芝麻SNP和InDel标记遗传多样性、群体结构及连锁不平衡分析

Genetic Diversity, Population Structure and Linkage Disequilibrium Analysis of Sesame Using SNP and InDel Markers

为了利用关联分析发掘芝麻种质资源中所携带的优异等位基因,并了解其对目标性状的贡献值。本研究利用随机分布于芝麻基因组中的206对多态性分子标记(167对SNP标记和39对In Del标记),对101份来自国内外的芝麻材料进行遗传多样性、亲缘关系、群体结构及连锁不平衡分析。206对标记共检测到413个等位基因;标记位点的基因多样性范围在0.01~0.53,平均为0.35;多态性信息含量(PIC)变幅为0.01~0.46,平均为0.28。供试芝麻材料间的遗传距离变幅为0.08~0.88,平均为0.43。聚类结果显示101份芝麻材料被划分为两大亚群:中国绝大部分(93.42%)芝麻材料被划分为第一大亚群,国外绝大部分(80.0%)芝麻材料被划分为第二大亚群。中国北方区(NR)与美洲区(AMR)的材料遗传距离最远(0.36);中国北方区(NR)与中部区(CR)的遗传距离最近(0.04)。群体结构分析显示供试芝麻群体由2个亚群组成,该结果与聚类分析以及主坐标分析结果一致。另外,绝大多数芝麻材料(>84%)间的亲缘关系较远(亲缘关系值<0.2)。连锁不平衡分析显示不同位点组合间存在一定程度的LD。利用SNP和InDel标记成功分析了101份芝麻品种的遗传多样性、亲缘关系、群体结构和连锁不平衡程度,本研究结果为后期芝麻杂交组合的配置以及利用关联分析准确挖掘芝麻有利基因提供了依据。

In order to discover the excellent alleles carried in sesame germplasm resources by using association analysis and understand their contributions to aimed traits, 101 sesame accessions from all over the world were scanned with 206 pairs of polymorphic molecular markers（167 SNP and 39 In Del markers） located randomly on sesame genome, then the analysis of genetic diversity, relationship, population structure and linkage disequilibrium（LD） were performed.A total of 413 alleles were detected from 206 pairs of markers. The value of gene diversity varied from 0.01 to 0.53, with the average of 0.35; The value of polymorphism information content（PIC） varied from 0.01 to 0.46, with the average of 0.28; the average of genetic distance among these sesame accessions was0.43 and varied from 0.08 to 0.88. The phylogeny showed that the 101 accessions were divided into two subgroups. Most（93.42%） Chinese sesame accessions were clustered into G1 subgroup, and most（80.0%） exoticaccessions were clustered into G2 subgroup. Furthermore, the genetic distance between sesame accessions from China northern region（NR） and American region（AMR） was the farthest（0.36）, and the accessions from China northern region（NR） and center region（CR） had the nearest genetic distance（0.04）. Population structure analysis revealed that sesame population was composed of two subpopulations, with consistence to the results of clustering analysis and principal coordinate analysis（PCo A）. In addition, most sesame accessions（ 〉84.0%） had a lower relationship（〈0.2）. Linkage disequilibrium analysis showed that a certain degree of LD existed among these marker loci pairs. The genetic diversity, relationship, population structure and linkage disequilibrium were analyzed by SNP and In Del markers and the results would provide a basis for disposition of further sesame hybrid combination and accurate selection of sesame beneficial genes by association analysis.