Tissue-Specific Transcriptome and Metabolome Analysis Reveals the Response Mechanism of Brassica napus to Waterlogging Stress

During the growth period of rapeseed, if there is continuous rainfall, it will easily lead to waterlogging stress, which will seriously affect the growth of rapeseed. Currently, the mechanisms of rapeseed resistance to waterlogging stress are largely unknown. In this study, the rapeseed (Brassica napus) inbred lines G230 and G218 were identified as waterlogging-tolerant rapeseed and waterlogging-sensitive rapeseed, respectively, through a potted waterlogging stress simulation and field waterlogging stress experiments. After six days of waterlogging stress at the seedling stage, the degree of leaf aging and root damage of the waterlogging-tolerant rapeseed G230 were lower than those of the waterlogging-sensitive rapeseed G218. A physiological analysis showed that waterlogging stress significantly increased the contents of malondialdehyde, soluble sugar, and hydrogen peroxide in rape leaves and roots. The transcriptomic and metabolomic analysis showed that the differential genes and the differential metabolites of waterlogging-tolerant rapeseed G230 were mainly enriched in the metabolic pathways, biosynthesis of secondary metabolites, flavonoid biosynthesis, and vitamin B6 metabolism. Compared to G218, the expression levels of some genes associated with flavonoid biosynthesis and vitamin B metabolism were higher in G230, such as CHI, DRF, LDOX, PDX1.1, and PDX2. Furthermore, some metabolites involved in flavonoid biosynthesis and vitamin B6 metabolism, such as naringenin and epiafzelechin, were significantly up-regulated in leaves of G230, while pyridoxine phosphate was only significantly down-regulated in roots and leaves of G218. Furthermore, foliar spraying of vitamin B6 can effectively improve the tolerance to waterlogging of G218 in the short term. These results indicate that flavonoid biosynthesis and vitamin B6 metabolism pathways play a key role in the waterlogging tolerance and hypoxia stress resistance of Brassica napus and provide new insights for improving the waterlogging tolerance and cultivating waterlogging-tolerant rapeseed varieties.