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Isolation and Characterization of Microsatellite Loci and Genetic Diversity in Cassava (Manihot esculenta Crantz)

Cassava is an economically important crop in Thailand. ‘Hanatee’, a Thai variety of cassava, was used to develop microsatellite markers from an enriched-genomic DNA library using (GAT)8, (GGA)8, and (AAAC)6 oligonucleotide repeats. Thirty-two primer pairs were developed and used to evaluate 40 M. esculenta Crantz samples originating from 15 countries. Nine polymorphic loci were identified with 2-9 alleles per locus and 0.0476–0.8179 polymorphic information content (PIC). The observed heterozygosity (Ho) and the expected heterozygosity (He) ranged from 0.0500 to 0.8500 and 0.0488 to 0.8356, respectively. Four loci showed significant deviation from the Hardy-Weinberg Equilibrium (HWE) and two pairs of loci revealed significant linkage disequilibrium (LD). Cross-species amplification was tested with four different Manihot sp. and one subspecies. All nine polymorphic primers were able to amplify DNA of these samples with the number of alleles ranging from one to four. The polymorphic SSR markers could be useful for accessing genetic diversity, including transferability, as well as for cassava breeding.