Genetic diversity analysis of indigenous pomegranate (Punica granatum L.) germplasm lines

Pomegranate (Punica granatum L.) is an ancient edible fruit crop well recognized for its immense nutraceutical and medicinal properties. Precise morphological characterization of wild, exotic and commercial (cultivar) varieties and understanding the molecular variability in perennial crops like pomegranate is essential for developing varietal DNA fingerprints, identifying true-to-type of genotypes, to avoid duplication and overcome the problem of clonal admixture. It has become a challenge to identify varieties based solely on observable phenotypic traits due to dynamic environmental factors that influence physical traits and increasing number of varieties. Hence, the implementation of stable molecular markers is the best complementary biotechnological tool, which fulfil the above requirements. In our first objective, we identified 24 polymorphic SSR markers out of 40. These SSRs screened on 13 different varieties of pomegranate. The PIC value ranged from 0.13 to 0.37 (mean 0.25) and heterozygosity percent ranged from 0.14% to 0.50% (mean 0.35%). Highest PIC value and heterozygosity observed in PgSSR78 marker. Similarity coefficient matrix showed the genetic distance between the twenty-four varieties, ranged from 0.58 to 0.99. Maximum similarity was observed between Alah and Khandari. Minimum similarity was found between IC318743 and 1185 followed by Maha and 1185. PgSSR16, PgSSR23, PgSSR49, PgSSR60, PgSSR32, PgSSR40, PgSSR78 markers were found with high PIC value and heterozygosity and these primers could be useful for pomegranate cultivar identification. From this study, microsatellite markers have proven to be very useful marker for developing varietal identification marker at early growth stage due to its high polymorphism, abundance, multi-allelic and co-dominant inheritance