogen specificity was observed in cvs. Alpha and Rosita. Suppression of lesion area and sporulation were the host resistance components identified only for the variety Nortena.}, keywords = {central mexico, clonal lineages, compatibility, field-resistance, genetic differentiation, genetic resistance, host-pathogen specificity, isozymes, late blight, mating types, metalaxyl, metalaxyl resistance, population-structure, solanum, toluca valley}, isbn = {1405-3195}, author = {Lozoya-Saldana, H. and Guzman-Galindo, L. and Fernandez-Pavia, S. P. and Niklaus J. Gr{\"u}nwald and McElhinny, E.} } @article {167, title = {Plant pathogen culture collections: It takes a village to preserve these resources vital to the advancement of agricultural security and plant pathology}, journal = {Phytopathology}, volume = {96}, number = {9}, year = {2006}, note = {078GCTimes Cited:9Cited References Count:64}, month = {Sep}, pages = {920-925}, abstract = {
Plant pathogen culture collections are essential resources in our fight against plant disease and for connecting discoveries of the present with established knowledge of the past. However, available infrastructure in support of culture collections is in serious need of improvement, and we continually face the risk of losing many of these collections. As novel and reemerging plant pathogens threaten agriculture, their timely identification and monitoring depends on rapid access to cultures representing the known diversity of plant pathogens along with genotypic, phenotypic, and epidemiological data associated with them. Archiving such data in a format that can be easily accessed and searched is essential for rapid assessment of potential risk and can help track the change and movement of pathogens. The underexplored pathogen diversity in nature further underscores the importance of cataloguing pathogen cultures. Realizing the potential of pathogen genomics as a foundation for developing effective disease control also hinges on how effectively we use the sequenced isolate as a reference to understand the genetic and phenotypic diversity within a pathogen species. In this letter, we propose a number of measures for improving pathogen culture collections.}, keywords = {california, collar rot, database, disease diagnosis, diversity, DNA barcodes, epidemiology, fungi, fusarium, identification, informatics, management, pathogen taxonomy and systematics, phytophthora-ramorum, population genetics, sp-nov.}, isbn = {0031-949X}, author = {Kang, S. C. and Blair, J. E. and Geiser, D. M. and Khang, C. H. and Park, S. Y. and Gahegan, M. and O{\textquoteright}Donnell, K. and Luster, D. G. and Kim, S. H. and Ivors, K. L. and Lee, Y. H. and Lee, Y. W. and Niklaus J. Gr{\"u}nwald and Martin, F. M. and Coffey, M. D. and Veeraraghavan, N. and Makalowska, I.} } @article {174, title = {Potential application of TRAP (targeted region amplified polymorphism) markers for mapping and tagging disease resistance traits in common bean}, journal = {Crop Science}, volume = {46}, number = {2}, year = {2006}, note = {021NYTimes Cited:30Cited References Count:40}, month = {Mar-Apr}, pages = {910-916}, abstract = {
Genetic resistance is an important component of integrated strategies used to control problematic diseases in common bean (Phaseolus vulgaris L.). Molecular linkage maps have been used to identify, tag, and map disease resistance genes and QTL in common bean, leading to improved breeding strategies and implementation of marker-assisted selection. Most widely used marker types, random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphisms (AFLP), for linkage mapping in bean are located randomly throughout the genome and associate with particular traits by chance. We sought to determine the potential application of a new marker system, TRAP, which uses expressed sequence information and a bioinformatics approach to generate polymorphic markers around targeted candidate gene sequences. TRAP markers were amplified by fixed primers designed against sequenced expressed sequence tag (EST) associated with disease resistance in the Compositae Genomics database or against sequenced resistance gene analog (RGA) from common bean. Seventeen of 85 TRAP markers located in the BAT 93/Jalo EEP558 core mapping population mapped in the vicinity of R genes. Six of 21 TRAP markers generated in the Dorado/XAN 176 mapping population were linked with newly identified QTL, two conditioning resistance to ashy stem blight (14\% and 16\% of the phenotypic variation explained, R 2), and one each conferring resistance to Bean golden yellow mosaic virus (BGYMV) (15\%) and common bacterial blight (30\%). The TRAP marker system has potential for mapping regions of the common bean genome linked with disease resistance.}, keywords = {anthracnose, candidates, colletotrichum-lindemuthianum, gene analogs, linkage map, loci, microsatellite, pcr, phaseolus-vulgaris, selection}, isbn = {0011-183X}, author = {Miklas, P. N. and Hu, J. G. and Niklaus J. Gr{\"u}nwald and Larsen, K. M.} } @article {176, title = {Screening techniques and sources of resistance to root diseases in cool season food legumes}, journal = {Euphytica}, volume = {147}, number = {1-2}, year = {2006}, note = {039UYTimes Cited:19Cited References Count:193}, month = {Jan}, pages = {201-221}, abstract = {
Soil-borne fungal diseases are among the most important factors, limiting the yield of grain legumes in many countries worldwide. Root rot, caused by Aphanomyces euteiches, Rhizoctonia solani, Fusarium solani and wilt, caused by several formae speciales of Fusarium oxysporum are the most destructive soil-borne diseases of pea, chickpea, lentil, fababean and lupin. The most effective control of these diseases is achieved through the use of resistant varieties. In this paper, recent advances in conventional and innovative screening methods for disease resistance are presented. Many grain legume accessions, which are maintained in national and international germplasm collections, have been evaluated for disease resistance and numerous resistant varieties have been released following incorporation of identified resistance genes from these sources. Recent identification of molecular markers tightly linked to resistance genes has greatly enhanced breeding programs by making marker assisted selection (MAS) possible and allowing the development of varieties with multiple disease resistance. Progress in the understanding of the biology of soil-borne fungal pathogens of grain legumes is also reviewed with particular reference to the genetic structure of their populations, diagnosis and host-pathogen interaction.}, keywords = {amplified polymorphic DNA, aphanomyces-euteiches drechs, f-sp ciceris, genetic variability, green dry pea, kabuli chickpea germplasm, oxysporum f.sp ciceris, pisum core collection, polymerase-chain-reaction, quantitative trait loci, real-time pcr, resistant varieties, soil-borne fungi}, isbn = {0014-2336}, author = {Infantino, A. and Kharrat, M. and Riccioni, L. and Coyne, C. J. and McPhee, K. E. and Niklaus J. Gr{\"u}nwald} } @article {164, title = {Selection for fungicide resistance within a growing season in field populations of Phytophthora infestans at the center of origin}, journal = {Phytopathology}, volume = {96}, number = {12}, year = {2006}, note = {108SSTimes Cited:11Cited References Count:51}, month = {Dec}, pages = {1397-1403}, abstract = {
