Integrative analyses of transcriptome, microRNA-seq and metabolome reveal insights into exogenous melatonin-mediated salt tolerance during seed germination of maize

Melatonin is an important phytohormone influencing plant growth and defense responses. However, the mechanism mediating the regulatory effects of melatonin on the salt tolerance of germinating maize seeds remains unexplored. In this study, the application of exogenous melatonin enhanced the salt tolerance of germinating maize seeds. A transcriptome analysis indicated that complex regulatory pathways may be associated with the melatonin-mediated salt tolerance. Remarkably, antioxidant activities, transcriptional regulation, and phytohormone (e.g., cytokinin and auxin) pathways were induced following the exogenous application of melatonin. The microRNA (miRNA)-seq analysis result indicated that exogenous melatonin obviously altered the expression of a set of miRNAs. Notably, many differentially expressed miRNAs and their target genes, including several transcription factor genes, were revealed to contribute to salt stress responses. According to metabolite profiles, the abundance of diverse metabolites, like secondary metabolites, nucleotides, cofactors, and vitamins, increased significantly after using exogenous melatonin. The combined analysis of the transcriptome and metabolome indicated that several gene–metabolite networks related to amino acid metabolism and secondary metabolite biosynthetic pathways are essential for melatonin-mediated maize tolerance to salt stress. Consistent with these findings, exogenously applied melatonin altered the phytohormone levels and increased the antioxidant enzyme activities and energy supply. Our results reflect the significance of melatonin for enhancing the salt tolerance of germinating maize seeds, which is achieved through the regulation of antioxidant capacity, phytohormone content, and metabolic adaptation.