苦荞全基因组SSR位点挖掘及遗传多样性分析

苦荞是一种重要的杂粮作物.利用GenBank数据库中苦荞的8条染色体基因组序列进行SSR标记挖掘,并基于Primer 3.0设计SSR引物,筛选多态性高的引物进行遗传多样性评价.共检测到51 485个SSR位点,平均发生频率为114.07 Mb-1,二核苷酸重复型最多(78.20％),其次为三核苷酸重复型(17.76％...

Mining SSR Loci and Analysis the Genetic Diversity of Tartary Buckwheat Based on the Whole Genome Sequence

Tartary buckwheat （Fagopyrum tataricum） is an important minor crop. In this study， molecular markers of the simple sequence repeat （SSR） were mined from 8 chromosomes sequence of tartary buckwheat in GenBank database. SSR primers were designed by primer 3.0 software and those with high polymorphism were employed to evaluate the genetic diversity. A total of 51 485 SSR loci were screened with average frequency of 114.07 Mb^-1. Among these SSR motifs， dinucleotide repeat was the main type accounting for 78.20%， followed by trinucleotide repeat （17.76%）. There were 361 types of repeat motifs， while AT/AT （69.60 %）， AAT/TTA （2.49%） and AGA/TCT （2.10%） were the main repeat types. The SSRs length ranged from 12 to 228 bp， and the ratio of SSRs with length ranging from 12 to 20 bp was 57.93%， the ratio with length above 20 bp was 42.07%. It was found that the SSR types detected were specific to the chromosomes. Based on the type of SSR loci， 156 pairs of primers were designed and 17 pairs of primers were screened with high polymorphism to analyze the genetic diversity of the 42 local varieties of tartary buckwheat. The diversity of black tartary buckwheat samples in Meigu County was the highest. The diversity of samples in Butuo County was significantly lower than that in the other two counties. It was of great significance to identify and analyze tartary buckwheat germplasm resources and molecular marker-assisted breeding through a large number of SSR mining， especially the chromosome specific SSR loci mining. In this study， a large number of SSRs were mined， especially the chromosomal specific SSR sites were mined， which was of great significance for the identification and analysis of tartary buckwheat germplasm resources and the molecular marker-assisted breeding of tartary buckwheat. Genetic diversity analysis also revealed the availability of SSR markers and the level of genetic diversity of tartary buckwheat， which provided a new approach for the study of the conservation of genetic diversity of tartary buckwheat.