The central highlands of Mexico should provide an optimal testing ground for evaluating the potential threat of selection for resistance to fungicides in the population of Phytophthora infestans. We evaluated the hypotheses that exposure to the fungicides azoxystrobin, cymoxanil, dimethomorph. fluazinam, mancozeb, metalaxyl, and propamocarb hydrochloride would lead to (i) a shift in the sensitivity distributions (i.e., selection) and (ii) a lower genotypic diversity of the population. We compared populations from unsprayed plots with populations that had been exposed to several applications of each of the fungicides within a single field season. This study provides novel baseline data and shows that the Toluca valley P. infestans population has a wide range of sensitivities to the fungicides fluazinam, cymoxanil, dimethomorph, metalaxyl, and propamocarb. Directional selection toward resistance combined with a reduction in genetic diversity of the P. infestans population was observed only for the fungicide metalaxyl. The results obtained provide direct experimental support for continuing vigilance regarding further introductions of exotic strains of P. infestans into the United States.}, keywords = {central mexico, durable resistance, evolution, fungal resistance, late-blight management, metalaxyl, phenylamide, potato, quantification, sensitivity, toluca valley}, isbn = {0031-949X}, author = {Niklaus J. Gr{\"u}nwald and Sturbaum, A. K. and Montes, G. R. and Serrano, E. G. and Lozoya-Saldana, H. and Fry, W. E.} } @article {166, title = {Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus}, journal = {BMC Genomics}, volume = {7}, year = {2006}, note = {095UXTimes Cited:17Cited References Count:58}, month = {Sep 28}, abstract = {
Background: Members of the genus Phytophthora are notorious pathogens with world-wide distribution. The most devastating species include P. infestans, P. ramorum and P. sojae. In order to develop molecular methods for routinely characterizing their populations and to gain a better insight into the organization and evolution of their genomes, we used an in silico approach to survey and compare simple sequence repeats (SSRs) in transcript sequences from these three species. We compared the occurrence, relative abundance, relative density and cross-species transferability of the SSRs in these oomycetes.Results: The number of SSRs in oomycetes transcribed sequences is low and long SSRs are rare. The in silico transferability of SSRs among the Phytophthora species was analyzed for all sets generated, and primers were selected on the basis of similarity as possible candidates for transferability to other Phytophthora species. Sequences encoding putative pathogenicity factors from all three Phytophthora species were also surveyed for presence of SSRs. However, no correlation between gene function and SSR abundance was observed. The SSR survey results, and the primer pairs designed for all SSRs from the three species, were deposited in a public database.Conclusion: In all cases the most common SSRs were trinucleotide repeat units with low repeat numbers. A proportion (7.5\%) of primers could be transferred with 90\% similarity between at least two species of Phytophthora. This information represents a valuable source of molecular markers for use in population genetics, genetic mapping and strain fingerprinting studies of oomycetes, and illustrates how genomic databases can be exploited to generate data-mining filters for SSRs before experimental validation.}, keywords = {coding DNA, DNA-sequences, drosophila-melanogaster, eukaryotic genomes, infestans populations, molecular markers, pathogen, point mutations, slippage events, tandem repeats}, isbn = {1471-2164}, author = {Garnica, D. P. and Pinzon, A. M. and Quesada-Ocampo, L. M. and Bernal, A. J. and Barreto, E. and Niklaus J. Gr{\"u}nwald and Restrepo, S.} } @article {182, title = {The biology of Phytophthora infestans at its center of origin}, journal = {Annual Review of Phytopathology}, volume = {43}, year = {2005}, note = {970DZTimes Cited:62Cited References Count:87Annual Review of Phytopathology}, pages = {171-190}, abstract = {
The central highlands of Mexico are considered to be a center of genetic diversity for both the potato late blight pathogen and for tuber-bearing Solanum spp. Recent work conducted in Mexico and South America sheds new light on the biology and evolution of Phytophthora infestans and other related Phytophthora pathogens. It now appears that Mexican Solanum species, which coevolved with P. infestans and were previously known for providing a source of R-genes, also provide a source of quantitative, rate-reducing resistance that is highly effective, stable, and durable. It is now apparent that Mexico is the center of origin not only of the potato late blight pathogen P. infestans, but also of several related Phytophthora species including R mirabilis, P ipomoeae, and possibly P phaseoli. We close with the hypothesis that these Phytophthora species evolved sympatrically from one ancestral host through adaptive radiation onto their respective four host families.}, keywords = {broad-spectrum resistance, central mexico, coevolution, epidemiology, genetic differentiation, germplasm collecting expedition, interspecific hybridization, mont debary, nevado-de-toluca, potato late blight, potato late-blight, resistance, solanum-bulbocastanum, speciation, western slopes}, isbn = {0066-4286}, author = {Niklaus J. Gr{\"u}nwald and Flier, W. G.} } @article {177, title = {Qualification of a plant disease simulation model: Performance of the LATEBLIGHT model across a broad range of environments}, journal = {Phytopathology}, volume = {95}, number = {12}, year = {2005}, note = {987QRTimes Cited:11Cited References Count:37}, month = {Dec}, pages = {1412-1422}, abstract = {
