Association mapping and genomic prediction for processing and end-use quality traits in wheat (Triticum aestivum L.)

Authors: GILL, HARSIMARDDEP - University Of Minnesota; CONLEY, EMILY - University Of Minnesota; BRAULT, CHARLOTTE - University Of Minnesota; Dykes, Linda; WIERSMA, JOCHUM - University Of Minnesota; FRELS, KATHERINE - University Of Nebraska; ANDERSON, JAMES - University Of Minnesota

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/21/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: Hard red spring wheat is primarily grown in the Northern Great Plains of the U.S. and is known around the world for its outstanding end-use quality traits such as high protein content and excellent baking characteristics. In a wheat breeding program, end-use quality traits are often evaluated only in the advanced stages because their evaluations are expensive, time-consuming, and require large quantities of flour. Recent advances in genomics have provided an opportunity for wheat breeding programs to characterize quality-related traits and use marker-assisted selection in earlier generations. In this study, 56 significant associations for grain or flour characteristics, mixograph, farinograph, and bread-baking traits were identified and mapped, which could be used for marker-assisted selection. In addition, genomic prediction could have the ability to predict for mixograph and bread-baking traits, and only 46 markers from the genome-wide association study (GWAS) could be used to predict dough rheology traits (i.e. mixograph, farinograph). These results suggest the practical application of genomic prediction in early generations via the use of mixograph and farinograph as opposed to directly predicting bread-baking traits, which would accelerate wheat breeding for end-use quality.

Technical Abstract: End-use and processing traits in wheat are crucial for varietal development but are often evaluated only in the advanced stages of the breeding program due to challenging phenotyping and limited resources. Advances and availability of genomic resources have provided new tools to address the breeding for these complex traits. We used association mapping to identify key variants underlying various end-use quality traits and evaluate the usefulness of genomic prediction for these traits in hard red spring wheat. A panel of 383 advanced lines and cultivars representing the diversity of the University of Minnesota wheat breeding program was genotyped using the Illumina 90K SNP Array and evaluated in extensive multilocation trials using standard assessments of end-use quality. We identified 56 significant associations for grain or flour characteristics, mixograph, farinograph, and baking traits, the majority of which were mapped in the vicinity of glutenin/gliadin or other known loci and could be used for marker-assisted selection. In addition, a putative novel multi-trait association was identified on chromosome 6AL and candidate gene analysis revealed eight genes of interest. Further, genomic prediction had a high predictive ability (PA) for mixograph and baking traits, with PA up to 0.62 and 0.50 in cross-validation and forward prediction, respectively. The employment of only 46 markers from GWAS to predict dough-rheology traits yielded PA similar to or higher than genome-wide markers. Our results suggest the practical application of genomic prediction in early generations via the use of indirect assays such as mixograph and farinograph instead of directly predicting baking traits.