Insights into the salt stress response of allotetraploid Brassica napus from epigenetic modification and expression changes

• A n subgenome of Brassica napus plays a major role in the changes of gene expression, while C n subgenome is more active in the changes of epigenetic modification under salt stress. • H3K27 methylation cooperates with DNA methylation to inhibit gene expression under salt stress and is antagonistic to H3K4 methylation in most cases. • Transposable elements widely affect differentially expressed genes and further expand the level of epigenetic modification differences in the regions where they are inserted. • The response of Brassica napus to salt stress is jointly regulated by multiple factors including gene expression, epigenetic modification and transposable elements. Polyploid plants are widely recognized that have superior advantages in abiotic stress responses, yet the complexity of epigenetic regulation networks mediating stress response mechanisms persists as an unresolved issue. Salt stress poses persistent challenges to global crop productivity through ionic toxicity and osmotic imbalance. Evidence reveals that epigenetic modifications play a critical role in gene regulation under salt stress. Genome-wide profiles of DNA methylation and histone modification landscapes were analyzed in Brassica napus under salt stress, then combined them with the RNA-seq data to uncover the mechanism of polyploid plants in response to abiotic stress. Our study set a control group and four treatment groups subjected to salt stress for 0 h, 6 h, 12 h, 24 h, and 48 h respectively. A total of 5540, 1414, 3541, and 1444 differentially expressed genes (DEGs) were identified among four comparable groups, with the majority of them exhibiting preference to A n subgenome. In contrast, differential epigenetic modifications tend to be distributed on the C n subgenome, with methylation level decreased and histone modification level increased after salt stress. Transposable elements generally regulated genes expression by inserting over 80% of DEGs, accompanied with impacts on epigenetic modifications. These findings highlight the substantial effect of epigenetic modifications on gene expression, indicating B. napus had unique regulation strategies under different periods of salt stress. Subgenomes also exhibited relatively independent functions under salt stress, in which A n subgenome was more active in expression changes and more conserved in epigenetic modifications.