Structural variation in grapevine domestication

Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and especially their population dynamics. Understanding these dynamics are critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here we identify SVs and study their evolutionary genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalog SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using the integrative comparison between Chardonnay and Cabernet Sauvignon by whole-genome alignment, long- and short read- alignment, we extended SV detection to a population sample. We found that strong purifying selection acts against SVs, but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex determination region and the berry color locus, where independent large, complex inversions have driven convergent phenotypic evolution.