Abstract
Although rapeseed (Brassica napus L.) is known to be affected by waterlogging, the genetic basis of waterlogging tolerance by rapeseed is largely unknown. 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 most highly expressed genes illustrated that 144 under normal conditions were down-regulated by waterlogging, while up to 191 under waterlogging were those induced in response to 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.
Highlights
Waterlogging is one of the most widespread abiotic determinants for crop growth, leading to the depletion of oxygen, which is vital to plants [1]
The induction of plant growth regulators under waterlogging stress are involved in signaling cascades that influence cellular responses, including increases in ethylene [19,20], abscisic acid (ABA) [21,22,23,24,25], gibberellic acid (GA) [26], and auxin (IAA) [27,28] and a reduction in cytokinin (CK) [29,30]
To gain comprehensive insight into how rapeseed responds to waterlogging and to identify the genes important in mounting a response of waterlogging tolerance, here we report a detailed analysis of gene expression profiling in ZS9, a waterlogging-tolerant variety [29,30], at the vegetative growth stage under waterlogging using digital gene expression (DGE) method, a powerful tool for studying high-throughput gene expression profiling [34,35]
Summary
Waterlogging is one of the most widespread abiotic determinants for crop growth, leading to the depletion of oxygen, which is vital to plants [1]. The expression of a majority of global genes was depressed, the accumulation of mRNAs was revealed for many genes under hypoxia. These genes included anaerobic proteins (ANPs) involved in sugar phosphate metabolism [15]. The induction of plant growth regulators under waterlogging stress are involved in signaling cascades that influence cellular responses, including increases in ethylene [19,20], abscisic acid (ABA) [21,22,23,24,25], gibberellic acid (GA) [26], and auxin (IAA) [27,28] and a reduction in cytokinin (CK) [29,30]. In Arabidopsis, studies have revealed that oxygen sensing is mediated by group VII ERF (ethylene response factor) TFs through the N-End rule pathway [33]
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