Elucidation of genetic diversity and population structure in okra (Abelmoschus esculentus (L.) Moench) using SSR markers

A total of 72 okra genotypes, including 70 cultivated accessions and two wild relatives (Abelmoschus manihot var. tetraphyllus and A. moschatus), collected from diverse agro-ecological regions of India, were evaluated using 30 simple sequence repeat (SSR) markers to assess genetic diversity, population structure, and phylogenetic relationships. The SSR markers generated 65 scorable alleles, with an average of 1.90 alleles per locus and amplicon sizes ranging from 140 to 550 bp. The overall polymorphism rate was 85.71%, and AVRDC Okra-57 was identified as the most informative marker, exhibiting the highest polymorphic information content (PIC = 0.97), expected heterozygosity (He = 0.50), and Shannon’s information index (I = 0.693). Genetic diversity analysis revealed moderate levels of variation across the germplasm, with mean values of PIC, He, unbiased expected heterozygosity (UHe), Shannon’s index (I), and effective number of alleles (Ne) of 0.39, 0.23, 0.24, 0.36, and 1.41, respectively. Analysis of molecular variance (AMOVA) indicated that most of the genetic variation was distributed within individuals (66%), while 19% and 15% of the variation occurred among and within populations, respectively. Neighbor-joining cluster analysis separated the cultivated accessions from the wild relatives and grouped the cultivated genotypes into 11 sub-clusters, reflecting substantial genetic differentiation associated with domestication. Principal coordinate analysis (PCoA) supported the clustering pattern, with the first three axes explaining 52.69% of the total genetic variation (PC1 = 29.31%, PC2 = 14.24%). Population structure analysis identified four distinct genetic subpopulations (K = 4; ΔK = 57), with several admixed genotypes indicating historical gene flow among groups. These findings provide valuable insights into the genetic architecture of Indian okra germplasm and offer a useful resource for germplasm conservation, parental selection, and accelerated marker-assisted genetic improvement of okra.