Integrated Physiological and Multi-Omics Analyses Reveal the Coordinated Regulation of Carbon and Nitrogen Metabolism in Rapeseed (Brassica napus L.) Tolerance to Saline-Alkaline Stress

Background/Objectives: Soil salinization and alkalization critically limit global agricultural production. This study aimed to investigate the differential response mechanisms of rapeseed (Brassica napus L.) varieties to saline and alkaline stresses at the seedling stage. Methods: Seedlings of a salt-tolerant variety, Huayouza 62 (H62), and a non-salt-tolerant variety, Xiangyou 15 (X15), were exposed to saline (NaCl:Na2SO4 = 1:1) and alkaline (Na2CO3:NaHCO3 = 1:1) stresses. An integrated analysis combining physiology, biochemistry, transcriptomics, and metabolomics was conducted to systematically elucidate their differential stress responses. Results: (1) H62 maintained favorable photosynthetic and carbon–nitrogen homeostasis. Notably, under saline and alkaline stresses, the activity of glutamate dehydrogenase (GDH) in H62 showed a significant increasing trend, whereas it was inhibited in X15. (2) Alkaline stress triggered more differential genes than saline stress, with H62 exhibiting broader transcriptional up-regulation in carbon–nitrogen metabolism. (3) Metabolomic profiling showed that H62 accumulated more beneficial metabolites than X15 under both stresses, such as phenolic acids, amino acids, and their derivatives. (4) In multi-omics analysis, key genes in starch–sucrose and amino acid metabolism in H62 were up-regulated to accumulate osmolytes, enabling an efficient defense network. However, X15’s responses were disordered. Conclusions: H62 leverages robust transcriptional reprogramming to coordinate carbon–nitrogen metabolism, constituting a multidimensional defense network. This study provides potential physiological indicators, candidate genes, and metabolite markers associated with short-term saline–alkaline stress responses, laying a foundation for further exploration of stress response mechanisms.