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

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.

Genome-wide association study of seed coat color in sesame (Sesamum indicum L.)

“…Discussion [27]. In the present study, the panel of sesame accessions with wide geographic distribution, plentiful phenotype variation, sufficient genetic variation and weak population structure is advantageous for GWAS implementation [30]. However, the reliability of GWAS is usually disturbed by phenotypic variance associated with the environment.…”

“…In this study, 366 diverse sesame lines, which were assembled into an association-mapping panel [30], were used to evaluate the phenotypic variation of seed coat color, and three color space values (L-value, a-value, and b-value) with 2 replications were analyzed in 12 environments. Descriptive statistics for seed coat color are presented in Table 1.…”

Genome-Wide Discovery of InDel Markers in Sesame (Sesamum indicum L.) Using ddRADSeq

“…A few mapping and marker-assisted selection studies have also been conducted with the use of AFLP markers for the closed capsule mutant trait [ 26 ]; RAPD markers for corolla color [ 27 ]; and SSR markers for determinate growth habit [ 12 ], male-sterile gene [ 28 ], and oil and protein content [ 2 ] to improve the efficiency of sesame breeding programs. A large number of single nucleotide polymorphisms (SNPs) have also been identified with the advent of next-generation sequencing technology and have been used for the exploitation of genetic diversity [ 29 , 30 ], the construction of high-density linkage mapping [ 31 , 32 , 33 ], and the identification of candidate genes for the improvement of sesame production [ 34 , 35 , 36 , 37 ].…”

A Combinatorial Approach of Biparental QTL Mapping and Genome-Wide Association Analysis Identifies Candidate Genes for Phytophthora Blight Resistance in Sesame

“…Alternatively, SSRs are also widely used in genetic analyses because of their locus specificity, multi-allelic and codominant nature (Tautz, 1989). Using these and other markers systems, several interspecific and intraspecific genetic linkage maps have been developed in sesame (Mei et. al., 2017; Liu et al, 2015; Wei et.…”

“…Four main complexity reduction methods have been described to date: deep resequencing according to the principal of paired-end sequencing and de novo sequencing (RNA-Seq) using Illumina HiSeq 2000 platform can detect SNPs, small InDels and structural variants, restriction site-associated DNA (RAD) sequencing, reduced representation libraries (RRL), specific-locus amplified fragment (SLAF) sequencing, and GBS. Using the SLAF approach in sesame, 89,924, 71,793, and 9378 in three different studies (Cui et al, 2017; Mei et al, 2017; Zhang et al, 2013b). Recently, RAD sequencing has been applied in sesame for fine mapping of plant height and seed coat color (Wang et al, 2016).…”