Global Genetic Diversity and Population Structure of Mango (Mangifera indica L.) Germplasm Conserved in Oman Revealed Through SSR Markers

Mangifera indica L. (mango) is a major tropical fruit tree valued for its nutritional, economic, and cultural importance. Understanding the genetic diversity within mango germplasm is essential for conservation and for selecting parents in breeding programs. This study assessed the genetic variation of 126 mango accessions (378 samples) maintained in the National Mango GenBank in Oman, originating from 15 geographical regions across the Middle East, Africa, Asia, Australia, and the Americas. A total of 55 polymorphic SSR loci generated 706 alleles, averaging 12.8 alleles per locus, with allele number ranging from 4 (MiSHRS-23, MGDSSR17) to 25 (MiSHRS-18). Polymorphic information content (PIC) values ranged from 0.184 (SSR22) to 0.903 (LMMA01), indicating high marker informativeness. Expected and observed heterozygosity ranged between 0.024–0.496 and 0.048–0.992, respectively. Fixation indices (Fis, Fit, Fst) averaged − 0.978, 0.430, and 0.714, reflecting excess heterozygosity within accessions and strong differentiation among populations. Molecular variance partitioned approximately 87% of diversity among populations and 13% within populations. Cluster, PCoA, and STRUCTURE analyses separated accessions into two major genetic groups, with Oman forming a distinct cluster alongside a small number of foreign cultivars. This study demonstrates extensive genetic diversity in Oman’s mango germplasm and highlights SSR markers as an effective tool for distinguishing genotypes. The findings provide a critical foundation for cultivar preservation, parent selection, and future genome-wide association and marker-assisted breeding in mango.