Genome-wide transcriptional analysis of rapeseed (Brassica napus L.) responses to heat stress: an integrated RNA-Seq meta-analysis, gene co-expression, and gene regulatory network study

Brassica napus L. (rapeseed) represents one of the world’s most important oilseed crops, yet its yield is increasingly impacted by heat—a threat that is intensifying under climate change. Here, we employed an integrative framework combining RNA‑Seq meta‑analysis, weighted gene co‑expression network analysis (WGCNA), and gene regulatory network (GRN) inference to dissect the transcriptional programs activated during the response of rapeseed to heat stress. WGCNA partitioned the transcriptome into three principal modules—green, black, and brown—with genes in the black and brown modules exhibiting predominantly decreased expression under heat, whereas the green module was largely characterized by upregulation. The green module promoted energy conservation, transcriptome flexibility through alternative splicing, endoplasmic reticulum remodeling, proteostasis via chaperone activity, redox balance, and reduced ABA sensitivity to enhance transpirational cooling. In contrast, the black and brown modules, largely downregulated, restricted carbon fixation, cyclic electron flow, chlorophyll turnover, and PSII repair while sustaining stomatal opening, highlighting a trade-off between photosynthetic efficiency and thermotolerance. Within GRNs, upregulated hub TFs reinforced chaperone function, ROS detoxification, (post-)transcriptional reprogramming, and photosynthetic support whereas downregulated hub TFs suppressed photosynthesis, metabolism, growth, transport, and basal immunity thereby redirecting resources toward essential heat stress responses. Our results illuminate the key regulatory mechanisms and co‑expressed gene clusters that orchestrate adaptive response of rapeseed to heat, offering valuable molecular targets for the development of varieties with improved tolerance to heat stress conditions.