Differential response to waterlogging stress in rapeseed (Brassica napus L.): insights from physiological, transcriptomic, and metabolomic analyses.

Waterlogging stress severely impacts the yield and quality of rapeseed (Brassica napus L.), necessitating the elucidation of tolerance mechanisms through a comparative analysis of contrasting varieties. To elucidate the mechanisms of tolerance, this study employed an integrative approach combining physiological, transcriptomic, and metabolomic analyses to compare the waterlogging-tolerant genotype D199 with the sensitive genotype N1983. Physiological profiling indicated that D199 exhibited 24% higher superoxide dismutase (SOD) activity and 94% higher catalase (CAT) activity, alongside a 7% reduction in superoxide anion accumulation compared to N1983 under stress conditions, effectively mitigating reactive oxygen species (ROS) damage. Integrated transcriptomic and metabolomic profiling has revealed three synergistic adaptation mechanisms: the upregulation of AHP4 (3.0-fold), associated with cytokinin signaling pathways, enhances the leaf’s antioxidant capacity via the activation of RR1/RR2. Additionally, auxin biosynthesis genes IAA14 (2.9-fold) and GH3.6 (2.2-fold) facilitate root remodeling through the induction of SAUR4/5/78 (3.6-4.0-fold). Crucially, the spatiotemporal coordination between auxin and cytokinin pathways orchestrates aerial ROS scavenging and root plasticity, involving co-expressed genes SAUR (auxin-responsive) and AHP4 (cytokinin-related). This systematic decoding of the hormone crosstalk network identifies actionable breeding targets (IAA14, AHP4, SAUR78) for the development of waterlogging-resilient cultivars. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-026-08099-4.