Genome-wide SNP analysis uncovers population structure and genetic differentiation in longan (Dimocarpus longan Lour.)

Lour.) is an economically important fruit tree in tropical and subtropical Asia, yet population-level genomic resources supporting germplasm conservation and breeding remain limited. We resequenced 185 longan accessions and generated a high-density genome-wide SNP dataset for population genomic analyses, including phylogenetic inference, principal component analysis, model-based ancestry estimation, linkage disequilibrium analysis, and genome-wide diversity/differentiation scans. The analyses consistently resolved the panel into four genetic groups, while several accessions showed mixed ancestry, suggesting historical germplasm exchange. Genome-wide diversity and differentiation analyses indicated heterogeneous within-group variation but overall low differentiation among groups, with comparatively greater divergence involving group 4. Linkage disequilibrium decay revealed differences in haplotype structure among groups. A genome-wide scan integrating diversity reduction and elevated differentiation identified a narrow candidate interval on chromosome 11 (17.79-17.98 Mb) showing a localized sweep-like signature. These results provide a population-genomic framework for longan germplasm classification, conservation, and breeding-oriented follow-up.