Genetic diversity and population structure of the Mediterranean sesame core collection with use of genome-wide SNPs developed by double digest RAD-Seq

Abstract

The Mediterranean sesame core collection contains agro-morphologically superior sesame accessions from geographically diverse regions in four continents. In the present investigation, the genetic diversity and population structure of this collection was analyzed with 5292 high-quality SNPs discovered by double-digest restriction site associated DNA (ddRAD) sequencing, a cost-effective and flexible next-generation sequencing method. The genetic distance between pairs of accessions varied from 0.023 to 0.524. The gene diversity was higher in accessions from Asia than from America, Africa, and Europe. The highest genetic differentiation was observed between accessions collected from America and Europe. Structure analysis showed the presence of three subpopulations among the sesame accessions, and only six accessions were placed in an admixture group. Phylogenetic tree and principal coordinate analysis clustered the accessions based on their countries of origin. However, no clear division was evident among the sesame accessions with regard to their continental locations. This result was supported by an AMOVA analysis, which revealed a genetic variation among continental groups of 5.53% of the total variation. The large number of SNPs clearly indicated that the Mediterranean sesame core collection is a highly diverse genetic resource. The collection can be exploited by breeders to select appropriate accessions that will provide high genetic gain in sesame improvement programs. The high-quality SNP data generated here should also be used in genome-wide association studies to explore qualitative trait loci and SNPs related to economically and agronomically important traits in sesame.

DArT-seq based SNP analysis of diversity, population structure and linkage disequilibrium among 274 cowpea (Vigna unguiculata L. Walp.) accessions

“…This may also imply that there is a degree of relatedness between accessions from different regions, which can be attributed to the transfer and or exchange of seeds between regions through breeding programs, human migration and or farmers exchanging preferred planting materials. Similar observations were reported in cowpea [18] and sesame [36]. In terms of population structure within each country, accessions from Nigeria, Ghana, Benin, Uganda, and India were predominant in the collection, and distributed in all clusters, regardless of the clustering approaches used.…”

“…The cowpea germplasm comprises 274 accessions from 33 countries (Fig. 1 were assigned to their respective cluster using the coe cient of ancestry values generated from the Structure software (Additional le 2), with the assumption that an individual is a true member of a given cluster if its coe cient of ancestry in this cluster is above 0.52 [36].…”

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

“…We performed quality filtering and then generated 349.86 M raw sequence reads by sequencing 95 sesame accessions using the Illumina HiSeq platform. Among these accessions, the mean number of reads was 3.68 M and the guanine-cytosine (GC) content was 38% [ 30 ]. We processed these filtered data using bioinformatic analysis and identified 7477 InDel sites ( Table 1 ).…”

“…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 ].…”

Genome-wide SNP detection in Darjeeling tea: unravelling genetic structure, functional impact and trait associations

“…With the advent of molecular genetic approaches, efficient genotyping with high throughput markers has led to an in-depth understanding of crop genetic resources, their management, and utilization in breeding programs (Basak et al, 2019;Sudan et al, 2019). Development of SNP markers along with the determination of their genomic position assisted the trait association analyses in plants and their diversity at an individual, community as well as species level (Guajardo et al, 2020;Huq et al, 2016;Luo et al, 2019;Mammadov et al, 2012).…”