Transcriptomic analysis of genotypes derived from Rosa wichurana unveils molecular mechanisms associated with quantitative resistance to Diplocarpon rosae

Black spot disease, caused by the hemibiotrophic fungus Diplocarpon rosae , is a major constraint for garden rose cultivation. Developing resistant cultivars requires a better understanding of the genetic and molecular mechanisms underlying resistance. A hybrid of Rosa wichurana (RW) displays quantitative resistance to black spot that has been previously associated with two major Quantitative Trait Loci (QTLs), B3 and B5, located on linkage groups 3 and 5, respectively. Our objective was to investigate the molecular mechanisms associated with these QTLs by comparing the transcriptome of RW and four F1 individuals carrying different QTL combinations. Differential expression analyses comparing inoculated and mock-treated samples within each genotype revealed that the strongest transcriptional response occurred at 3 days post-inoculation, which was therefore considered the most informative stage for functional interpretation. Genotypes carrying QTL B3 displayed transcriptional signatures consistent with pathogen perception, defense signaling, reactive oxygen species production, cell wall-associated responses and localized cell death. In contrast, genotypes carrying QTL B5 shared relatively fewer transcriptional responses, preventing the identification of a clear QTL-specific contribution. Overall, these results provide new insight into the molecular basis of quantitative resistance to black spot in rose and suggest that resistance inherited from RW involves coordinated and background-dependent regulation of multiple defense-related processes.