Assessment of genetic diversity and species relationship of genus Cotoneaster in the Kashmir Himalaya

The characterization of the genus Cotoneaster is crucial for its use, conservation, and breeding programs. In this study, we evaluated the genetic diversity of 102 individuals from seven species (C. nummulariodes, C. microphyllus, C. roseus, C. confusus, C. nummularius, C. horizontalis, and C. affinis) collected from various locations in the Kashmir Himalaya, India. Using 10 simple sequence repeat (SSR) markers, we identified a total of 51 alleles. The average polymorphic information content (PIC) value of 0.54, indicated high polymorphism. Eleven private alleles were detected across seven SSR loci. The percentage of polymorphic loci ranged from 80 to 90% across species, with an overall percentage of 87.14%. Observed heterozygosity varied from 0.15 to 0.29 (average 0.23) and expected heterozygosity ranged from 0.30 to 0.49 (average 0.43). The fixation index values showed moderate to significant inbreeding. Interspecific diversity analysis showed that C. nummularius had the highest genetic diversity, while C. microphyllus had the lowest. The analysis of molecular variance (AMOVA) indicated that 85% of genetic variation existed within species and 15% variation between species, with an Fst value of 0.15, thereby suggesting moderate genetic differentiation among species. The unweighted pair group method with arithmetic mean (UPGMA) and STRUCTURE analysis divided the individuals of the seven species into two main clusters with distinct species compositions and admixed patterns suggesting ongoing gene flow and hybridization. To our knowledge, this is the first analysis of the genetic diversity and relationships of Cotoneaster species in the Kashmir Himalayan region. The findings will assist in the efficient utilization, conservation, and marker-assisted selection-based breeding programs of Cotoneaster.