The concept of model qualification, i.e., discovering the domain over which a validated model may be properly used, was illustrated with LATEBLIGHT, a mathematical model that simulates the effect of weather, host growth and resistance, and fungicide use on asexual development and growth of Phytophthora infestans on potato foliage. Late blight epidemics from Ecuador, Mexico, Israel, and the United States involving 13 potato cultivars (32 epidemics in total) were compared with model predictions using graphical and statistical tests. Fungicides were not applied in any of the epidemics. For the simulations. a host resistance level was assigned to each cultivar based on general categories reported by local investigators. For eight cultivars, the model predictions fit the observed data. For four cultivars, the model predictions overestimated disease, likely due to inaccurate estimates of host resistance. Model predictions were inconsistent for one cultivar and for one location. It was concluded that the domain of applicability of LATEBLIGHT can be extended from the range of conditions in Peru for which it has been previously validated to those observed in this study. A sensitivity analysis showed that, within the range of values observed empirically, LATEBLIGHT is more sensitive to changes in variables related to initial inoculum and to weather than to changes in variables relating to host resistance.}, keywords = {confidence interval test, cultivars, envelope of acceptance test, genetic-structure, integrated control, management, metamodelling, phytophthora-infestans, potato late-blight, quantification, resistance, revalidation, toluca valley, validation}, isbn = {0031-949X}, author = {Andrade-Piedra, J. L. and Forbes, G. A. and Shtienberg, D. and Niklaus J. Gr{\"u}nwald and Chacon, M. G. and Taipe, M. V. and Hijmans, R. J. and Fry, W. E.} } @article {181, title = {Use of real-time PCR to examine the relationship between disease severity in pea and Aphanomyces euteiches DNA content in roots}, journal = {European Journal of Plant Pathology}, volume = {111}, number = {4}, year = {2005}, note = {927SLTimes Cited:6Cited References Count:31}, month = {Apr}, pages = {309-316}, abstract = {
Aphanomyces euteiches causes severe root rot of peas. Resistance is limited in commercial pea cultivars. Real-time fluorescent PCR assay specific for A. euteiches was used to study the relationship between disease severity and pathogen DNA content in infected peas. Five pea genotypes ranging in levels of resistance were inoculated with five isolates of A. euteiches. Plants were visually rated for disease development and the amount of pathogen DNA in roots was determined using the PCR assay. The susceptible genotypes Genie, DSP and Bolero tended to have significantly more disease and more pathogen DNA than the resistant genotypes 90-2079 and PI 180693. PI 180693 consistently had less disease, while 90-2079 had the lowest amount of pathogen DNA. The Spearman correlation between pathogen DNA quantity and disease development was positive and significant (P \< 0.05) for three isolates, but was not significant for two other isolates. This suggests that the real-time PCR assay may have limited application as a selection tool for resistance in pea to A. euteiches. Its utility as a selection tool would be dependent on the correlation between disease development and pathogen DNA content for a given pathogen isolate. The accuracy and specificity of the real-time PCR assay suggests considerable application for the assay in the study of mechanisms of disease resistance and the study of microbial population dynamics in plants.}, keywords = {damping off, disease resistance, drechs, fatty-acids, identification, lines, pea root rot, pisum-sativum, polymerase, populations, quantitative pcr, registration, resistance, rot}, isbn = {0929-1873}, author = {Vandemark, G. and Niklaus J. Gr{\"u}nwald} } @article {183, title = {First report of blight on Ipomoea purpurea caused by Phytophthora ipomoeae}, journal = {Plant Disease}, volume = {88}, number = {11}, year = {2004}, note = {865GBTimes Cited:2Cited References Count:2}, month = {Nov}, pages = {1283-1283}, keywords = {toluca valley}, isbn = {0191-2917}, author = {Badillo-Ponce, G. and Fernandez-Pavia, S. P. and Niklaus J. Gr{\"u}nwald and Garay-Serrano, E. and Rodriguez-Alvarado, G. and Lozoya-Saldana, H.} } @article {186, title = {First report of Pythium irregulare on lentils in the United States.}, journal = {Plant Disease}, volume = {88}, number = {3}, year = {2004}, note = {804QRTimes Cited:0Cited References Count:1}, month = {Mar}, pages = {310-310}, isbn = {0191-2917}, author = {Paulitz, T. C. and Dugan, F. and Chen, W. and Niklaus J. Gr{\"u}nwald} } @article {185, title = {Low diversity of vegetative compatibility types and mating type of Cryphonectria parasitica in the southern Balkans}, journal = {Plant Pathology}, volume = {53}, number = {3}, year = {2004}, note = {829MKTimes Cited:27Cited References Count:44}, month = {Jun}, pages = {325-333}, abstract = {
The diversity of vegetative compatibility (vc) types and mating type was estimated in populations of the chestnut blight fungus, Cryphonectria parasitica, throughout Macedonia and from selected areas in Greece. Nearly all of the 786 isolates (94\%) from Macedonia were in a single vc type, EU-12; all 379 isolates from Greece were EU-12. Only six of 20 populations in Macedonia had more than one vc type. The diversity of vc types in the most diverse populations of Macedonia was comparable with the least diverse populations found previously in Italy. All but six of the 313 isolates assayed had the same mating type, MAT-1, and no perithecia of Cryphonectria parasitica were observed in any population. These results lead to the conclusion that sexual reproduction does not occur in these populations. The lack of vc type diversity may indicate a high potential for the spread of hypoviruses and successful biological control with transmissible hypovirulence. However, if sexual reproduction should occur in Macedonian populations, up to 32 vc types would be possible by recombination among vegetative incompatibility loci.}, keywords = {biological-control, chestnut blight fungus, cryphonectria parasitica, cryphonectria radicalis, endothia-parasitica, genetic-structure, genotypic diversity, hypovirulence, incompatibility, magnaporthe-grisea, mating type, population-structure, subpopulations, vegetative incompatibility}, isbn = {0032-0862}, author = {Sotirovski, K. and Papazova-Anakieva, I. and Niklaus J. Gr{\"u}nwald and Milgroom, M. G.} } @article {187, title = {Soilborne oospores of Phytophthora infestans in central Mexico survive winter fallow and infect potato plants in the field}, journal = {Plant Disease}, volume = {88}, number = {1}, year = {2004}, note = {804QNTimes Cited:17Cited References Count:30}, month = {Jan}, pages = {29-33}, abstract = {
