Whole-genome sequencing reveals genomic diversity and population structure of mango germplasm from the Jazan region of Saudi Arabia

Background Mango ( Mangifera indica L.) is an economically important tropical fruit crop, yet the genomic diversity of mango germplasm from the Jazan region of Saudi Arabia—the country's primary production hub—remains poorly characterized. This knowledge gap limits the effective use of regional genetic resources in breeding programs and conservation strategies under arid conditions. Methods We conducted whole-genome resequencing of 64 mango accessions from the Jazan region. Reads were mapped to the M. indica reference genome, and variants were called. After stringent quality control and filtering, 5,079,569 high-quality SNPs were retained for genetic diversity and population structure analysis. A compact 150-SNP fingerprinting panel was subsequently designed for routine cultivar identification. Results The genome-wide dataset revealed substantial genetic diversity (mean expected heterozygosity He = 0.3003, nucleotide diversity π = 5.87 × 10 -4 per bp). Population structure analysis resolved three genetically differentiated ancestry groups (K = 3): a South Asian-associated cluster (n = 25), an admixed Saudi/Southeast Asian cluster enriched for local Jazan breeding selections (n = 19), and an Egyptian/Americas-associated cluster (n = 16). Pairwise FST values ranged from 0.048 to 0.089, indicating low-to-moderate differentiation with appreciable within-cluster diversity. Linkage disequilibrium decayed to r 2 = 0.1 at approximately 142.5 kb. The 150-SNP fingerprinting panel distinguished all accessions with unique multilocus profiles (mean PIC = 0.3749, probability of identity = 5.25 × 10 -91 ). Conclusion Mango germplasm from the Jazan region harbors broad and structured genetic variation, establishing a regional genomic reference for accessions of diverse origin. The three-group structure reflects a complex introduction history with substantial admixture. The 150-SNP panel provides a practical tool for cultivar authentication, redundancy detection, and conservation prioritization, while the genome-wide SNP resource enables future trait-mapping studies and marker-assisted selection for mango improvement in tropical and subtropical dry regions.