We used an eQTL approach to further investigate the association between expression of candidate genes and the resistance locus. For this, 12 resistant and 12 susceptible vines from the ‘Chardonnay’ × V. cinerea B9 progeny were sampled, 14 of which exhibited recombination within 15 cM of the Rda1 locus (Fig. 5). The total number of quality reads was 32.01 million per treatment (± Rda1 allele), with a sample mean and median of 2.67 million reads and 2.20 million reads per progeny, respectively (Supplementary Figure S1).Fig. 5Genotypes on chromosome 15 of the Vitis cinerea B9 map for individuals selected for RNA-Seq. Resistant (upper) and susceptible (lower) progeny showed genotype segregation at the Rda1 locus. The marker with highest LOD score is indicated. White and black dots indicate the allelic states AAxBA and AAxAB, respectively