Abstract
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 × 10-3, with averages of 1.0 × 10-4, 2.7 × 10-4, and 3.6 × 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 ∼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.
Highlights
Sesame (Sesamum indicum L., 2n = 26), a member of the Pedaliaceae family, is one of the most ancient oil crops and it is grown widely in both tropical and subtropical areas (Bedigian and Harlan, 1986; Ashri, 1998)
After excluding the singlenucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) < 0.01, there were left 89,924 (∼65.15%) high-quality SNPs (Supplementary Table 3) evenly distributed across the whole genome that could be used for further analysis
The proportion of rare SNPs (i.e., MAF < 0.05) we examined amounted to ∼68.04%, which was similar to those reported for the genomes of Arabidopsis and Alfalfa (Clark et al, 2007; Zhang et al, 2015)
Summary
In China, two sets of sesame germplasm collections are preserved by the Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (OCRI-CAAS), and by the Henan Sesame Research Center, Henan Academy of Agricultural Sciences (HSRC-HAAS). This OCRI-CAAS collection contains 4,251 accessions, most of which were sent to the National Genebank for long-term storage, and a core collection of 453 representative samples that was established in 2000 (Zhang et al, 2000). With support from the China Agriculture Research System (CARS15), there has been an extensive collecting effort conducted in the past 7 years: to date more than 5,200 accessions are preserved in the HSRC-HAAS collection, and a core collection of 501 representative samples was amassed by Liu et al (2017)
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