Distinct physiological and transcriptomic responses between tolerant and susceptible rapeseed (Brassica napus) germplasm to flooding stress

Waterlogging and submergence are major abiotic stresses impairing rapeseed development and hence evaluation of submergence tolerance ability is crucial for the development of tolerant lines through breeding approaches. This study investigated submergence impact on the survival rate, physiological responses, and transcriptomic variation of the young seedlings of 706 Brassica napus germplasm. We identified 57 highly tolerant and 109 highly susceptible accessions underwent six days submergence. Most accessions originated from the downstream of Yangtze River region had higher tolerance level. SOD enzymic activity increased both in the five representative tolerant and susceptible genotypes under submergence stress. POD activity also increased in the tolerant genotypes whereas CAT activity decreased, showing a opposite trend compared to the susceptible genotypes. The tolerant genotypes showed less chlorosis and produced less malondialdehyde than that in the susceptible group, while soluble protein content increased more than that in the susceptible genotypes. Transcriptome analysis detected 5,072 and 5,063 up-regulated genes, as well as 3,512 and 3,889 down-regulated genes in the tolerant / susceptible group in comparison to their respective control. Many genes encoding the transcription factors in AP2/ERF, bHLH, MYB, WRKY, and NAC families were also significantly regulated. The differentially expressed genes shared by the two pairs comparison were mainly enriched in such KEGG pathways as circadian rhythm, tryptophan metabolism, and porphyrin and chlorophyll metabolism. The specific pathways in the tolerant group were enriched in carbon metabolism, phenylpropanoid biosynthesis, and biosynthesis of amino acid, while the susceptible group was more distributed in hormone signal transduction, sucrose and starch metabolism, and vitamin B6 metabolism etc. The results uncovered distinct physiological and transcriptomic differences between tolerant and susceptible genotypes.