Mining of microsatellite markers using next generation sequencing data and its application in genetic relationship analysis of tartary buckwheat (Fagopyrum tataricum Gaertn)

Fagopyrum genus is composed of about 20 species and among them two major species, common buckwheat (F. esculentum) and tartary buckwheat (F. tataricum). SSR markers are only reported in common buckwheat with lower numbers based on enriched repeat libraries and next-generation sequencing (NGS) is a cost-effective alternative. Here we report the development of new cDNA SSR (cSSR) markers characterized from transcriptome sequence data of F. esculentum and F. tataricum using NGS and these cSSR markers were applied for the validation of buckwheat germplasm. From the transcriptome sequences, a total of 8,360 and 6,518 putative cSSR markers were identified in common and tartary buckwheat, respectively, using SSR Locator. Among the cSSR markers, tetra-mer repeats are most abundant and occurred in rates of 54.9 and 37.3% in common and tartary buckwheat, respectively. To test the usefulness of newly developed cSSR markers with previously developed SSR markers based on the SSR motif enrichment library, in analysis of genetic relationship in tartary buckwheat, we selected five representative cSSR markers and applied to investigate the polymorphism of tartary buckwheat germplasm and found these markers can be applied in genetic diversity of germplasm with high polymorphism.