Waterlogging stress reshapes epigenetic regulation of gene expression in Brassica napus

Waterlogging stress significantly impairs early development and yield in Brassica napus, yet the underlying epigenetic regulatory mechanisms remain poorly understood. We applied a multi-omics strategy integrating RNA-seq, WGBS, and ChIP-seq to dissect multi-layered regulatory dynamics during waterlogging stress and recovery. We found that waterlogging stress globally repressed gene expression and enhanced expression divergence between homoeologous genes of the two subgenomes. Transposable element (TE) activation, together with dynamic epigenetic changes, is associated with altered expression of neighboring genes under waterlogging stress. This study provides novel insights into the multilayered epigenetic regulation of waterlogging responses in a polyploid crop and highlights the regulatory potential of TEs in stress adaptation.