Genome‐wide association study of six quality traits reveals the association of the <i>TaRPP13L1</i> gene with flour colour in Chinese bread wheat

<jats:title>Summary</jats:title><jats:p>Flour colour, kernel hardness, grain protein content and wet gluten content are important quality properties that determine end use in bread wheat. Here, a wheat 90K genotyping assay was used for a genome‐wide association study (GWAS) of the six quality‐related traits in Chinese wheat cultivars in eight environments over four years. A total of 846 significant single nucleotide polymorphisms (SNPs) were identified, explaining approximately 30% of the phenotypic variation on average, and 103 multienvironment‐significant SNPs were detected in more than four environments. Quantitative trait loci (QTL) mapping in the biparent population confirmed some important SNP loci. Moreover, it was determined that some important genes were associated with the six quality traits, including some known functional genes and annotated unknown functional genes. Of the annotated unknown functional genes, it was verified that <jats:italic>TaRPP13L1</jats:italic> was associated with flour colour. Wheat cultivars or lines with <jats:italic>TaRPP13L1‐B1a</jats:italic> showed extremely significantly higher flour redness and lower yellowness than those with <jats:italic>TaRPP13L1‐B1b</jats:italic> in the Chinese wheat natural population and the doubled haploid (DH) population. Two tetraploid wheat lines with premature stop codons of the <jats:italic>TaRPP13L1</jats:italic> gene mutagenized by ethyl methanesulfonate (EMS) showed extremely significantly higher flour redness and lower yellowness than wild type. Our data suggest that the <jats:italic>TaRPP13L1</jats:italic> gene plays an important role in modulating wheat flour colour. This study provides useful information for further dissection of the genetic basis of flour colour and also provides valuable genes or genetic loci for marker‐assisted selection to improve the process of breeding quality wheat in China.</jats:p>