Integrated physiological, metabolomic and transcriptomic analyses provide insights into the roles of exogenous melatonin in promoting rice seed germination under salt stress

Melatonin is an important phytohormone in plant development and stress responses. However, the functions of melatonin in rice salt tolerance during seed germination is largely undetermined. In this study, we investigated its potential molecular mechanism during rice seed germination under salinity through comprehensive transcriptome sequencing, metabolome profiling, and physiological assays. Transcriptome analysis revealed 4794 differentially expressed genes (DEGs) after melatonin pretreatment under salinity, including 2843 upregulated and 1951 downregulated genes. Functional annotation showed that many DEGs were associated with antioxidative activity and phytohormone biosynthesis and signal transduction. Consistent with the transcriptome results, physiological analysis revealed enhanced activity of antioxidant capacity, increased indole-3-acetic acid (IAA) level, and reduced abscisic acid (ABA) level under melatonin pretreatment. The enhanced antioxidative activity was also supported by metabolome assay that melatonin pretreatment increased the levels of non-enzymatic antioxidant organic acids and amino acids. The results demonstrated that exogenous melatonin can enhance rice seed tolerance to salinity during germination via activating antioxidants and modulating phytohormones.