Fig. 5: Selective sweep on chromosome 17 and allele specific expression (ASE) of the LRR–receptor kinase VIT_217s0000g05570.

a Chromosomal plot of haplotype diversity. Haplotype diversity was calculated in blocks of five consecutive variant sites and plotted as the average of 50 consecutive blocks (blue dots) and a cubic smoothing spline (black line). The scale indicates Mb. The yellow background indicate the interval magnified in b. b V2.1 gene models (exons in blue), manually curated gene predictions (green) in the isopiperitenol/carveol dehydrogenase gene cluster (gene IDs 7 → 11), annotated transposable elements (light gray). c Frequency of 19 haplotypes shown in Supplementary Fig. 38 in 196 grapevine accessions. d Genotype frequency in 121 cultivated varieties. e VIT_217s0000g05570 (gene 6 in b) gene phylogeny. Numbers indicate the proportion of bootstrap trees supporting that clade. f ASE of the LRR–receptor kinase VIT_217s0000g05570 alleles in representative varieties of 15 haplotypic combinations, in softening berries (lower panel) and leaves (upper panel). The asterisks indicate statistically significant ASE levels (p-value <0.05) according to a Stouffer’s meta-analysis with weight and direction effect using n = 2 biologically independent samples. Cumulative expression is reported for each haplotypic combination lacking exonic SNPs in VIT_217s0000g05570 (H1-A/H1-G, H1-A/H10, H1-A/AX) and for a control variety homozygous for the H1-A haplotype. Gene expression for three haplotype combinations (H1-A/H10, H1-A/H6, H1-A/H4) was quantified in leaves of three different representative varieties (Tschvediansis Tetra, Picolit, Lambrusco Grasparossa) with the same genotype with respect to those used for berry gene expression. Source data of gene expression are provided as a Source Data file.