Genetic dissection of soil acidity tolerance in wheat by combining genome-wide association study and linkage mapping

Low pH stress is a major constraint to wheat production in China, severely impacting wheat yield and quality. However, the genetic basis of low pH tolerance remains unclear. We evaluated seven seedling traits under control (pH 7.0) and low pH stress (pH 4.5) conditions, calculated an acidity tolerance coefficient (ATC) for each trait and used it in subsequent analyses. A stable QTL on chromosome 2A (13.85–21.27 Mb) associated with low pH tolerance was identified by integrating genome-wide association study (GWAS) and quantitative trait locus (QTL) mapping. Haplotype analysis refined this interval to ∼ 489 kb containing 11 genes. Through parental re-sequencing, bulked segregant RNA-seq (BSR-seq), and haplotype dissection, we identified TaMT-2A , a methyltransferase-encoding gene, as a candidate regulator. Sequence analysis identified a SNP at position −791 in the TaMT-2A promoter, defining two genotypes (CC and TT). CC genotype had significantly higher ATCs for multiple traits (plant height, shoot fresh weight, shoot dry weight, and root dry weight) compared with the TT genotype. These findings provide mechanistic insights into soil acidity tolerance in wheat and a molecular marker for selection.