Genetic diversity and population structure of a large usda sesame collection

Authors: Seay, Damien; Szczepanek, Aaron; DE LA FUENTE, GERALD N. - Sesaco; VOTAVA, ERIC - Sesaco; Abdel-Haleem, Hussein

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/24/2024
Publication Date: 6/26/2024
Citation: Seay, D., Szczepanek, A.E., De La Fuente, G., Votava, E., Abdel-Haleem, H.A. 2024. Genetic diversity and population structure of a large usda sesame collection. Plants. 13. Article 1765. https://doi.org/10.3390/plants13131765.
DOI: https://doi.org/10.3390/plants13131765

Interpretive Summary: The rapid advancements in next generation sequencing technologies reduces the cost, time, and efforts to develop and utilize high-throughput genotyping pipelines. Using Genotype-by-sequencing (GBS) technology, the current study genotyped a panel of 501 sesame accessions with 24K SNP markers to explore their genetic diversity and population structure. The 24K high-quality SNP markers covered the 13 chromosomes with an average 1900 SNP/chromosome, thus providing sufficient marker information for further genetic and breeding studies. Population structure and phylogenetic tree analyses identified two distinct subpopulations. Variation in polymorphism, genetic diversity indexes and Linage disequilibrium (LD) decay patterns indicate that directed selection and geographical adaptation may have affected the formation and differentiation within sesame natural populations at the chromosomal and, consequently, genome-wide level. This information can be used in future studies for allele/gene identification using genome-wide association analysis studies (GWAS), and ultimately providing a tool to enhance genetic gain in sesame breeding programs using innovative breeding methodologies such as marker assisted selection and genomic selection.

Technical Abstract: Sesame, Sesamum indicum L., is one of the oldest domesticated crops used for its oil and protein in many parts of the world. To build genomic resources for sesame that could be used to improve sesame productivity and responses to stresses, a USDA sesame germplasm collection of 501 accessions originating from 36 countries was used in this study. The panel was genotyped using genotyping-by-sequencing (GBS) technology to explore its genetic diversity and population structure and the relatedness among its accessions. A total of 24,735 high-quality single-nucleotide polymorphism (SNP) markers were identified over the 13 chromosomes. The marker density was 1900 SNP per chromosome, with an average polymor-phism information content (PIC) value of 0.267. The marker polymorphisms and heterozygosity estimators indicated the usefulness of the identified SNPs to be used in future genetic studies and breeding activities. The population structure, principal components analysis (PCA), and unrooted neighbor-joining phylogenetic tree analyses classified two distinct subpopulations, indicating a wide genetic diversity within the USDA sesame collection. Analysis of molecular variance (AMOVA) revealed that 29.5% of the variation in this population was due to subpopulations, while 57.5% of the variation was due to variation among the accessions within the subpopulations. These results showed the degree of differentiation between the two subpopulations as well as within each subpopulation. The high fixation index (FST) between the distinguished subpopulations in-dicates a wide genetic diversity and high genetic differentiation among and within the identified subpopulations. The linkage disequilibrium (LD) pattern averaged 161 Kbp for the whole sesame genome, while the LD decay ranged from 168 Kbp at chromosome LG09 to 123 Kbp in chromo-some LG05. These findings could explain the complications of linkage drag among the traits during selections. The selected accessions and genotyped SNPs provide tools to enhance genetic gain in sesame breeding programs through molecular approaches.