Drought-mitigation of Verticillium longisporum colonization in Brassica napus is associated with transcriptome and DNA methylation reprogramming.

Climate is becoming more variable, and the frequency and magnitude of drought and pathogen epidemics are changing. This creates a need to understand how limited water availability influences plant responses to biotic challenges. In Brassica napus L., drought decreases the disease progression and fungal colonization of the vascular pathogen Verticillium longisporum, yet the underlying regulatory mechanisms remain unclear. Here, we used an integrative approach combining transcriptome profiling, co-expression network analysis, and DNA methylation analysis to investigate host responses in hypocotyl tissues of water-stressed plants at early and later stages of infection. Relative to infected hypocotyls of well-watered plants, imposition of drought evokes extensive transcriptome rewiring centered around three distinct events: the activation of detoxification/defence pathways, including glucosinolate and glutathione metabolism and redox-related processes, induction of cell wall components contributing to formation of apoplastic barriers, and hormonal responses linked to ethylene signalling. Many of these changes were temporally regulated. Co-expression network analysis in infected water-stressed tissue identified tightly connected co-expression modules and highly connected candidate hub genes, including receptor-like kinases and transcription factors, whose expression patterns were associated with stress-responsive pathways. DNA methylation profiling following combined imposition of drought and fungus infection revealed predominantly localized and context-dependent changes, with differentially methylated loci associated with genes annotated to diverse stress-related functions, including defence signalling, hormone-related pathways, and cell wall processes. Integration of methylome and transcriptome data identified genes exhibiting coordinated epigenetic and transcriptional changes, consistent with a context-dependent association between DNA methylation and early defence-associated transcriptional responses. Together, these findings demonstrate that the effect of drought in delaying V. longisporum colonization is associated with specific regulation of detoxification processes, hormone signalling, and cell wall modification, coordinated by specific variations in epigenomic landscape.