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Genetic Diversity, Population Structure, and Linkage Disequilibrium of an Association-Mapping Panel Revealed by Genome-Wide SNP Markers in Sesame

文献类型： 外文期刊

作者： Cui, Chengqi 1 ; Mei, Hongxian 2 ; Liu, Yanyang 2 ; Zhang, Haiyang 2 ; Zheng, Yongzhan 2 ;

作者机构： 1.Nanjing Agr Univ, Cotton Res Inst, Natl Key Lab Crop Genet & Germplasm Enhancement, Nanjing, Jiangsu, Peoples R China

2.Henan Acad Agr Sci, Henan Sesame Res Ctr, Zhengzhou, Peoples R China

3.Minist Agr, Key Lab Oil Crops Huanghuaihai Plain, Zhengzhou, Peoples R China

4.Henan Prov Key Lab Oil Crops Improvement, Zhengzhou, Peoples R China

关键词： Sesamum indicum L.;SNPs;genetic diversity;population structure;linkage disequilibrium

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.753； 五年影响因子：6.612 ）

ISSN： 1664-462X

年卷期： 2017 年 8 卷

页码：

收录情况： SCI

摘要： The characterization of genetic diversity and population structure can be used in tandem to detect reliable phenotype-genotype associations. In the present study, we genotyped a set of 366 sesame germplasm accessions by using 89,924 single-nucleotide polymorphisms (SNPs). The number of SNPs on each chromosome was consistent with the physical length of the respective chromosome, and the average marker density was approximately 2.67 kb/SNP. The genetic diversity analysis showed that the average nucleotide diversity of the panel was 1.1 x 10(-3), with averages of 1.0 x 10(-4), 2.7 x 10(-4), and 3.6 x 10(-4) obtained, respectively for three identified subgroups of the panel: Pop 1, Pop 2, and the Mixed. The genetic structure analysis revealed that these sesame germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in the panel. The genome-wide linkage disequilibrium (LD) analysis showed that an average LD extended up to similar to 99 kb. The genetic diversity and population structure revealed in this study should provide guidance to the future design of association studies and the systematic utilization of the genetic variation characterizing the sesame panel.

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