Correlative Transcriptome and Metabolome Analysis of the Maize Shoot Response to Salt Stress

Soil salinity increasingly jeopardizes maize productivity. Although previous studies have documented maize physiological responses under salt stress, the integrated regulatory networks linking signal perception, transcriptional reprogramming, and metabolic adjustment in shoots remain poorly understood. Here, we combined phenotypic, physiological, enzymatic, transcriptomic, and metabolomic analyses to systematically dissect maize seedling leaf responses to NaCl. Salt stress significantly inhibited photosynthesis, reduced plant biomass, and disturbed ion homeostasis, as evidenced by increased Na⁺/K⁺ ratio, elevated MDA level, and enhanced antioxidant enzyme activities (SOD, CAT, POD). Through transcriptomic profiling analysis, 1558 DEGs were identified, which were predominantly associated with MAPK and hormone signal transduction and secondary metabolism. Among the DEGs, transcription factors (AP2, bHLH, bZIP, MYB, NAC, WRKY) showed marked expression changes. Moreover, metabolomic analysis detected 232 DAMs, spanning amino acids and derivatives, phenolic acids, alkaloids, organic acids, and lipids. Integrated omics revealed that salt stress induced widespread transcriptional reprogramming of signaling genes, which was correlated with metabolic adjustments favoring osmolyte accumulation, antioxidant biosynthesis, and membrane stabilization. These findings provide a comprehensive multi-omics resource for understanding maize shoot responses to salinity and highlight potential targets to breed salt-tolerant varieties.