Multilayered Transcriptional Regulation Underlying Salt Tolerance in Rapeseed (Brassica napus L.) Revealed by Integrated Physiological and Transcriptomic Analyses

Soil salinity represents a significant abiotic constraint limiting the productivity and geographical expansion of rapeseed (<i>Brassica napus</i> L.), yet the coordination among the signaling, hormonal, metabolic, and regulatory layers underlying salt tolerance remains incompletely understood. This study elucidates the physiological, biochemical, and transcriptomic responses of <i>B. napus</i> inbred line 383-5 to moderate salt stress (100 mM NaCl at day 10), identifying key lncRNA-mRNA regulatory networks. Salt stress induced pronounced, dose-dependent growth inhibition, oxidative damage, and osmotic adjustment, accompanied by extensive transcriptional reprogramming. Genome-wide analyses identified 6215 differentially expressed protein-coding genes and 941 salt-responsive long non-coding RNAs (lncRNAs), revealing coordinated regulation of ion transport, redox homeostasis, phytohormone signaling, and secondary metabolism. Functional enrichment analyses highlighted the central involvement of abscisic acid and ethylene signaling pathways, MAPK cascades, membrane transporters, and antioxidant systems. Notably, salt stress strongly activated the phenylpropanoid and lignin biosynthesis pathways, suggesting reinforced cell wall remodeling and enhanced oxidative stress mitigation. Integration of lncRNA-mRNA regulatory networks further indicated that non-coding transcripts act as important modulators linking hormone signaling, redox balance, and metabolic adaptation. Collectively, these results reveal a multilayered and tightly synchronized regulatory framework underlying salinity tolerance in <i>B. napus</i> and provide valuable molecular targets for the genetic improvement of salt-resilient rapeseed cultivars.