ABSTRACT
The domestication history of grapes (Vitis vinifera ssp. vinifera) has not yet been investigated with genome sequencing data. We gathered data for a sample of 18 cultivars and nine putatively wild accessions to address three features of domestication history. The first was demography. We estimated that the wild and cultivated samples diverged ~22,000 years ago. Thereafter the cultivated lineage experienced a steady decline in population size (Ne), reaching its nadir near the time of domestication ~8,000 years ago. The long decline may reflect low intensity cultivation by humans prior to domestication. Ne of the wild sample fluctuated over the same timeframe, commensurate with glacial expansion and retraction. Second, we characterized regions of putative selective sweeps, identifying 309 candidate-selected genes in the cultivated sample. The set included genes that function in sugar metabolism, flower development and stress responses. Selected genes in the wild sample were enriched exclusively for functions related to biotic and abiotic stresses. A genomic region of high differentiation between wild and domesticated samples corresponded to the sex determination region, which included a candidate gene for a male sterility factor and additional genes that vary in gene expression among sexes. Finally, we investigated the cost of domestication. Despite the lack of a strong domestication bottleneck, grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. We confirm that clonal propagation leads to the accumulation of recessive deleterious mutations, which is a likely cause of severe inbreeding depression in grapes.
