Genetic Diversity, Population Structure Analysis Using Ultra-High Throughput Diversity array Technology (DArTseq) in Different Origin Sesame (Sesamum indicum L)

Abstract Background Sesame is an important oil crop widely cultivated in Africa and Asia continent. Characterization of genetic diversity and population structure of sesame genotypes in these continents can be used to designing breeding methods. In the present study, 300 sesame genotypes comprising 209 local, and 75 exotic collection, and 16 released varieties provided from the Ethiopian Biodiversity Institute and research centers were used in the present study. Results The panel was genotyped using two ultra-high-throughput diversity array technology (DArT) markers (silicoDArT and SNP). Both markers were used to identify the genetic diversity and population structure of sesame germplasm. A total of 6115 silicoDArT and 6474 SNP markers were reported, of which 5002 silicoDArT and 4638 SNP markers were screening with quality control parameters. The average polymorphic information content values of silicoDArT and SNP markers were 0.07 and 0.08, respectively. For further analysis, the allele frequency for each SNP site was calculated and purified with MAF < 0.01 and left 2997 high-quality SNPs evenly distributed across the whole genome that could be used for subsequent analysis. All genotypes used in this study were descended from eight 8 geographical origins. The genetic diversity analysis showed that the average nucleotide diversity of the panel was 0.14. Considering the genotypes based on their geographical origin, Africa collections (0.21) as a whole without Ethiopian collection was more diverse than Asia and when further portioned Africa, North Africa (0.23) collection was more diverse than others, but at the continent level, Asia (0.17) was more diverse than Africa (0.14). The genetic distance among the sesame populations was ranged from 0.015 to 0.394, with an average of 0.165. The sesame populations was clustered into four groups. The structure analysis divided the panel into four subgroups and 21 genotypes were clustered as an admixture. These indicates genotypes from the same origin didn’t classify properly on the premise of the country of origin. Conclusions The genetic diversity and population structure revealed in this study should guide the future research work to design association studies and the systematic utilization of the genetic variation characterizing the sesame panel.