Effects of waterlogging stress on rapeseed yield, oil content, fatty acid composition, and transcriptome differences

Brassica napus (rapeseed) frequently suffers from waterlogging, resulting in large decrease in seed yield and quality. In this study, we imposed a 14-day waterlogging treatment during the pod development stage of rapeseed, which will be referred to as WL. Plants without waterlogging were used as the control group, referred to as CK. The composition of fatty acids (FAs) in the seed was determined at 3, 6, 9, and 14 day after waterlogging (DAW). Comparative transcriptome analysis between WL and CK was conducted from the 3-DAW seeds, and a total of 2761 DEGs were identified. A large number of up-regulated DEGs were found to be involved in the biosynthesis and signaling of abscisic acid and ethylene, which could lead to earlier senescence of plants and seed maturation. Meanwhile, DEGs related to fatty acid degradation were up-regulated under waterlogging. As a result, seed yield and oil content decreased largely at harvest time. Moreover, pathway of linolenic and linoleic acid metabolism was significantly enriched by DEGs. A total of four triacylglycerol lipases and two fatty acid desaturases were up-regulated, facilitating the supply of linoleic and linolenic acid at the expense of triacylglycerol and oleic acid. However, seven lipoxygenases involved in the oxidation of linolenic acid were highly up-regulated, potentially promoting jasmonic acid biosynthesis. As a result, the content of linolenic acid decreased significantly during the 14-day waterlogging period. This study elucidated the molecular mechanisms of fatty acid metabolism in response to waterlogging, offering valuable insights for enhancing rapeseed quality under waterlogging conditions.