Varietal Identification of Promising Pomegranate Cultivars Using Novel Genomic and Genic Markers

This study deals with characterization of 12 popular Indian pomegranate varieties based on 36 morphological descriptors and 76 DNA markers. Twenty seven of 36 morphological descriptors showed polymorphism and identified 52 DNA markers that produced variety‐specific (30) and rare alleles (27). The low probability of identity (PI) values (4.0 × 10 −12 ) of 27 rare allele‐producing loci attested to their high discrimination power. Furthermore, principal coordinates analysis based on 27 rare alleles was consistent with the relationship of 12 pomegranate varieties inferred from their breeding records. Then selected a subset of eight markers to generate unique identifiers in the form of marker IDs and digital codes for 12 pomegranate varieties. Furthermore, multiplexing of 40 SSR markers allowed us to develop a low‐cost molecular assay for rapid and accurate identification of pomegranate varieties. Finally, tested the efficacy of eight markers by diversity analysis of 40 pomegranate genotypes and confirmed their ability to distinguish pomegranate genotypes. Through this study, we clearly demonstrated the application of 52 markers for varietal fingerprinting, construction of digital marker IDs and multiplex assay development for twelve Indian pomegranate varieties. Also demonstrated the application of these markers for germplasm characterization. These findings have implications for germplasm management and breeding efforts of pomegranate.