Integrated Analyses Reveal the Physiological and Molecular Mechanisms of Brassinolide in Modulating Salt Tolerance in Rice.

Salt stress poses a significant threat to crop growth. While brassinolide (BR) has been shown to alleviate its adverse effects and modulate plant development, the precise mechanism underlying BR-induced salt tolerance in rice remains unclear. In this study, the Chaoyouqianhao and Huanghuazhan rice varieties were employed to investigate the effects of BR seed soaking on the seedling phenotype, physiology, transcriptome, and metabolome under salt stress. The results demonstrated that BR treatment significantly enhanced rice plant height, root length, biomass, and antioxidant enzyme activities, while reducing leaf membrane damage, promoting ion homeostasis, and improving the photosynthetic capacity and salt tolerance. The transcriptome analysis revealed that BR regulated the expression of 1042 and 826 genes linked to antioxidant activity, ion homeostasis, photosynthesis, and lipid metabolism under salt stress. These included genes involved in Na efflux (, , and , photosynthetic electron transport ( and ), photosystem II (, , and ), and CO fixation. The metabolomic analysis identified 91 and 57 metabolite alterations induced by BR, primarily linked to amino acid, flavonoid, and lipid metabolism, with notable increases in antioxidant metabolites such as lignanoside, isorhamnetin, and L-glutamic acid. The integrated analysis highlighted the pivotal roles of 12-OPDA in α-linolenic acid metabolism and genes related to lipid metabolism, JA metabolism, and JA signal transduction in BR-mediated salt tolerance.