Survival and infectivity of oospores in soils naturally infested with R infestans oospores were studied in central Mexico. Sporangia were selectively eliminated from soil samples to determine infectivity attributable to the presence of oospores. Selective elimination of sporangia was achieved by two cycles of wetting and drying the soil. Oospore concentration, viability, and infectivity varied among soils collected during the winter fallow in different locations of central Mexico. In some soils, oospores were infective regardless of the time at which they were collected during the winter fallow. However, oospore viability and infectivity decreased following 2 years of intercropping. The number of stem lesions and initial disease, severity were significantly higher in soils with moderate (20 to 39 oospores g(-1) soil) oospore infestation compared with soils with low (0 to 19 oospores g-1 soil) infestation. Our study confirms that oospores can survive winter fallow and serve as a source of primary inoculum in the central highlands of Mexico. Oospore survival appeared lower in the Toluca Valley soil, which may be an indication of soil suppressiveness.}, keywords = {bioassay, germination, late-blight, oomycete, potato late blight, soil, toluca valley, viability}, isbn = {0191-2917}, author = {Fernandez-Pavia, S. P. and Niklaus J. Gr{\"u}nwald and Diaz-Valasis, M. and Cadena-Hinojosa, M. and Fry, W. E.} } @article {189, title = {Analysis of genotypic diversity data for populations of microorganisms}, journal = {Phytopathology}, volume = {93}, number = {6}, year = {2003}, note = {682CATimes Cited:78Cited References Count:47}, month = {Jun}, pages = {738-746}, abstract = {
Estimation of genotypic diversity is an important component of the analysis of the genetic structure of plant pathogen and microbial populations. Estimates of genotypic diversity are a function of both the number of genotypes observed in a sample (genotype richness) and the evenness of distribution of genotypes within the sample. Currently used measures of genotypic diversity have inherent problems that could lead to incorrect conclusions, particularly when diversity is low or sample sizes differ. The number of genotypes observed in a sample depends on the technique used to assay for genetic variation; each technique will affect the maximum number of genotypes that can be detected. We developed an approach to analysis of genotypic diversity in plant pathology that makes specific reference to the techniques used for identifying genotypes. Preferably, populations that are being compared should be very similar in sample size. In this case, the number of genotypes observed can be used directly for comparing richness. In most cases, sample sizes differ and use of the rarefaction method to calculate richness is more appropriate. In all cases, scaling either Stoddart and Taylor\&$\#$39;s G or Shannon and Wiener\&$\#$39;s H\&$\#$39; by sample size should be avoided. Under those circumstances where it might be important to distinguish whether richness or evenness contribute more to diversity, a bootstrapping approach, where confidence intervals are calculated for indices of diversity and evenness, is recommended.}, keywords = {chestnut blight fungus, cryphonectria-parasitica, dynamics, epidemiology, evenness, genetic-structure, microbial ecology, mycosphaerella-graminicola, pathogen populations, phytophthora-infestans, population genetics, setosphaeria-turcica populations, sexual reproduction}, isbn = {0031-949X}, author = {Niklaus J. Gr{\"u}nwald and Goodwin, S. B. and Milgroom, M. G. and Fry, W. E.} } @article {190, title = {The population structure of Phytophthora infestans from the Toluca Valley of central Mexico suggests genetic differentiation between populations from cultivated potato and wild Solanum spp.}, journal = {Phytopathology}, volume = {93}, number = {4}, year = {2003}, note = {659CJTimes Cited:43Cited References Count:50}, month = {Apr}, pages = {382-390}, abstract = {
The Population structure of Phytophthora infestans in the Toluca Valley of central Mexico was assessed using 170 isolates collected front cultivated potatoes and the native wild Solanum spp., S. demissum and S. xedinense. All isolates were analyzed for mitochondrial DNA (mtDNA) haplotype and amplified fragment length polymorphism (AFLP) multi-locus fingerprint genotype. Isolate samples were monomorphic for mtDNA haplotype because all isolates tested were of the la haplotype. A total of 158 multilocus AFLP genotypes were identified among the 170 P. infestans isolates included in this study. P. infestans populations sampled in the Toluca Valley in 1997 were highly variable and almost every single isolate represented a unique genotype based on the analysis of 165 AFLP marker loci. Populations of P infestans collected from the commercial potato-growing region in the valley, the subsistence potato production area along the slopes of the Nevado de Toluca, and the native Solanum spp. on the forested slopes of the volcano showed a high degree of genetic diversity. The number of polymorphic loci varied from 20.0 to 62.4\% for isolates collected from the field station and wild Solanum spp. On average, 81.8\% (135) of the AFLP loci were polymorphic. Heterozygosity varied between 7.7 and 19.4\%. Significant differentiation was found at the population level between strains originating from cultivated potatoes and wild Solanum spp. (P = 0.001 to 0.022). Private alleles were observed in individual isolates collected from all three populations, with numbers of unique dominant alleles varying from 9 to 16 for isolates collected from commercial potato crops and native Solanum spp.. respectively. Four AFLP markets were exclusively found present in isolates collected from S. demissum. Indirect estimation of gene flow between populations indicated restricted gene flow between both P. infestans populations front cultivated potatoes and wild Solanum hosts. There was no evidence found for the presence of substructuring at the subpopulation (field) level. We hypothesize that population differentiation and genetic isolation of P infestans in the Toluca Valley is driven by host-specific factors (i.e., R-genes) widely distributed in wild Solanum spp. and random genetic drift.