Simple sequence repeats (SSRs)-based characterization of cultivated and indigenous wild pomegranates (Punica granatum L.) revealed evolutionary relationships with considerable insights to native resource exploration

Pomegranate (Punica granatum L.) is an important commercial crop that has been cultivated for economic, ornamental and medicinal purposes since ancient times. In this study, simple sequence repeats (SSRs) markers were used to speculate the genetic association and mutations in cultivated and indigenous wild pomegranate germplasm. Twenty-two highly polymorphic SSR primers from 102 pairs amplified a total of 46 alleles with an average of 2.14 alleles per locus among the total 60 pomegranate genotypes. The size of the alleles varied from 50 to 300 bp. The primer pairs Pg4 and Pg14 amplified up to three alleles, while the remaining primers amplified only two alleles. The PIC value ranges from 0.03 for PGKVR-11 to 0.50 for Pg4, with an average of 0.27. Cluster analysis divided the pomegranate strains into four groups and further correlated with PCA. The first two major coordinates described the maximum cumulative variation between cultivated and wild genotypes. According to AMOVA analysis, the majority of genetic variation was found within the population that indicated the emergence of cultivated genotypes from the wild types through artificial selection. Furthermore, a mixed analysis performed using Bayesian gene structure and STRUCTURE software with accessions assigned to each of the two gene clusters that showed the existence of two gene pools and the nature of self-pollination of pomegranate crops. The present study revealed evolutionary relationships among cultivated and indigenous wild pomegranate with considerable insights to native resource exploration in various breeding and hybrid development programs.