Regional Genetic Signatures in Underrepresented Mediterranean Grapevine Germplasm: Comparative SSR Analysis Reveals Distinct Diversity Patterns in Greek, Moroccan, and Slovenian Landraces

Traditional Mediterranean grapevine landraces represent irreplaceable reservoirs of adaptive diversity, yet many regional germplasm pools remain poorly characterized, limiting conservation strategies and climate-resilient breeding. This study presents the first comparative genetic assessment of 154 local Vitis accessions from three historically interconnected but genomically underrepresented Mediterranean regions: Greece, Morocco, and Slovenia. Using 12 highly polymorphic nuclear SSR markers, we detected substantial genetic diversity (168 alleles; mean heterozygosity He = 0.881) with distinct regional signatures. Moroccan accessions exhibited the highest allelic richness and 11 private alleles, reflecting diverse agroecological adaptation. Slovenian germplasm formed a cohesive, genetically stable cluster with high effective allele numbers. Greek accessions exhibited the highest observed heterozygosity and 14 private alleles, consistent with the Aegean’s role as a major diversification hotspot. Despite >90% of variance occurring within individuals, AMOVA and pairwise FST (0.050–0.061) revealed low to moderate but significant geographic differentiation. Multivariate analyses (PCA, UPGMA) and Bayesian clustering (sNMF, K = 3) consistently resolved three regional genetic groups with varying admixture levels, consistent with a mosaic domestication model, as previously proposed for the Mediterranean basin, shaped by recurrent introductions, wild introgression, and region-specific selection. Our results show that peripheral Mediterranean germplasm harbors meaningful, regionally distinctive, substantial, non-redundant diversity not fully represented in surveys focused on climate adaptation, disease resistance breeding, and long-term genetic resource conservation. These findings challenge simplistic diffusion models and emphasize the strategic importance of geographically comprehensive sampling in grapevine conservation programs.