Genome-wide Association Study of Common Wheat’s Alkali Tolerance at the Germination Stage

Soil alkalization poses a severe threat to global wheat production, and deciphering the genetic basis of alkali tolerance during germination is critical for breeding resistant varieties. Here, a genome-wide association study (GWAS), with a comprehensive analysis, of 314 wheat accessions was executed under 0.15% Na ₂ CO ₃ stress and control conditions. The phenotypic screening showed seedling biomass and root growth were suppressed under stress, while germination rate remained stable. The 314 accessions were classified by a principal component analysis, as follows: 6 highly tolerant, 57 tolerant, 92 moderate, 110 sensitive, and 35 highly sensitive. The GWAS indicated that 206 significant marker-trait associations (MTAs) were identified for nine germination-related traits. Notably, five loci (MTA25, MTA29, MTA80, MTA129, and MTA166) demonstrated stability across both tested conditions. The alleles effect analysis and candidate gene analysis for three stable loci (MTA25, MTA29, and MTA80) were executed. A principal component analysis-integrated GWAS identified 198 significant MTAs, of which 51 were co-localized with phenotype location-based MTAs, and they were verified as core stress-responsive loci. In addition, Kompetitive Allele Specific PCR markers for sheath length and germination percentage were developed. These findings provide a theoretical foundation for the selection of alkali-resistant wheat and provide important resources for wheat molecular breeding.