Genetic diversity and population structure analysis of papaya (Carica papaya L.) germplasm using simple sequence repeat (SSR) markers

Papaya (Carica papaya L.) is a versatile tropical fruit crop with economic and nutritional benefits. Assessing genetic diversity of the germplasm is essential for effective collection, conservation management and utilization of resources for breeding purposes. Genetic variability and population structure were studied for 55 papaya accessions including landraces, cultivars, and exotic collections, using 15 simple sequence repeat (SSR) markers. SSR analysis data revealed a total of 95 alleles with an average of 6.3 alleles per marker and an average heterozygosity of 0.75. All the markers were polymorphic, with an average PIC value of 0.72. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on shared allele distance grouped the accessions into four main clusters. Genetic structure based on the structure algorithm identified two populations, whereas discriminant analysis of principal components revealed four distinct genetic clusters. Remarkably, these clusters were not linked to the geographic regions. The analysis of molecular variance (AMOVA) indicated a variation of 75% within individuals and 22% between populations. Fst = 0.216 and N_m = 0.205 showed moderate genetic relationship within populations. These findings have implications for marker-assisted breeding, improvement of conservation strategies, detection of duplicates, and framing policies for sustainable crop utilization.