Effects of waterlogging stress on early seedling development and transcriptomic responses in Brassica napus

In this study, we performed a transcriptomic analysis to investigate genome-wide gene profiles of a rapeseed ( Brassica napus ) cultivar Zhongshuang 11 (ZS11) in response to waterlogging stress at germination stage. The root and shoot development of ZS11 was dramatically inhibited by waterlogging stress. As a result, 7472 downregulated DEGs (differentially expressed genes) and 3869 upregulated DEGs were identified by the RNA-seq experiments. KEGG analyses show that enriched pathways of these DEGs mainly include “plant hormone signal transduction,” “phenylpropanoid biosynthesis,” and “starch and sucrose metabolism.” Among them, there are 41, 19, and 26 DEGs involved in the regulatory pathways of root, shoot, and hypocotyl growth, respectively. In detail, the downregulated IAA17 , IAA28 , YUCCA9 , UPBEAT1 , and ARR1 and the upregulated ACR4 probably affect the balance between cell differentiation and division in the root apical meristem (RAM), while the downregulated CLV1 , CRN , AHK4 , and FAS2 might disturb stem cell fate in the shoot apical meristem (SAM). Taken together, the current results provide valuable information for understanding molecular mechanisms of seedling development in response to waterlogging stress at germination stage in rapeseed.