Genome-Wide Association Study and Functional Analysis of Alkali Tolerance in Maize (Zea mays L.) Seedlings Based on Biomass-Related Traits

Salinization stress poses a major environmental factor that adversely affects maize (Zea mays L.) growth and development. Thus, identifying and utilizing alkaline tolerance-related genes in maize is crucial for enhancing resistance to alkaline stress. In this study, a genome-wide association study (GWAS) was conducted to analyze alkali tolerance in seedlings, focusing on biomass-related traits at the seedling stage across a panel of 212 maize inbred lines. The analysis found nine single-nucleotide polymorphism (SNP) loci significantly associated with alkali tolerance during the seedling stage. Within the confidence intervals of these loci, 57 genes with clear functional annotations were identified, among which eight were predicted to be involved in alkali tolerance based on functional annotation and homology analysis. qRT-PCR expression validation of selected candidate genes revealed that the relative expression level of GRMZM2G028089 was similar between in L99 and M-J244-3 lines. In contrast, the expression levels of GRMZM2G071196, GRMZM2G313162 and GRMZM5G883126 were higher in the L99 line compared to M-J244-3, suggesting their potential positive regulatory roles in the response to alkaline stress. These findings provide important theoretical support for the targeted breeding of alkali-resistant maize varieties.