Multi-locus genome-wide association study on the rheological traits in wheat flour dough

The rheological properties of wheat dough exert a profound influence on the baking process and the quality of the final food products. Previous studies have partially elucidated the genetic basis of wheat flour rheological characteristics; however, multi-locus genome-wide association studies (ML-GWAS) investigating these traits under multi-year single-location field trials remain scarce and have yielded highly variable results. Therefore, the identification of stable genetic loci associated with dough rheological properties has become particularly critical. This study conducted a comprehensive analysis of a diverse natural population comprising 273 wheat varieties (lines) using a 55 K SNP array and an ML-GWAS model. This approach identified with high precision 239 quantitative trait nucleotides (QTNs) significantly associated with wheat flour dough rheological properties. Among these QTNs, 13 mono-effect QTNs were consistently detected across at least two environments and two distinct models, with only 3 classified as major-effect QTNs. Additionally, 7 pleiotropic QTNs were identified. Eleven of the mono-effect QTNs exhibited significant differences in phenotypic traits, while 3 pleiotropic QTNs demonstrated highly significant differences across all associated traits. Within a 4 Mb flanking region surrounding these major-effect and pleiotropic QTNs, a total of 606 genes were co-annotated. Gene annotation indicated these genes primarily participate in critical biological functions, including protein modification and degradation, and the regulation of seed development and maturation. Subsequent Gene Ontology (GO) enrichment analysis rigorously screened 18 promising candidate genes, and their expression profiles were analyzed throughout wheat tissue development and endosperm maturation. Ultimately, 6 SNP loci and 9 key candidate genes strongly linked to wheat flour dough rheological properties were identified. This study employed ML-GWAS combined with the 55 K SNP array to analyze six dough rheological traits in 273 wheat germplasm accessions. SNP loci and candidate genes associated with dough rheological properties were identified, advancing molecular breeding technology in wheat and thereby establishing a theoretical foundation for genetic improvement and the cultivation of high-quality varieties.