Georgian wild grapevine germplasm is confirmed to be genetically distinct from Mediterranean germplasm

The wild progenitor of the cultivated grapevine, Vitis vinifera subsp. sylvestris is a key reservoir of genetic diversity and adaptive traits. Georgia, one of the primary centres of grapevine domestication, still hosts remaining populations of wild grapevines that preserve unique genetic lineages. In this study, the genetic diversity and structure of 23 Georgian wild grapevine accessions were investigated using 18k SNP loci and compared with those of 112 additional wild genotypes from the Mediterranean basin. Genetic analyses revealed that wild Georgian grapevine populations from eastern Georgia constitute a single, highly diverse genetic pool with limited population stratification; however, cluster analysis detected geographically associated substructures, particularly within Kakheti. In the context of the Mediterranean basin, genetic analysis revealed a genetic distinctiveness of the Georgian grapevine population. Clustering and PCA consistently identified Georgian samples as a coherent and genetically distinct group, showing limited overlap with Mediterranean accessions. Population structure analyses supported three ancestral populations, with the Georgian group forming an independent cluster (POP2), while North African and Iberian Peninsula (POP1) and Western–Central European samples constituted the others. A minimum spanning network revealed three main populations, with the North African group acting as a genetic bridge between Georgian and Western–Central European wild grapevine samples. TreeMix analysis indicated a clear tree-like divergence among the three populations, with POP1 and POP2 forming sister groups and POP3 diverging earlier. Georgian samples showed the highest genetic drift, and no evidence of admixture or post-divergence gene flow was detected. Altogether, these results emphasise the importance of preserving Georgian wild grapevine germplasm for future conservation and breeding strategies.