The set of DE genes identified in the eQTL study of progeny vines differs from that in the DE study of the V. cinerea B9 parent. This is expected as consequences of distinct experimental designs. Differences in the V. cinerea B9 DE study reflected changes in expression between time points (0 and 48 hpi) for a single parental genotype. In contrast, differential expression in the eQTL study was among different genotypes (full siblings) at a single time point (14 hpi), obscuring whether genes were constitutively or dynamically differential. As the resistant Rda1 allele is dominant, observing the effect of the susceptible allele was only possible in the eQTL study, in which the two Rda1 alleles segregate, but not in the V. cinerea B9 DE study. Moreover, in the eQTL experiment, ‘Chardonnay’ alleles are also present, which can change the transcriptome profiles related to the V. cinerea B9 DE study. Regardless of these differences, both approaches suggest that NB-LRR gene-mediated host responses may be critical in determining the outcome of infection.