Comparative Physiological and Transcriptomic Analysis Reveals Candidate Salt-Responsive Transcription Factors in Two Rapeseed (Brassica napus L.) Cultivars with Contrasting Salt Tolerance

Salt stress severely limits rapeseed growth and productivity, with varietal differences in tolerance, yet the molecular responses remain poorly understood. In this study, we compared the physiological and transcriptomic responses of a salt-tolerant cultivar ‘ZY821’, and a salt-sensitive cultivar ‘HS3’ under salt stress. Physiological analysis confirmed that ‘ZY821’ exhibited significantly higher plant height, shoot and root biomass, chlorophyll content, and SOD and CAT activities, while accumulating lower level of H2O2 under salt stress compared to ‘HS3’. Transcriptome analysis revealed 1542 and 2348 differentially expressed genes (DEGs) in ‘ZY821’ and ‘HS3’ under salt stress, respectively. A formal genotype × treatment interaction analysis further identified 1011 genes with genotype-dependent salt responses. GO and KEGG enrichment analyses indicated that upregulated genes in ‘ZY821’ were primarily associated with environmental sensing, starch and sucrose metabolism, and phenylpropanoid biosynthesis, whereas downregulated genes involved lipid metabolism. In contrast, ‘HS3’ exhibited broad upregulation of ribosome-related genes and downregulation of secondary metabolism and glutathione-mediated redox pathways. Analysis of transcription factors (TFs) identified 569 differentially expressed TFs under salt stress. Basic characterization revealed that three candidate TFs (BnaERF106, BnaNFYA6, and BnaCOL13) localized to the nucleus, with BnaERF106 exhibiting transcriptional activation activity. BnaERF106 and BnaNFYA6 were downregulated in both cultivars under salt stress, while BnaCOL13 showed contrasting gene expression patterns. Heterologous expression of BnaERF106 and BnaCOL13 reduced yeast salt tolerance, consistent with a possible negative regulatory role that requires validation in plants. Collectively, these findings provide a candidate gene resource and testable hypotheses for future functional validation.