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Genetic Diversity of Buckwheat Cultivars (Fagopyrum tartaricum Gaertn.) Assessed with SSR Markers Developed from Genome Survey Sequences

Hou, Siyu, Sun, Zhaoxia, Linghu, Bin, Xu, Dongmei, Wu, Bin, Zhang, Bin, Wang, Xingchun, Han, Yuanhuai, Zhang, Lijun, Qiao, Zhijun, Li, HongYing
Plant molecular biology reporter 2016 v.34 no.1 pp. 233-241
Fagopyrum, alleles, breeding, buckwheat, cluster analysis, cultivars, genetic markers, genetic variation, genomics, germplasm, loci, medicinal plants, microsatellite repeats, plateaus, surveys, Bhutan, China, Nepal, United States
Tartary buckwheat is an important edible crop as well as medicinal plant in China. More and more research is being focused on this minor grain crop because of its medicinal functions, but there is a paucity of molecular markers for tartary buckwheat due to the lack of genomics. In this study, a genome survey was carried out in tartary buckwheat, from which SSR markers were developed for analysis of genetic diversity. The survey generated 21.9 Gb raw sequence reads which were assembled into 348.34 Mb genome sequences included 204,340 contigs. The genome size was estimated to be about 497 Mb based on K-mer analysis. In total, 24,505 SSR motifs were identified and characterised from this genomic survey sequence. Most of the SSR motifs were di-nucleotide (67.14 %) and tri-nucleotide (26.05 %) repeats. AT/AT repeat motifs were the most abundant, accounting for 78.60 % of di-nucleotide repeat motifs. SSR fingerprinting of 64 accessions yielded 49.71 effective allele loci from a total of 63 with the 23 polymorphic SSR primer combinations. Analyses of the population genetic structure using SSR data strongly suggested that the 64 accessions of tartary buckwheat clustered into two separate subgroups. One group was mainly distributed in Nepal, Bhutan and the Yunnan-Guizhou Plateau regions of China; the other group was mainly derived from the Loess Plateau regions, Hunan and Hubei of China and USA. The cluster analysis of these accession’s genetic similarity coefficient by UPMGA methods strongly supported the two subgroup interpretation. However accessions from Qinghai of China could be grouped into either of the two subgroups depending on which classification method was used. This region is at the intersection of the two geographical regions associated with the two subgroups. These results and information could be used to identify and utilize germplasm resources for improving tartary buckwheat breeding.