The elevated number of NB-LRR gene transcripts up-regulated in the susceptible progeny compared with the resistant progeny suggests that susceptibility and not resistance is mediated by the action of NB-LRR genes, which may facilitate the necrotrophic phase of the hemibiotrophic fungus. This is reminiscent of the wheat NB-LRR protein Tsn1, which confers sensitivity to ToxA from the necrotrophic fungi Stagonospora nodorum and Pyrenophora tritici-repentis (Faris et al. 2010). Alternatively, sequence divergence between the resistance allele and the reference transcriptome derived from V. vinifera ‘Pinot noir’ may have resulted in a misalignment of reads, resulting in lower FPKM values for the resistance allele. To elucidate this issue, a de novo transcriptome for the resistant parent was constructed using the DE study total reads, eQTL analysis was repeated and associated transcripts were annotated. We obtained the same eQTL as reported when using the reference genome; specifically, three of the four most significant DE genes were NB-LRR genes 80- to 410-fold up-regulated in susceptible versus resistant progeny (data not shown).