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Although rapeseed (Brassica napus L.) is known to be affected by waterlogging, the genetic basis of waterlogging tolerance is largely unknown in this crop.In this study, the transcriptome under 0 h and 12 h of waterlogging was assayed in the roots of ZS9, a tolerant variety, using digital gene expression (DGE).A total of 4432 differentially expressed genes were identified, indicating that the response to waterlogging in rapeseed is complicated.The assignments of the annotated genes based on GO (gene ontology) revealed there were more genes induced under waterlogging in "oxidation reduction", "secondary metabolism", "transcription regulation", and "translation regulation", suggesting these four pathways are enhanced under waterlogging.Analysis of the 200 highly expressed genes illustrated 144 under normal condition were down-regulated by waterlogging, while up to 191 under waterlogging were those induced in response to the stress.The expression of genes involved under waterlogging is mediated by multiple levels of transcriptional, post-transcriptional, translational, and post-translational regulation, including phosphorylation and protein degradation; in particular, protein degradation might be involved in the negative regulation in response to this stress.Our results provide new insight into the response to waterlogging and will help to identify important candidate genes.