Dual Regulation of DNA Methylation Orchestrates the Saline-Alkali Stress Response in Salt-Tolerant <i>Brassica napus</i>

Soil salinization is a threat to global agriculture. This study used whole-genome bisulfite sequencing and transcriptomics to explore epigenetic regulation in salt-tolerant <i>Brassica napus</i> (cv. Huayouza 62) under NaCl (salt), Na₂CO₃ (alkali), and combined salt-alkali stresses. All stresses induced genome-wide DNA hypermethylation (combined > alkali > salt). The Cn subgenome had significant methylation changes (most at CHH, then at CHG), with more differentially methylated regions in transposable elements than protein-coding genes. Hypermethylation, driven by DNA methyltransferases (e.g., DRM2), inhibited growth by repressing photosynthetic genes (<i>RBCS-1A</i>, <i>RBCS-1B</i>). <i>B. napus</i> adapted via targeted demethylation activated stress resistance (ROS scavenging under salt, redox buffering under alkali, and protein homeostasis under combined stress). 5-Azacytidine validation confirmed that methylation balances photosynthesis and stress response, clarifying the epigenetic network and providing strategies for crop stress resistance improvement.