Molecular mechanisms of melatonin in mitigating compound salt stress in Sophora alopecuroides revealed by physiological and transcriptomic profiling

• Melatonin can significantly enhance the photosynthetic performance and antioxidant enzyme system activity of Sophora alopecuroides seedlings. • Exogenous melatonin helps plants resist salt stress by reshaping endogenous hormone balance, and high concentrations of exogenous melatonin may increase endogenous melatonin levels in plants. • At the molecular level, exogenous melatonin treatment resulted in significant upregulation of riboflavin and zeaxanthin metabolic pathways and intermediate genes. Melatonin is a conserved multifunctional signaling molecule in plants, which regulates many developmental processes and responds to stress. Although many studies have involved melatonin in plants, it is not clear whether the application of exogenous melatonin can improve their tolerance to salt damage NaCl + Na 2 SO 4 (2:1). This study investigated the effects of different concentrations of melatonin (0, 50, 100, 150, 200, and 250 μmol·L -1 ) on seed germination, physiological characteristics, and transcriptome (12d) of Sophora alopecuroides under salt stress at different time (3d, 6d, 9d and 12d). The results showed that on the 12th day of salt stress, the germination rate (37.88 %), radicle (16.67 %), germ (38.87 %), total chlorophyll content (72.48 %), transpiration rate (45.17 %) decreased, and H 2 O 2 (24.26 %), malondialdehyde content (10.95 %) increased. In particular, exogenous melatonin at 50 μmol·L -1 can improve the germination index of Sophora alopecuroides seeds under salt stress, increase plant growth, biomass accumulation, root activity, regulate stomatal conductance and intercellular CO 2 concentration, and improve photosynthetic efficiency. In addition, exogenous melatonin also reduced MDA content and reactive oxygen species (ROS)accumulation, alleviated oxidative damage and increased enzymatic and non-enzymatic antioxidant activities, including catalase, superoxide dismutase, polyphenol oxidase, peroxidase, flavonoids and carotenoids. Exogenous melatonin also promoted the accumulation of growth-related endogenous hormones (GA, IAA, MT) and the ability to change gene expression patterns. Discussion Transcriptomics analysis revealed significant changes in gene expression, especially in the comparison of T0 and T1 treatment groups. 4761 differentially expressed genes (DEGs) were identified, including arginine and proline metabolism, zeatin biosynthesis, pentose and glucuronic acid mutual transformation, galactose metabolism, and peroxisome synthesis pathways, which are essential for plant responses to salt stress. Our results provide preliminary mechanistic insights into how melatonin alleviates the combined salt stress of S. alopecuroides , and lay the foundation for molecular breeding strategies to enhance the salt tolerance of this crop.