Maize (Zea mays L.) is one of the most important food crops. Salt stress can hinder crop growth and development, but the molecular mechanisms underlying maize’s response to salt tolerance remain unclear. In this study, we conducted comparative transcriptome, metabolome, and physiological analyses of a salt-tolerant maize inbred line (J1285) subjected to different NaCl concentrations during the seedling stage. The results demonstrated that, with increasing salt concentration, seedling growth parameters and antioxidant enzyme activities (SOD, POD, CAT) exhibited initially increases before subsequently decreasing, peaking at 50–150 mmol/L. Transcriptome data analysis revealed that the experimental groups subjected to 50, 100, 150, and 200 mmol/L treatments had 375, 1043, 2504, and 2328 differentially expressed genes (DEGs) compared to the control group, respectively. Additionally, through GO and KEGG analysis, we found that the DEGs were primarily enriched in the MAPK signaling pathway and plant hormone signal transduction, especially the abscisic acid (ABA) signaling pathway, both of which play instrumental roles in orchestrating the maize response to salt-induced stress. Transcription factors involved in the salt stress response, including WRKY, TIFY, bZIP, and bHLH, were identified. Metabolomic data analysis revealed that the experimental groups subjected to 50, 100, 150 and 200 mmol/L treatments had 44, 335, 278, and 550 differentially expressed metabolites (DEMs) compared to the control group, respectively. The DEMs were mainly enriched in metabolic pathways and the biosynthesis of secondary metabolites. Transcriptomics and metabolomics combined analysis were performed on J1285 seedling leaves, and it was found that the co-enrichment pathways included starch and sucrose metabolism, linoleic acid metabolism, α-linolenic acid metabolism, phenylpropanoid biosynthesis pathway, etc. Collectively, these results will aid in identifying resistance genes and elucidating the molecular mechanisms underlying salt tolerance for maize.

Soil salinization, recognized globally as a significant environmental issue, can directly impact the sustainable development of agriculture worldwide. As a key crop driving the global agricultural economy, maize is particularly vulnerable to the detrimental effects of salt–alkali stress, which can impede its growth and development from germination through the seedling stages. In this study, 32 maize inbred lines were screened for saline–alkali resistance identification. We performed four treatments—200 mmol/L NaCl, 100 mmol/L Na₂CO₃, 200 mmol/L NaCl with 25 mmol/L Na₂CO₃—and distilled water (CK) served as a control with a complete randomized design. Principal component analysis and the membership function value method were employed to evaluate the salt–alkali tolerance of these lines. The results indicate complex correlations among various traits at different growth stages. The relative correlation of each index was established by measuring the key physiological indexes (germination rate, root length and seedling height) of different maize inbred lines at the germination stage and seedling stage and standardizing them via the membership function value method. Subsequently, the principal component analysis method was used to reduce the dimensions of the standardized data, and the main factors affecting maize germination and seedling growth were extracted. The salt–alkali tolerance of maize inbred lines was comprehensively evaluated, and the salt–alkali tolerance and sensitive materials of maize germination and seedling stage were identified. This study found that the coefficient of variation of each trait is relatively rich. Therefore, in the preliminary screening of breeding germplasm resources, different reference indexes can be selected according to different periods and stress conditions. The enzyme activity results revealed significant variations in enzyme activity across different treatments and materials, with changes in superoxide dismutase (SOD) and peroxidase (POD) exhibiting relative stability, thereby reflecting the physiological response mechanisms of maize under salt–alkali stress. In this study, through principal component analysis, it was found that the germ and germination factors at the germination stage of maize and the root weight, root length, and seedling development factors at the seedling stage affected its saline–alkali resistance. The root weight factor, seedling development factor, and root length factor may affect the growth and development of maize at the seedling stage. Through the comprehensive analysis of the data of the germination stage and seedling stage, it can be seen that the materials with better salt resistance are Zm4 and Zm32; the material with better alkali resistance is Zm30; the material with better salt and alkali resistance is Zm2. Through the application of comprehensive evaluation system, researchers can more effectively screen out maize germplasm resources with excellent genetic characteristics to promote maize variety improvement and genetic diversity protection.