Soil salinization significantly impairs the growth and development of maize, resulting in reduced yields. Investigating the salt tolerance of various maize inbred lines and identifying favorable allelic variants associated with salt tolerance can provide valuable SNP markers and candidate gene resources for salt-tolerant maize varieties.

This study utilized a natural population comprising 238 inbred maize lines as experimental materials. Twenty-day-old maize seedlings at the three-leaf stage were subjected to treatment with a 300 mmol·L^-1 NaCl solution, and changes in biomass, moisture contents as well as salt damage phenotypes were evaluated after 40 days of salt stress. A genome-wide association study (GWAS) was subsequently performed to identify favorable allelic variants associated with salt tolerance in maize.

Through salt tolerance assessment of a maize natural population at the seedling stage, the materials were categorized into five distinct salt tolerance grades based on the salt damage rate: 22 highly tolerant materials (Grade 1), 93 tolerant materials (Grade 2), 62 moderately tolerant materials (Grade 3), 41 salt-sensitive materials (Grade 4), and 20 highly sensitive materials (Grade 5). The number of materials with different salt tolerance levels shows a normal distribution characteristic, with high-tolerance and highly sensitive materials comprising 17.6% of the total, while intermediate-grade materials accounted for 82.4%. Statistical analysis revealed that the salt damage rate was significantly and negatively correlated with the fresh weight, dry weight, and moisture content of plants under salt stress. The investigated traits exhibited considerable variability, indicating substantial differences among the genotypes. Genome-wide association analysis identified a total of 40 SNP loci associated with maize salt tolerance. Further investigation revealed one significantly associated SNP locus on chromosome 1 and another on chromosome 10. Analysis of the candidate genes within the 100 Kb confidence interval upstream and downstream of these two loci identified a total of 18 functional genes, including 9 genes with functional annotations and 9 genes with unknown functions.

22 first-class salt-tolerant maize inbred line materials were selected from a natural population consisting of 238 lines. 40 SNP loci associated with salt tolerance in maize seedlings were identified, among which two key SNPs showed significant association with the trait. Two salt tolerance-related candidate genes, ZmSTYK46 and Zm00001eb004810, were identified. ZmSTYK46 encodes a serine/threonine protein kinase, while the function of Zm00001eb004810 remains unknown.