}, keywords = {diversity, flow, mont debary, nevado-de-toluca, oospores, p-infestans, pcr amplification, resistance, sympatric speciation, western slopes}, isbn = {0031-949X}, author = {Flier, W. G. and Niklaus J. Gr{\"u}nwald and Kroon, L. P. N. M. and Sturbaum, A. K. and van den Bosch, T. B. M. and Garay-Serrano, E. and Lozoya-Saldana, H. and Fry, W. E. and Turkensteen, L. J.} } @conference {298, title = {Second International Aphanomyces Workshop}, booktitle = {Proceedings of the Second International Aphanomyces Workshop}, year = {2003}, publisher = {U.S. Department of Agriculture, Agricultural Research Service}, organization = {U.S. Department of Agriculture, Agricultural Research Service}, address = {Pasco, Washington}, abstract = {
This report comprises papers presented at the Second International Aphanomyces Workshop, June 17-18, 2003, Pasco, Washington. These proceedings summarize scientific contributions from the workshop on the genus Aphanomyces that emphasized the importance of these pathogens on legumes and sugar beets. The workshop covered a broad range of subject matter including disease management, host-parasite interactions, epidemiology, population genetics, breeding for resistance, and economic impact. These proceedings also include a bibliography on the genus Aphanomyces.}, keywords = {alfalfa, Aphanomyces, Aphanomyces cochlioides, aphanomyces euteiches, crop pathology, legumes, peas, phytopathogen, root rot, sugar beets}, author = {Niklaus J. Gr{\"u}nwald and Coyne, C. J.} } @article {188, title = {Sources of partial resistance to fusarium root rot in the Pisum core collection}, journal = {Plant Disease}, volume = {87}, number = {10}, year = {2003}, note = {722XWTimes Cited:12Cited References Count:17}, month = {Oct}, pages = {1197-1200}, abstract = {
Fusarium root rot, caused by Fusarium solani f. sp. pisi, is one of the most important fungal diseases of pea and is found in most pea-growing areas around the world. Currently, no commercial cultivars are resistant to this pathogen. Availability of new sources of partial resistance could provide another tool for managing Fusarium root rot. In all, 387 accessions from the Pisum core collection were evaluated for resistance to Fusarium root rot in two independent experiments. Nonparametric analysis of variance conducted on ranks of disease severity for each accession indicated that the two experiments corresponded well. Forty-four plant introduction lines with a disease severity rating of 2.5 or less on a 0-to-5 scale (where 5 = completely rotted) were selected as being partially resistant to root rot. Immunity to Fusarium root rot was not found. Comparison of disease resistance data for Aphanomyces root rot and Fusarium, root rot showed a weak, but significant and positive correlation. A complete listing of the data for the partial resistance of all accessions tested can be found at the National Plant Germplasm System website, United States Department of Agriculture-Agricultural Research Service.}, keywords = {pea, pisum sativum}, isbn = {0191-2917}, author = {Niklaus J. Gr{\"u}nwald and Coffman, V. A. and Kraft, J. M.} } @article {193, title = {Phytophthora ipomoeae sp nov., a new homothallic species causing leaf blight on Ipomoea longipedunculata in the Toluca Valley of central Mexico}, journal = {Mycological Research}, volume = {106}, year = {2002}, note = {Part 7606MGTimes Cited:29Cited References Count:28}, month = {Jul}, pages = {848-856}, abstract = {
A Phytophthora species was found on blighted foliage of Ipomoea longipedunculata, a morning glory native to the highlands of central Mexico. Based on host range, morphology, allozymes, mitochondrial DNA haplotype and rDNA sequences it is concluded that a new Phytophthora species, P. ipomoeae sp. nov., is the causal agent of leaf blight disease on I. longipedunculata.}, keywords = {infestans, phylogeny, population-structure, potato}, isbn = {0953-7562}, author = {Flier, W. G. and Niklaus J. Gr{\"u}nwald and Kroon, L. P. N. M. and van den Bosch, T. B. M. and Garay-Serrano, E. and Lozoya-Saldana, H. and Bonants, P. J. M. and Turkensteen, L. J.} } @article {192, title = {Potato cultivars from the Mexican National Program: Sources and durability of resistance against late blight}, journal = {Phytopathology}, volume = {92}, number = {7}, year = {2002}, note = {565ZATimes Cited:17Cited References Count:54}, month = {Jul}, pages = {688-693}, abstract = {
The Mexican National Potato Program has produced several cultivars with high levels of field resistance. We evaluated the durability of resistance to potato late blight of a selection of 12 such cultivars using data from 1960 to the present. Data were extracted from the field notebooks located in the archives of the Mexican National Potato Program in the John S. Niederhauser Library in Toluca, Mexico. There was a trend indicating that field resistances to potato late blight of Mexican cultivars released between 1965 to 1999 were durable. At least two of the cultivars, namely \&$\#$39;Sangema\&$\#$39; and \&$\#$39;Tollocan\&$\#$39;, have been gown on at least 4 to 5\% of the potato acreage and over long periods of time without decay in levels of field resistance. Pedigrees of the 12 cultivars indicate that most of the field resistance was introgressed from Solanum demissum. Field resistance might also be derived from commonly grown land-race cultivars such as \&$\#$39;Amarilla de Puebla\&$\#$39; and \&$\#$39;Leona\&$\#$39;. These have been grown in Mexico since about the 1780s. They have the appearance of S. andigena-derived material but their genetic background is unknown.}, keywords = {breeding, disease resistance, field-resistance, general resistance, germ plasm, host-resistance, intraracial variation, mont debary, nevado-de-toluca, phytophthora infestans, phytophthora-infestans populations, polygenic resistance, s. tuberosum, western slopes}, isbn = {0031-949X}, author = {Niklaus J. Gr{\"u}nwald and Hinojosa, M. A. C. and Covarrubias, O. R. and Pena, A. R. and Niederhauser, J. S. and Fry, W. E.} } @article {191, title = {Potato late blight management in the Toluca Valley: Field validation of SimCast modified for cultivars with high field resistance}, journal = {Plant Disease}, volume = {86}, number = {10}, year = {2002}, note = {596NETimes Cited:20Cited References Count:17}, month = {Oct}, pages = {1163-1168}, abstract = {
