Fig. 3: Sex-linked polymorphisms along the sex-determining region in Vitis spp.

The number of all (a) and nonsynonymous sex-linked SNPs (b) per kbp across the sex-determining region (SDR). SNPs were identified by aligning all Vitis haplotypes to Vv vinifera Cabernet Sauvignon hap1 (H). Only SNPs strictly (100%) linked to one sex type were plotted. c Linkage disequilibrium (LD) across the region represented as the median of the squared correlation coefficients (r²) between all pairs of SNPs calculated within 20 kbp windows. d TF-binding motif conservation per gene promoter detected in the SDR. The x-axis denotes the location on the Cabernet Sauvignon hap1 (H) SDR, and the two black triangles along this axis mark the position of the genetic markers VVIB23¹⁷ and VSVV010¹⁰ that are closely linked to the SDR. The potential position of the recombination event responsible for the reversion to hermaphroditism in domesticated Vv vinifera is also indicated. e Gene composition of the H haplotype of Vv vinifera Cabernet Sauvignon hap1. Genes are colored as in Fig. 2d and white-colored genes are not sex-linked. Genes affected by nonsense mutations are indicated with an X followed by the affected haplotype and the gene name in parentheses. f Neighbor-joining clustering of the protein sequences encoded by each gene of the SDR. Yellow, purple and gray colors represent F, M and H haplotypes, respectively. Source data underlying Figs. 3a–d, f are provided as a Source Data file.