Genome-wide SNP analysis reveals genetic diversity and structure of wild and cultivated olives (Olea europaea L.) in Oman

The olive (Olea europaea L.) crop has significant cultural, nutritional, and economic importance worldwide. While its genetic diversity has been extensively studied in the Mediterranean Basin, little is known about olive germplasm in the Arabian Peninsula, including Oman, where it represents a unique environment for olive cultivation. In Oman, both wild and cultivated olives are exposed to arid conditions, which may have led to unique genetic adaptations. Leaf samples were collected from 44 olive accessions, including wild populations (MN and UT) distributed across northern and southern Oman and introduced cultivars originating from the Mediterranean Basin and cultivated in Oman, as a comparative reference. Genomic DNA was extracted and genotyping-by-sequencing (GBS) libraries were prepared and sequenced on the Illumina NovaSeq X platform. High-quality reads were aligned to the Mediterranean olive reference genome, and single-nucleotide polymorphisms (SNPs) were called, filtered for quality, and annotated to assess their genomic distribution. Genetic diversity indices, population structure (PCA, DAPC, STRUCTURE), phylogenetic relationships, analysis of molecular variance (AMOVA), pairwise Fst/PhiST, and linkage disequilibrium were calculated to evaluate variation, differentiation, and evolutionary patterns among wild and cultivated olives. After quality filtering, 167,875 high-confidence SNPs were retained. Functional annotation revealed that many variants were located in coding and regulatory regions. For linkage disequilibrium analysis, a more stringent SNP filtering scheme was applied, and genome-wide LD showed a progressive decay of r2 with increasing physical distance. Introduced cultivars used as comparative reference genotypes exhibited moderate genetic diversity (He = 0.100–0.162) and negative or near-zero FIS values, indicating heterozygote excess likely due to clonal propagation, whereas Omani wild olive populations (MN and UT) showed markedly lower diversity (He = 0.060–0.106) and positive FIS values, reflecting reduced heterozygosity and limited gene flow. Multivariate (PCA and DAPC), STRUCTURE, and phylogenetic analyses consistently revealed strong genetic differentiation between wild and cultivated olives, with AMOVA indicating that ~ 51% of genetic variation was explained by differences among predefined groups, dominated by the contrast between wild and cultivated olives. This study provides an early genome-wide SNP analysis of Omani wild and cultivated olives. Clear genetic differentiation was observed between wild and cultivated groups, with wild populations showing distinct variation. These findings can inform future conservation and breeding efforts for olive germplasm in arid environments.