Genetic diversity and population structure of Omani date palm assessed by SSR markers

Date palm ( Phoenix dactylifera L.) is a dioecious, clonally propagated crop in which accurate genetic characterization is essential for germplasm management and breeding. This study used 12 SSR loci to quantify genetic diversity and resolve population structure within a sex-stratified Omani collection (Oman female and Oman male accessions), interpreted against a limited international reference panel (IRD) used strictly for contextual comparison. Across groups, SSR loci were highly polymorphic and captured moderate to high diversity, with mean allelic richness ranging from Na = 9.75–12.58 and expected heterozygosity from He = 0.736–0.797. Observed heterozygosity was consistently lower (Ho = 0.596–0.646), yielding positive inbreeding coefficients (Fis = 0.164–0.193). Pairwise differentiation indicated very weak sex-based subdivision within Oman (Fst = 0.021; Nei’s D = 0.143), whereas comparisons between Oman groups and IRD showed higher but still modest differentiation (Fst ≈ 0.057–0.059; D ≈ 0.508–0.534). AMOVA supported this pattern, with 92% of variation within populations and 8% among populations. Multivariate and model-based structure analyses identified clear genetic clustering overall (optimal K = 4), driven primarily by separation involving the IRD panel rather than by sex within Oman. Collectively, these findings demonstrate substantial within-Oman diversity with minimal sex-based structuring, while highlighting measurable divergence between the Omani collection and the contextual IRD reference panel.