Management of potato late blight in the highland tropics is very costly and remains difficult. Reducing the impact of late blight through the use of resistant cultivars in combination with a fungicide forecasting system could lower the number of costly fungicide applications. Previously, we evaluated the fungicide advisory SimCast for use with Mexican cultivars of high levels of field resistance for use in the central highlands of Mexico and found that it predicted too many fungicide applications for cultivars of moderate to high levels of resistance. We adapted SimCast for cultivars with higher levels of resistance, and field validations conducted in 1999 and 2000 show that SimCast resulted in good disease control on cultivars ranging from susceptible to highly resistant. The number of fungicide applications forecast for cultivars with moderate to high levels of resistance was reduced. Precipitation was the environmental variable responsible for most of the forecasts made, Our work demonstrates that a predictive system can be portable from the temperate climate to a tropical highland climate. A user-friendly decision support system consisting of just a rain-gauge and the exclusive use of SimCast\&$\#$39;s fungicide units could be a valuable and affordable tool in managing potato late blight in the highland tropics.}, keywords = {central mexico, epidemiology, forecasts, phytophthora-infestans populations, plant pathogen, yield loss}, isbn = {0191-2917}, author = {Niklaus J. Gr{\"u}nwald and Montes, G. R. and Saldana, H. L. and Covarrubias, O. A. R. and Fry, W. E.} } @article {195, title = {Formation, production and viability of oospores of Phytophthora infestans from potato and Solanum demissum in the Toluca Valley, central Mexico}, journal = {Mycological Research}, volume = {105}, year = {2001}, note = {Part 8473FCTimes Cited:16Cited References Count:36}, month = {Aug}, pages = {998-1006}, abstract = {
Aspects of the ecology of oospores of Phytophthora infestans were studied in the highlands of central Mexico. From an investigation of a random sample of strains, it was found that isolates differed in their average capability to form oospores when engaged in compatible pairings. Most crosses produced large numbers of oospores but a few yielded none and some yielded only a few oospores. The results reveal that oospore production and fecundity is dependent on both isolates and the combining ability of a specific combination of parental strains. On average, 14\% of the oospores produced were viable as determined by the plasmolysis method. Viability ranged from a low 1\% in one cross to a high of 29\% in another cross. Oospores were found in 10-20\% of naturally infected Solanum demissum leaves from two different collections, and leaflets with two lesions per leaflet produced more oospores than did leaflets with 3-5 lesions per leaflet. There was no consistent trend for preferential mating between isolates from the same location or host.}, keywords = {genetics, inheritance, populations, resistance, segregation, sympatric speciation, virulence}, isbn = {0953-7562}, author = {Flier, W. G. and Niklaus J. Gr{\"u}nwald and Fry, W. E. and Turkensteen, L. J.} } @article {194, title = {Population structure of Phytophthora infestans in the Toluca valley region of central Mexico}, journal = {Phytopathology}, volume = {91}, number = {9}, year = {2001}, note = {466NLTimes Cited:56Cited References Count:43}, month = {Sep}, pages = {882-890}, abstract = {
We tested the hypothesis that the population of Phytophthora infestans in the Toluca valley region is genetically differentiated according to habitat. Isolates were sampled in three habitats from (i) wild Solanum spp. (WILD), (ii) land-race varieties in low-input production systems (RURAL), and (iii) modern cultivars in high-input agriculture (VALLEY). Isolates were sampled in 1988-89 (n = 179) and in 1997-98 (n = 389). In both sampling periods, the greatest genetic diversity was observed in RURAL and VALLEY habitats. Based on the Glucose-6-phosphate isomerase and Peptidase allozymes, the subpopulations from the three habitats were significantly differentiated in both sampling periods. In contrast to allozyme data for 1997-98, no differences were found among the three subpopulations for sensitivity to metalaxyl. Two groups of isolates identical for allozyme and mating type were further investigated by restriction fragment length polymorphism fingerprinting; 65\% of one group and 85\% of another group were demonstrated to be unique. The genetic diversity data and the chronology of disease occurrence during the season are consistent with the hypothesis that populations of P. infestans on wild Solanum populations are derived from populations on cultivated potatoes in the central highlands of Mexico near Toluca.}, keywords = {differentiation, diversity, evenness, fungicide resistance, genotypic diversity, mating-type loci, mont debary, nevado-de-toluca, potato late blight, rarefaction, resistance, richness, segregation, solanum, variability, western slopes}, isbn = {0031-949X}, author = {Niklaus J. Gr{\"u}nwald and Flier, W. G. and Sturbaum, A. K. and Garay-Serrano, E. and van den Bosch, T. B. M. and Smart, C. D. and Matuszak, J. M. and Lozoya-Saldana, H. and Turkensteen, L. J. and Fry, W. E.} } @article {196, title = {Potato late-blight management in the Toluca Valley: Forecasts and resistant cultivars}, journal = {Plant Disease}, volume = {84}, number = {4}, year = {2000}, note = {295XVTimes Cited:33Cited References Count:28}, month = {Apr}, pages = {410-416}, abstract = {
We evaluated host resistance and fungicide forecasting as components of integrated management in the Toluca Valley of central Mexico. Potato cvs. Rosita and Nortena showed high levels of resistance (20 and 4\% final disease severity, respectively) in the no-spray controls, whereas susceptible cv. Alpha was at 90\% defoliation well before the end of the season. Disease on Alpha was well managed with a weekly spray of chlorothalonil. None of three published forecast systems was entirely appropriate far this pathosystem. SIM-CAST accurately allocated fungicide for a susceptible cultivar but needs to be adapted for the high level of resistance of Rosita and Nortena. TOM-CAST and BLITECAST did not recommend the initial fungicide application until after disease was well established in the plots. We believe that the low-temperature response of Phytophthora infestans needs to be reevaluated for the highland tropics.}, keywords = {blitecast, epidemiology, fungicide applications, host-resistance, phytophthora-infestans, yield loss}, isbn = {0191-2917}, author = {Niklaus J. Gr{\"u}nwald and Rubio-Covarrubias, O. A. and Fry, W. E.} } @article {197, title = {Short-term cover crop decomposition in organic and conventional soils: Soil microbial and nutrient cycling indicator variables associated with different levels of soil suppressiveness to Pythium aphanidermatum}, journal = {European Journal of Plant Pathology}, volume = {106}, number = {1}, year = {2000}, note = {288GHTimes Cited:8Cited References Count:64}, month = {Jan}, pages = {51-65}, abstract = {
