Multi‐layered <scp>RNA</scp> decay mechanisms underlie subgenome‐biased homoeologous <scp>mRNA</scp> stability in salt‐stressed allopolyploid plants

Many crop species are polyploid plants, yet how post-transcriptional regulation influences the RNA abundance of homoeologous genes from different subgenomes under stress conditions remains poorly understood. In this study, we systematically investigated transcriptional and post-transcriptional regulation in the allopolyploid crop Brassica napus under salinity stress. Integrated transcriptome and degradome profiling on hypocotyl and cotyledon revealed tissue-specific gene expression and mRNA stability associated with their developmental changes under salt stress. Notably, mRNAs undergoing exon junction complex (EJC)-marked RNA decay (EMRD) and co-translational RNA decay (CTRD) exhibited higher degradation propensity. Transcriptome-wide profiling of mRNA abundance and mRNA decay in homoeologous genes revealed subgenome-specific patterns in both gene expression and mRNA stability. Dual-luciferase assays confirmed that the 3' UTR mediates the divergent mRNA stability observed between homoeologous gene pairs. Further analysis revealed that EMRD, CTRD, and miRNA cleavage are associated with asymmetric RNA degradation across subgenomes. These findings provide comprehensive insights into the multi-layered regulation of transcript stability under salt stress and reveal a critical role for RNA degradation in shaping tissue-specific and subgenome mRNA asymmetry in polyploid crops.