Population structure of wild and cultivated grapevines in Armenia

BACKGROUND: The South Caucasus region, including Armenia, is recognized as a center of early viticulture, home to the oldest known winery and a rich tradition of winemaking. Armenia's topography has contributed to the preservation of genetically diverse grapevine populations. Cultivated grapevines (Vitis vinifera ssp. vinifera or V.V. ssp. vinifera) and their wild ancestor (V. vinifera ssp. sylvestris or V.V. ssp. sylvestris) exhibit high genetic diversity, making them valuable resources for understanding domestication, adaptation, and breeding. Despite Armenia’s historical and economic importance, the genomic diversity of its wild and cultivated grapevines remains underexplored. We re-analyzed whole-genome sequencing data of 164 grapevine accessions from Armenia, including cultivated and wild individuals, taken from a previous study on worldwide collected vine accessions to characterize genomic diversity, population structure, and domestication history of this gene pool. RESULTS: Our analysis uncovered genetic patterns partly unique to Armenia. Population structure analysis revealed a clear genetic separation between wild and cultivated groups and three distinct ancestral components within the cultivated gene pool, reflecting a west-to-east geographical gradient in Armenia. This genetic cline correlates with a shift in usage, from table to wine grapes, and a transition in berry skin color from white to black. Additionally, we identified four distinct subgroups within wild populations in Syunik, suggesting notable diversity. Evolutionary history analysis indicates that wild and cultivated lineages began to separate ~18.5k years ago, with divergence intensifying ~4k years ago under human cultivation. Comparative genomic scans for divergent selection identified genomic regions associated with domestication traits, including disease resistance and biosynthesis of anthocyanin and flavanol. Genome-wide association, including k-mer-based approach studies, uncovered candidate markers linked to agronomic traits, such as berry skin color and bunch density. These results provide genomic resources and highlight targets for grapevine improvement and conservation. CONCLUSIONS: This whole-genome study on the genetic diversity of wild and cultivated grapevines from Armenia provides a valuable resource for identifying candidate genes and domestication-related regions associated with agronomic traits. The results underscore the importance of conserving local grapevine diversity in Armenia, a historically significant and genetically rich viticultural region.