The grape powdery mildew resistance loci , , , , , , and activate different transcriptional responses to .

Multiple grape powdery mildew (PM) genetic resistance () loci have been found in wild grape species. Little is known about the defense responses associated with each locus. In this study, we compare the defense mechanisms associated with PM resistance in interspecific crosses segregating for a single locus from (, , , ) () ( and ), and the interspecific hybrid Villard blanc (). By combining optical microscopy, visual scoring, and biomass estimation, we show that the eight loci confer resistance by limiting infection at different stages. We assessed the defense mechanisms triggered in response to PM at 1 and 5 days post-inoculation (dpi) RNA sequencing. To account for the genetic differences between species, we developed for each accession a diploid synthetic reference transcriptome by incorporating into the PN40024 reference homozygous and heterozygous sequence variants and assembled transcripts. Most of the loci exhibited a higher number of differentially expressed genes (DEGs) associated with PM resistance at 1 dpi compared to 5 dpi, suggesting that PM resistance is mostly associated with an early transcriptional reprogramming. Comparison of the PM resistance-associated DEGs showed a limited overlap between pairs of loci, and nearly half of the DEGs were specific to a single locus. The largest overlap of PM resistance-associated DEGs was found between , , and genotypes at 1 dpi, and between and accessions at 5 dpi. The , , and were also found to have the highest number of locus-specific DEGs in response to PM. Both shared and locus-specific DEGs included genes from different defense-related categories, indicating that the presence of triggered distinct transcriptional responses in the eight loci.