Metabolomics and Transcriptome Analysis of Rapeseed Under Salt Stress at Germination Stage

Salt stress is a significant abiotic factor that adversely impacts the yield of rapeseed (Brassica napus L.). Under salt stress conditions, the growth of rapeseed is markedly inhibited. This study integrates transcriptomic and metabolomic analyses to elucidate the molecular and physiological mechanisms underlying the salt stress response during the germination of the rapeseed variety ZS11. Metabolomic analysis revealed 175 differentially expressed metabolites, predominantly comprising amino acids, carbohydrates, and organic acids. Transcriptomic analysis highlighted the crucial roles of plant hormones and phenylpropanoid biosynthesis in enhancing the salt stress resistance of rapeseed. Comprehensive multi-omics analysis identified phenylpropanoid metabolism (p < 0.001), amino acid metabolism (FDR < 0.01), and carbohydrate metabolism (|log₂FC| ≥ 2) as the most significantly affected pathways. Crucially, we demonstrate that early-stage phenylpropanoid activation in hypocotyls dominates salt adaptation during germination. These findings provide actionable targets for molecular breeding and novel insights for optimizing crop establishment in salinized agroecosystems.