Physiological, biochemical, and multi-omics analyses reveal the mechanism underlying strigolactone-mediated waterlogging response in rapeseed

Global climate change has caused an increasing frequency of extreme rainfall events, which aggravates the waterlogging risk to pose serious threats to the production of rapeseed. Strigolactones (SLs) have been demonstrated to enhance crop stress resistance by modulating physiochemical processes and gene expression. However, little is known about the molecular mechanisms through which SLs alleviate waterlogging damage in rapeseed. Here, we comprehensively analyzed the regulatory effects of SLs on the phenotypic and physiochemical characteristics of waterlogged rapeseed and the underlying molecular mechanisms. The results indicated that waterlogging substantially inhibited the aboveground growth and root development, as well as reduced the net photosynthetic rate, stomatal conductance, mesophyll and spongy tissue thickness, APX activity, and N, P, and K contents in seedlings. Conversely, SLs activated the glutathione metabolism and phenylpropanoid biosynthesis pathways, upregulated GPX , GSH , and 4CL genes, increased amino acids and secondary metabolites, enhanced antioxidant enzyme system and absorption efficiency of N, P, and K elements, promoted photosynthesis and biomass accumulation, thereby effectively alleviating waterlogging damage. At the flowering stage, SLs activated alanine, aspartate, and glutamate metabolism and phenylpropanoid biosynthesis pathways, regulated the GLN1 , ASP and PAL genes, increased amino acid and phenolic compounds, which together effectively mitigated the waterlogging-induced yield and quality loss. Overall, this study demonstrates that SLs can effectively mitigate waterlogging damage to the phenotypic traits, physiochemical indicators, transcriptomics, and metabolomics in rapeseed. The findings provide practical guidance for improving waterlogging tolerance in cultivation management, and also an important theoretical basis for genetic improvement in rapeseed. • Waterlogging substantially inhibited the aboveground growth and root development in seedlings. • Waterlogging reduced the photosynthesis, mesophyll and spongy tissue thickness, and element content in seedlings. • Strigolactones activated the glutathione metabolism, phenylpropanoid biosynthesis pathways in seedlings. • Strigolactones activated alanine, aspartate, and glutamate metabolism and phenylpropanoid biosynthesis at flowering.