Stages of oat-vetch cover crop decomposition were characterized over time in terms of carbon and nitrogen cycling, microbial activity and community dynamics in organically and conventionally managed soils in a field experiment and a laboratory incubation experiment. We subsequently determined which variables describing soil microbial community dynamics, C and N cycling could be used as predictors of Pythium aphanidermatum damping-off incidence and relative growth. Disease incidence and relative growth of P. aphanidermatum were measured in growth chamber assays and in vitro growth tests. No significant differences were detected between the conventional and organic farming system with respect to either relative growth or disease incidence. Stepwise discriminant analysis on three classes of disease incidence or relative growth led to selection of qualitatively similar variables. Only one soil microbial variable, total biomass of actinomycetes, was selected. Total C and N content of debris extracted from soil as well as NH4-N content of soil were selected most consistently and show promise for assessment of potential damping-off incidence by P. aphanidermatum for young seedlings.}, keywords = {actinomycetes, bacteria, bioindicators, c : n ratio, container media, damping-off, decomposition rate constant, extraction method, fda hydrolytic activity, fungi, invertebrates, microbial activity, philippines, quality, root-rot, ultimum, yield}, isbn = {0929-1873}, author = {Niklaus J. Gr{\"u}nwald and Hu, S. and van Bruggen, A. H. C.} } @article {198, title = {Short-term cover crop decomposition in organic and conventional soils: Characterization of soil C, N, microbial and plant pathogen dynamics}, journal = {European Journal of Plant Pathology}, volume = {106}, number = {1}, year = {2000}, note = {288GHTimes Cited:22Cited References Count:53}, month = {Jan}, pages = {37-50}, abstract = {
Stages of oat-vetch cover crop decomposition were characterized over time in terms of carbon and nitrogen cycling, microbial activity and damping-off pathogen dynamics in organically and conventionally managed soils in a field and a controlled incubation experiment. A measurement of relative growth consisting of radial growth of a fungal colony over non-sterilized soil divided by that over sterilized soil was used as an assay of suppressiveness. No differences in relative growth of Pythium aphanidermatum and Rhizoctonia solani were detected between organic and conventionally managed soils amended with cover crop residue. Significant effects of cover crop decomposition stage on the relative growth of both pathogens were obtained. Relative growth of P. aphanidermatum was highest just after incorporation and decreased 3 weeks after incorporation. Relative growth of R. solani was highest about 20 days after incorporation, and decreased 2 weeks later in the organic system, but continued to increase in the conventional system. In both experiments, the N or C content, C:N ratio or dry weight of retrieved debris were significantly correlated with relative growth of P. aphanidermatum. Relative growth of R. solani was significantly correlated with the C:N ratio of soil or the C or N content of debris. Microbial activity was not consistently associated with relative growth of either pathogen.}, keywords = {biomass, carbon, cellulose, corky root, cover crop, damping-off, discriminant analysis, farming systems, fluorescein diacetate, lignin, nitrogen, potting mixes, pythium damping-off, severity, suppression, tomatoes}, isbn = {0929-1873}, author = {Niklaus J. Gr{\"u}nwald and Hu, S. and van Bruggen, A. H. C.} } @article {199, title = {Dynamics of bacterial populations in relation to carbon availability in a residue-amended soil}, journal = {Applied Soil Ecology}, volume = {13}, number = {1}, year = {1999}, note = {235YXTimes Cited:44Cited References Count:36}, month = {Sep}, pages = {21-30}, abstract = {
Bacterial response to alteration in C availability is important in understanding the microbial community structure and microbial interactions in soil ecosystems. Population dynamics of oligotrophic and copiotrophic bacteria in relation to soil C availability were examined and relationships between bacterial populations and water-extractable C, buffer-extractable C, mineralizable C or microbial biomass C were investigated. Both copiotrophs and oligotrophs were significantly stimulated by newly added C in the form of cover crop debris, but copiotrophs rapidly peaked at the very early stage of cover crop decomposition while peak populations of oligotrophs occurred at a later stage when available C decreased. Despite significant correlations between mineralizable C and water soluble C or buffer soluble C, dynamics of both copiotrophic and oligotrophic bacteria was best related to mineralizable C pool. Copiotrophs were logarithmically correlated to mineralizable C (p \< 0.0001), while oligotrophs were quadratically related to mineralizable C (p \< 0.0001), which is, to our knowledge, the first report showing that high C availability may have inhibited oligotrophs in natural soils. Oligotrophs were not significantly correlated to microbial biomass C, suggesting that oligotrophs only contributed a minor part to the soil microbial biomass pool. (C) 1999 Elsevier Science B.V. All rights reserved.}, keywords = {competition, environment, extraction method, forest soils, growth, microorganisms, oligotrophic bacteria, organic-carbon, rhizosphere, size}, isbn = {0929-1393}, author = {Hu, S. J. and van Bruggen, A. H. C. and Niklaus J. Gr{\"u}nwald} } @article {202, title = {Comparison of an in vitro and a damping-off assay to test soils for suppressiveness to Pythium aphanidermatum}, journal = {European Journal of Plant Pathology}, volume = {103}, number = {1}, year = {1997}, note = {Wj235Times Cited:17Cited References Count:34}, month = {Jan}, pages = {55-63}, abstract = {
