We found 16 DE genes between resistant and susceptible progeny 14 h after inoculation, at FDR ≤ 0.05, including three NB-LRR genes on chromosome 15 (Supplementary Table S3). Expression was significantly predicted by alleles at the Rda1 locus for 6 of these 16 genes: a mannitol dehydrogenase gene and the three aforementioned NB-LRRs on chromosome 15 were up-regulated in susceptible vines, while a cytochrome P450 monooxygenase gene (CYP78A3p) and an auxin-responsive protein IAA17 gene were up-regulated in resistant vines (Table 5). The NB-LRRs VIT_15s0046g02730 and VIT_15s0046g02800 located at 19.45 and 19.53 Mbp, respectively, were the only two eQTL located within the Rda1 interval in the PN40024 12X.0 reference genome.Table 5Differential expression (DE) and expression QTL (eQTL) mapping statisticsGeneGene chraGene position (bp)aGene functional annotationlogFCbDE p valueeQTL LODeQTL LOD ThrceQTL PVEdeQTL effectVIT_15s0046g027301519,454,696–19,457,671PRF disease resistance protein2–40.0016.33.570.16.06VIT_15s0021g00120159,388,654–9,389,448RPP13 recognition of Peronospora parasitica 1325.36 × 10−115.13.662.719.9VIT_15s0046g028001519,528,135–19,530,195PRF disease resistance protein6.50.0054.83.460.31.92VIT_00s0346g00110Un24,788,096–24,791,922Mannitol dehydrogenase4.50.0273.13.044.86.30VIT_15s0048g029001517,005,384–17,007,131Cytochrome P450 monooxygenase CYP78A3p− 3.40.0293.12.645.0− 5.90VIT_09s0002g0516094,853,689–4,862,025Auxin-responsive protein IAA17− 2.40.0293.63.050.1− 12.6Six genes showed association between transcription levels and the Rda1 locus, located between 19.3 and 19.6 Mbp of chromosome 15Genetic maps were used for multiple QTL mapping of transcription levels (FPKM) of differentially expressed genes on a subset of 24 progeny from ‘Chardonnay’ × V. cinerea B9aChr and gene positions correspond to the physical location in the 12X.0 PN40024 Vitis vinifera reference genome; chr Un corresponds to the unassembled pseudo chromosomeblogFC corresponds to the log2 fold changecLOD Thr (threshold) was determined by permutation test (10,000) at α = 0.05dPVE refers to the percentage of transcript variance explained by the Rda1 locus