Sesamum indicum L. of the Pedaliaceae family is considered an economically important oil-bearing plant that has been cultivated for more than 5000 years. In this research, we examined genetic diversity and seed fatty acid composition in 11 Iranian populations of S. indicum. We extracted the nuclear DNA using the CTAB protocol and then amplified the genomes using 10 SCoT molecular primers. For the phytochemical study, the seed fatty acid methyl esters were subjected to a GC apparatus and their composition was determined. The data were then analyzed using PAST, POPGENE, Geno-Dive, and STRUCTURE software. We determined that the percentage of polymorphic loci was 62%. According to the AMOVA test and estimated genetic diversity parameters, high genetic differentiation occurred between the examined populations, which was followed by a low rate of gene flow and Hs. Based on the Nei’s genetic distance and Structure analysis, the populations were divided into seven genotype groups. Most identified genotypes had homogeneous genetic structures indicating a limited genetic flow rate. The phytochemical evaluation revealed that a great part of the seed oils was composed of unsaturated fatty acids with linoleic and oleic acids as the main compounds. We detected palmitic acid as the major saturated fatty acid. The populations were divided into four chemotype groups based on the seed oil fatty acids composition. However, the population clustering patterns in the molecular genetic and seed fatty acid analyses were not identical. These results indicated that some environmental parameters strongly affect the seed oil fatty acids composition. We suppose that the populations under study are comprised of several genotypes or cultivars grown in various Iranian locations.
