GWAS links plateau winter wheat landraces to 62 stable quality loci

A genome-wide association study of 279 Chinese winter wheat landraces evaluated across four environments on the Qinghai–Tibet Plateau identified 62 stable single-nucleotide polymorphism loci associated with eight grain-quality traits. Together, the loci explained between 3.86% and 15.64% of the phenotypic variance in the measured traits, according to the study. Nineteen loci had pleiotropic effects, meaning they were associated with more than one quality trait.

The findings provide genetic markers and favorable haplotypes that may be useful for marker-assisted selection, although the research reports associations rather than demonstrated improvements in selected wheat. The researchers assessed moisture content, flour water absorption, grain protein content, wet gluten content, dough stability time, dough development time, grain hardness and test weight. All eight traits showed wide phenotypic variation among the landraces.

Associations were tested with a 120,000-SNP array, and loci detected consistently across the four environments were considered stable. One especially notable result occurred at chromosome 1B position 610760001. This pleiotropic locus was significantly associated with flour water absorption, grain protein content, dough stability time and dough development time in all four environments, making it a candidate for selecting wheat with several correlated quality characteristics.

The team also examined a 488-kilobase linkage-disequilibrium block at the chromosome 1B locus and identified four haplotypes, designated Hap1 through Hap4. Hap2 and Hap3 had significantly higher flour water absorption than Hap1. Hap2 also had significantly higher grain protein content and longer dough stability time than Hap1 and Hap4, while its dough development time was significantly longer than that of Hap1 and Hap4.

These haplotype comparisons were reported at P < 0.05. Based on the measured trait associations, the researchers identified Hap2 and Hap3 as favorable haplotypes relevant to wheat quality improvement, with Hap2 showing the broadest advantage across the compared flour-quality measurements. Ten candidate genes were predicted and annotated with functions involving signal transduction, metabolic regulation, cell development and stress response.

These functional annotations offer possible biological routes through which the associated genetic variation could affect grain-quality traits, but they do not establish which genes are causal. The results remain tied to the panel of 279 landraces, the eight measured characteristics and the four environmental conditions used in the study. Further evaluation would be needed to determine whether the associated markers and haplotypes retain their relationships with quality traits in independent populations and breeding material.

By testing the same collection in four environments and emphasizing signals detected across those environments, the study identified relationships that were more stable than associations observed in only one setting. Its principal findings are the 62 stable loci, including 19 with pleiotropic effects; the chromosome 1B locus associated with four quality traits in every environment; and the favorable Hap2 and Hap3 haplotypes. The authors describe these results as evidence of the breeding potential of Chinese winter wheat landraces on the Qinghai–Tibet Plateau.

For plant breeders, the loci may offer targets for marker-assisted selection, but the reported evidence concerns statistical associations and measured trait differences rather than a demonstrated gain in agricultural performance.

Subject of Research: Genome-wide association analysis of eight grain-quality traits in Chinese winter wheat landraces on the Qinghai–Tibet Plateau

Article Title: Evaluation and association analysis of quality traits in Chinese winter wheat landraces on the Qinghai-Tibet Plateau

Article References: Han, X., Zhang, Y., Hou, W., & Huang, M. (2026). Evaluation and association analysis of quality traits in Chinese winter wheat landraces on the Qinghai-Tibet Plateau. BMC Plant Biology, 26(1), Article 1619. https://doi.org/10.1186/s12870-026-09821-y

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09821-y

Keywords: winter wheat, grain quality, genome-wide association study, Chinese landraces, Qinghai–Tibet Plateau, stable SNP loci, pleiotropy, favorable haplotypes, flour quality, marker-assisted selection, Evaluation, association