Genomic evidence supports an independent history of Levantine and Eurasian grapevines

Grapevine is a major horticultural crop that has been intertwined with human culture for Millennia. The Levant was an important center of the ancient winemaking industry until the collapse of the Byzantine Empire. Consequently, the identity of the ancient grapevine varieties of the Levant was considered lost. Here, we study the domestication history of Levantine grapevine samples using whole-genome sequencing data and show that some of the samples are authentic descendants of ancient Levantine varieties and that they conform to an independent lineage. This precious germplasm paves a route to bridge the ancient culture of the Levant and modern grapevine varieties. However, accelerated anthropogenic development in this region poses a threat to sampling locations; thus, additional efforts are urged to explore and conserve grapevine and other crop germplasm collections in the Levant. Summary: The ancient wine varieties of the Levant have inspired beliefs and rituals in human societies. Despite their importance, the original Levantine wine-grape varieties were considered lost due to cultural turnovers commencing in the 7th century CE, leading to the collapse of a flourishing winemaking industry in this region. We generated whole-genome sequence data for a diversity panel of wild and domesticated grapevine accessions. Demographic models, pedigree analysis, and genome scans were conducted to estimate divergence among four distinct groups. Demographic models designated that the domestication in the Caucasus region predated the emergence of the Levantine varieties and that authentic descendants of ancient varieties are represented among the Levantine accessions. We further explored the pedigree relationship among domesticated grapevines and identified intriguing relationship between the “Chardonnay” variety and Levantine accessions. Genomic scans and genetic load analyses further supported the distinct lineage history of the Levantine and Eurasian accessions. Tracking the domestication history of crops is challenging especially in a perennial species like grapevine. Although the Levantine varieties represent a distinct genomic background, it remains unclear whether ancient extensive gene-flow or direct domestication of Levantine wild grapevines has sparked the emergence of the ancient Levantine varieties.