A genome-wide association study approach to identify novel major-effect quantitative trait loci for end-use quality traits in soft red winter wheat

Authors: SUBEDI, MADHAV - Cornell University; BAGWELL, JOHN - North Carolina State University; LOPEZ, BENJAMIN - University Of Georgia; Baik, Byung-Kee; BABAR, MD - University Of Florida; MERGOUM, MOHAMED - University Of Georgia

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/3/2024
Publication Date: 9/7/2024
Citation: Subedi, M., Bagwell, J.W., Lopez, B., Baik, B.V., Babar, M.A., Mergoum, M. 2024. A genome-wide association study approach to identify novel major-effect quantitative trait loci for end-use quality traits in soft red winter wheat. Genes. 15. Article 1177. https://doi.org/10.3390/genes15091177.
DOI: https://doi.org/10.3390/genes15091177

Interpretive Summary: The development of wheat varieties with improved milling and baking quality potentials requires extensive evaluation of a large number of breeding lines over multiple generations, which is both costly and time-consuming. Therefore, only the advanced breeding lines that are nearing selection as varieties are evaluated for milling and baking quality to avoid releasing inferior-quality varieties. Marker-assisted selection employing genetic markers linked to milling and baking quality traits would provide an efficient and reliable method for selecting traits of interest. Research on the genetics of, and markers for, wheat end-use quality is limited due to the numerous traits involved and their complex inheritance patterns. The large genome size of wheat necessitates extensive genetic studies to fully understand the complexities of wheat grain genetics. A genome-wide association study of 266 soft red winter wheat genotypes, grown in two locations over two years, identified 12 novel major quantitative trait loci (QTLs). These QTLs explained over 10% of the variance for milling and baking quality traits including kernel hardness, protein content, flour yield, flour particle size, damaged starch content, solvent retention capacity, and sugar-snap cookie diameter. Five of the QTLs had major effects on milling and baking quality traits and were consistently expressed across multiple datasets from different locations and crop years. Candidate genes linked to these quality traits were identified for eight of the major-effect QTLs. These results provide valuable insights for researchers and breeders aiming to improve the end-use quality of wheat. The development of genetic markers associated with these major-effect QTLs could facilitate marker-assisted and genomic selection in wheat improvement programs.

Technical Abstract: Wheat is used for making many food products due to its diverse quality profile found among different wheat classes. Since laboratory analysis of these end-use quality traits is costly and time-consuming, genetic dissection of the traits is preferential. This study used a genome-wide association study (GWAS) of 10 end-use quality traits, including kernel protein, flour protein, flour yield, softness equivalence, solvent’s retention capacity, cookie diameter, and top-grain, in soft red winter wheat (SRWW) adapted to US southeast. The GWAS study included 266 SRWW genotypes that were evaluated in two locations over two years (2020-2022). A total of 27,466 single nucleotide markers were used and a total of 80 significant marker-trait associations were identified. There were 13 major effect quantitative trait loci (QTLs) explaining > 10% phenotypic variance out of which 12 were considered as novel. Five of the major effect QTLs were found to be stably expressed across multiple datasets, and four showed associations with multiple traits. Candidate genes were identified for eight of the major-effect QTLs including genes associated with starch biosynthesis and nutritional homeostasis in plants. These findings increase genetic comprehension of these end-use quality traits and could potentially be used for improving the quality of SRWW.