Accelerating wheat breeding for end-use quality through association mapping and multivariate genomic prediction

Shichen Zhang-Biehn, Allan K. Fritz, Guorong Zhang, Byron Evers, Rebecca Regan, Jesse Poland

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


In hard-winter wheat (Triticum aestivum L.) breeding, the evaluation of end-use quality is expensive and time-consuming, being relegated to the final stages of the breeding program after selection for many traits including disease resistance, agronomic performance, and grain yield. In this study, our objectives were to identify genetic variants underlying baking quality traits through genome-wide association study (GWAS) and develop improved genomic selection (GS) models for the quality traits in hard-winter wheat. Advanced breeding lines (n = 462) from 2015–2017 were genotyped using genotyping-by-sequencing (GBS) and evaluated for baking quality. Significant associations were detected for mixograph mixing time and bake mixing time, most of which were within or in tight linkage to glutenin and gliadin loci and could be suitable for marker-assisted breeding. Candidate genes for newly associated loci are phosphate-dependent decarboxylase and lipid transfer protein genes, which are believed to affect nitrogen metabolism and dough development, respectively. The use of GS can both shorten the breeding cycle time and significantly increase the number of lines that could be selected for quality traits, thus we evaluated various GS models for end-use quality traits. As a baseline, univariate GS models had 0.25–0.55 prediction accuracy in cross-validation and from 0 to 0.41 in forward prediction. By including secondary traits as additional predictor variables (univariate GS with covariates) or correlated response variables (multivariate GS), the prediction accuracies were increased relative to the univariate model using only genomic information. The improved genomic prediction models have great potential to further accelerate wheat breeding for end-use quality.
Original languageEnglish (US)
JournalThe Plant Genome
StatePublished - Nov 24 2021
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2021-11-29
Acknowledgements: This project was supported by the USDA–National Institute of Food and Agriculture (Breeding and Phenomics of Food Crops and Animals grant no. 2017-67007-26464/project accession no. 1011754) and the Kansas Wheat Commission and Kansas Wheat Alliance. We thank Shuangye Wu for generating the GBS libraries; Sandesh Shrestha for optimizing the TASSEL 5 GBSv2 pipeline; Emily Delorean for providing insights and helping investigate the Gli-D2 locus in Norin 61, Mace, and Stanley genome assemblies; and all members of the Wheat Genetics Lab at Kansas State University for project support. Computational work was completed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, and EPS-0919443.

ASJC Scopus subject areas

  • Genetics
  • Agronomy and Crop Science
  • Plant Science


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