Testing of soil samples in greenhouse assays for suppressiveness to soilborne plant pathogens requires a considerable investment in time and effort as well as large numbers of soil samples. To make it possible to process large numbers of samples efficiently, we compared an in vitro growth assay with a damping-off assay using Pythium aphanidermatum as the test organism on tomato seedlings. The in vitro test compares the radial growth or relative growth of the fungus in soil to that in autoclaved soil and reflects suppressiveness of soils to the pathogen. We used soils from a field experiment that had been farmed either organically or conventionally and into which a cover crop (oats and vetch in mixture) had been incorporated 0, 10, 21, and 35 days previously. We obtained a significant, positive correlation between damping-off severities of tomato seedlings in damping-off assays and both relative and radial growth in vitro. In addition, radial and relative growth of P. aphanidermatum in the in vitro assay were positively correlated with several carbon and nitrogen variables measured for soil and incorporated debris. We did not find differences between the two farming systems for either growth measures of P. aphanidermatum or disease severities on tomato at different stages of cover crop decomposition. The in vitro assay shows potential for use with any fungus that exhibits rapid saprophytic growth, and is most suitable for routine application in suppressiveness testing.}, keywords = {cellophane, conduciveness, conventional, corky root, cover crops, damping-off, extraction method, farms, lycopersicon esculentum, microbial activity, organic, plant-disease, receptivity, root-rot, severity, systems, tomato, tomatoes}, isbn = {0929-1873}, author = {Niklaus J. Gr{\"u}nwald and Workneh, F. and Hu, S. and van Bruggen, A. H. C.} } @article {200, title = {Microbial suppression of in vitro growth of Pythium ultimum and disease incidence in relation to soil C and N availability}, journal = {Plant and Soil}, volume = {195}, number = {1}, year = {1997}, note = {Ye363Times Cited:21Cited References Count:35}, month = {Aug}, pages = {43-52}, abstract = {
Experiments were designed to examine effects of the soil microbial community, C and N availability on in vitro growth of Pythium ultimum and its infection of cotton seedlings by manipulating the stage of cellulose decomposition, size and activity of microbial populations, and N availability. In comparison to the untreated control (CONT), cellulose addition alone (CELL) reduced soil nitrate by 35-80 fold, but had no significant effect on soil ammonium. Soil microbial biomass C (SMBC) increased over 2 fold in 14 days following cellulose addition, but significantly decreased in the following 10 days due to N limitation. Addition of both cellulose and N (NCELL) resulted in sustained SMBC for 24 days and significantly reduced in vitro P. ultimum growth and disease incidence. In vitro growth of P. ultimum and disease severity were consistently reduced in the order: CONT \> CELL \> NCELL. In vitro growth of P. ultimum was lower in soils previously incubated for 24 days than in those incubated for 14 days, and was most closely correlated to cumulative soil CO2 evolution (CO2T). Correlations between P. ultimum growth rates and NO3-N or total available N were substantial (p \< 0.05), but much less significant than those between the growth rates and SMBC, microbial activity measured as CO2 evolution rates or CO2T (p \< 0.0001). Addition of available N (NH4NO3) and C (glucose) just before the assays did not increase the in vitro growth of P. ultimum or disease severity on cotton seedlings, suggesting that time-dependent microbial processes or microbial metabolites significantly contributed to suppression of P. ultimum growth.}, keywords = {biomass, carbon and nitrogen availability, corky root, damping-off, disease incidence, extraction method, fluorescein diacetate, microbial activity, microbial biomass c and n, microbial suppression, nitrogen, organic amendments, peat container media, predicting suppressiveness, pythium ultimum, rot}, isbn = {0032-079X}, author = {Hu, S. and van Bruggen, A. H. C. and Wakeman, R. J. and Niklaus J. Gr{\"u}nwald} } @article {201, title = {Short-term effects of cover crop incorporation on soil carbon pools and nitrogen availability}, journal = {Soil Science Society of America Journal}, volume = {61}, number = {3}, year = {1997}, note = {Xc996Times Cited:36Cited References Count:34}, month = {May-Jun}, pages = {901-911}, abstract = {
Winter cover crops are increasingly used to maintain water quality and agoecosystem productivity. Cover crop incorporation influences transient soil microbial dynamics and nutrient availability at an early growth stage of subsequent crops. Short-term (less than or equal to 35 d) effects of cover crop incorporation on soil C pools and N availability were evaluated using sandy loam soils from organically and conventionally managed fields. Field and incubation experimeuts were designed to investigate whether cover crop incorporation had differential effects on C pools and how they were related to N mineralization. Labile C pools (soil carbohydrates and soil microbial biomass C [SMBC]) and coarse organic debris (GOD) increased two- to threefold, whereas total organic C increased by only 20\% by Day 7 after incorporation, The COD decreased faster than other C pools and best predicted SMBC (P \< 0.0001), A rapid decrease in SMBC after Day 21 was accompanied by an increase in available N. Discriminant analyses revealed that organic soils were distinct from conventional soils by their higher total C, N, and SMBC, and lower available N, but cover crop incorporation obscured the distinction in the first 14 d. Residue decomposition was Slightly faster in organic soils than in conventional soils at the early stage (3-4,vk), but \>30\% of N in cover crop residues was mineralized in both soils by Day 35 after incorporation, suggesting that manipulations of soil microbial dynamics and N mineralization in the short term can be of particular significance in synchronizing N release with the need of subsequent crops.}, keywords = {corky root, decomposition, dynamics, extraction method, grassland, management, microbial activity, rot, suppression, tomatoes}, isbn = {0361-5995}, author = {Hu, S. and Niklaus J. Gr{\"u}nwald and van Bruggen, A. H. C. and Gamble, G. R. and Drinkwater, L. E. and Shennan, C. and Demment, M. W.} }