Genome-wide association study of alkali tolerance at germination stage in wheat

Six highly alkali-tolerant wheat germplasms were identified, 206 MTAs related to germination traits and 198 significant PC-MTAs were detected, and 2 KASP markers for resistance breeding were developed. Soil alkalization is a major constraint on global wheat production, making it essential to uncover the genetic mechanisms underlying alkali tolerance during germination. Here, a genome-wide association study (GWAS) was conducted on 314 wheat accessions evaluated under 0.15% Na₂CO₃ stress and control conditions. Phenotypic screening showed a strong suppression of seedling biomass and root growth under alkalinity stress, while germination rate remained largely unaffected. Based on principal component analysis, the accessions were classified into five tolerance groups: six highly tolerant, 57 tolerant, 92 moderate, 110 sensitive, and 35 highly sensitive. GWAS identified 206 significant marker-trait associations (MTAs) for nine germination-related traits, with five loci (MTA25, MTA29, MTA80, MTA129, and MTA166) consistently detected across both conditions. Allelic effect and candidate gene analyses were performed for three of these stable loci (MTA25, MTA29, and MTA80). Principal component analysis-integrated GWAS detected an additional 198 significant MTAs, 51 of which co-localized with phenotype-based MTAs and were validated as core stress-responsive loci. In addition, Kompetitive Allele Specific PCR markers associated with sheath length and germination percentage were developed. These findings enhance our understanding of the genetic basis of alkali tolerance during wheat germination and provide valuable molecular resources for breeding alkali-tolerant wheat varieties.