Pigment accumulation is an important trait related to wheat domestication, but there remains a limited understanding of its molecular mechanism. The genetic control of the red glume trait by a dominant allele, Rg-B1, on 1BS was reported in the last century, but the underlying gene and its molecular basis remained elusive. Here, we identified TraesTSP1B01G005700 (G57) encoding an R2R3-MYB transcription factor (TF) as the candidate Rg-B1 gene controlling red glume color by a combination of genome-wide association study (GWAS), bulked segregant RNA-sequencing (BSR-Seq), map-based cloning, and RNA-seq. The Rg-B1 locus had zero to five duplicate copies only one of which had high transcriptional activity. Genetic evidence suggested that promoter sequence variation in G57 in the glume leads to high expression of G57, resulting in the red glume phenotype. G57 could bind to the promoters of anthocyanin synthesis genes TaCHS, TaF3ʹH, and TaUFGT, activating their expression and contributing to anthocyanin accumulation in wheat glume. G57 also played a pivotal role in up-regulating expression of genes TaDREB1C and TaFLO2 associated with increased grain weight, thereby causing increased grain weight. Our research offers a better understanding of the molecular basis of red glume in bread wheat.

A large amount of genome-wide association study (GWAS) panels together with quantitative-trait locus (QTL) information associated with breeding-targeted traits have been described in wheat (Triticum aestivum L.). However, the application of mapping results from a GWAS panel to conventional wheat breeding remains a challenge. In this study, we first report a general genetic map which was constructed from 44 published linkage maps. It permits the estimation of genetic distances between any two genetic loci with physical map positions, thereby unifying the linkage relationships between QTL, genes, and genomic markers from multiple genetic populations. Second, we describe QTL mapping in a wheat GWAS panel of 688 accessions, identifying 77 QTL associated with 12 yield and grain-quality traits. Because these QTL have known physical map positions, they could be mapped onto the general map. Finally, we present a design approach to wheat breeding by using known QTL information and computer simulation. Potential crosses between parents in the GWAS panel may be evaluated by the relative frequency of the target genotype, trait correlations in simulated progeny populations, and genetic gain of selected progenies. It is possible to simultaneously improve yield and grain quality by suitable parental selection, progeny population size, and progeny selection scheme. Applying the design approach will allow identifying the most promising crosses and selection schemes in advance of the field experiment, increasing predictability and efficiency in wheat breeding.