Genetic diversity and hybridization potential of wild and commercial pomegranate populations for bacterial blight resistance

Abstract Pomegranate ( Punica granatum L.), valued for its nutritional and antioxidant properties, faces severe yield losses due to bacterial blight caused by Xanthomonas citri pv. punicae . Given the ecological resilience and genetic potential of wild populations, identifying resistant genotypes from indigenous germplasm is vital for sustainable breeding. This study assessed genetic diversity and structure among 23 pomegranate genotypes wild Daru accessions and commercial cultivars previously screened for blight resistance. Twenty simple sequence repeats markers yielded 1119 bands, with 1036 (92.58%) being polymorphic. Primers ESP05, ESP06, ESP13, and ESP14 exhibited 100% polymorphism. Polymorphism information content (PIC) values ranged from 0.08 to 0.460 (mean = 0.321), confirming moderate informativeness. Diversity indices revealed mean alleles per locus (Na = 2.14), effective alleles (Ne = 1.906), and Shannon’s index (I = 0.627). Commercial cultivars displayed greater diversity (Na = 3.00; He = 0.52) and private alleles (0.60) than wild populations, particularly Wild KL (from Kullu) (Na = 1.45; He = 0.25). Analysis of molecular variance revealed that 91% of the genetic variation observed is within populations. Pairwise population differentiation ranged from 0.091 to 0.289, indicating moderate to high differentiation, with gene flow values between 0.615 and 2.494. Principal coordinate analysis, Neighbor joining clustering, and STRUCTURE analysis (ΔK = 2) revealed two major clusters: commercial and wild types, with signs of admixture. Unique resistance-associated bands were identified in wild genotypes SH-14, SH-16, SR-15, and SL-23, linked to traits like acidity, tannins, and anthocyanins. Wild genotypes SR-11, SH-16, SL-22, and SL-23, selected as male parents, were hybridized with cultivars Bhagwa, Kandhari Kabuli, and Phule Super Bhagwa. The Bhagwa × SH-16 cross showed highest fruit set (88.90%), and Bhagwa × SL-23 had highest retention (66.67%). These F 1 progenies offer a promising genetic base for developing bacterial blight-resistant pomegranate cultivars with improved horticultural traits.