Evolutionary history of the grape sex-determining region in angiosperms and emergence of dioecy in Vitaceae

Dioecy, defined by the presence of either female or male flowers on separate individual plants, is rare in angiosperms. However, it has independently evolved multiple times from hermaphroditic ancestors. In Vitis spp., flower sex is determined by a ~200-kbp region with five genes involved in flower development and sexual identity. This study traces the evolutionary history of the Vitis sex-determining region (SDR) to assess whether it evolved in a conserved flowering-related locus. We analyzed the conservation of the Vitis SDR across 42 plant genomes and found collinearity in all 39 angiosperms, but not in non-flowering plants. The number of collinear genes and their rank-normalized gene conservation score were higher in the Vitis SDR compared to the rest of the genome, indicating its importance for flowering. We further explored SDR conservation within the Vitaceae family by long-read sequencing and haplotype phasing of eight species, including the outgroup Leea coccinea. Similarly, the Vitis SDR was highly conserved across the Vitaceae genomes, although variations in region size, primarily attributed to differences in repetitive elements, were observed. Interestingly, no recombination suppression was found in the dioecious Tetrastigma, suggesting a different sex determination mechanism. In Muscadinia rotundifolia, linkage disequilibrium analysis, haplotype comparison, and gene expression profiling showed that muscadine grapes have similar SDR boundaries and candidate sex-determining genes as Vitis. These results suggest that dioecy emerged in a common ancestor of the two grape genera at a locus associated with flower morphology and fertility, highly conserved in flowering plants.