Combining transcriptome and untargeted metabolome analysis to reveal the potential mechanism of 24-epibrassinolide alleviating low light stress in tomato

Low light stress seriously affects the growth and yield of crops and the phytohormone brassinosteroid (BRs) plays a vital role in regulating plant adaptation to low light conditions. However, the molecular mechanism underlying this process remains largely unknown. In this study, we showed that exogenous BR effectively alleviated damages to photosynthesis and antioxidant systems, improved the plant biomass under low light stress mimicking treatments in tomato (Lycopersicon esculentum Mill.). Comparative transcriptome profiling analysis revealed that genes related with photosynthesis and Calvin cycle pathways were enriched among the differentially expressed genes (DEG) co-regulated by low light stress and BR. The combination of transcriptome and metabolome analysis showed that BR could mitigate the down-regulation of photosynthesis and Calvin cycle caused by low light stress, and partially restore the up-regulation of Glycolysis / Gluconeogenesis and tricarboxylic acid (TCA) cycle through transcriptional and metabolic reprogramming to alleviate the effects of low light stress. Moreover, we further identified the crucial transcription factors, SIEPR1 and SIERF059, and their potential target genes involved in the regulation of low light stress alleviation mediated by BR signaling. Our results shed new light on the molecular mechanisms underlying the alleviation of low light stress by BR. [Display omitted] •Exogenous BR can alleviate low light stress in tomato effectively.•Exogenous BR can improve photosynthesis and Calvin cycle activity under low light.•BR can partially restore the changes in Glycolysis/Gluconeogenesis and TCA cycle.•Modules regulating photosynthesis in BR signaling under low light were identified.•SIEPR1 and SIERF059 probably be two key TFs in BR signaling under low light stress.