Genetic diversity assessment and population structure analysis of pomegranate cultivars from different countries and Himalayan wild accessions

Pomegranate (Punica granatum L.) is a hardy crop packed with nutritional and medicinal benefits. Exploitation of wild pomegranate germplasm is necessary to meet the modern-breeding objectives of superior quality, high yield and resistance to biotic and abiotic stresses. Genetic diversity and genetic relatedness among 61 cultivars of six countries and 35 wild accessions of Himalaya (India) were assessed using 60 SSR markers. Seventeen polymorphic markers produced 55 polymorphic alleles with an average of 3.24 alleles per locus, 1.69 effective alleles, moderate polymorphic information content (0.33) and moderate gene diversity (0.37). Low-to-moderate genetic differentiation was observed among the accessions from different countries with F-ST values ranging from 0.015 to 0.140. Himalyan wild accessions exhibited modest genetic differentiation of 0.152 from rest of the cultivars. Phenetic analysis based on genetic distance, clustered 97 genotypes into two major clusters of Himalayan wild accessions and cultivars, with no clear distinction between countries. Congruently, population STRUCTURE analysis revealed the presence of two sub-populations, one of Himalayan wild type and the other of cultivated type (Central Asian). Genetically distant Himalayan wild accessions with high gene diversity can be exploited in breeding for resistance to biotic and abiotic stresses using modern breeding tools.