Genetic architecture of end-use quality traits in soft white winter wheat

Meriem Aoun; Arron H Carter; Craig F Morris; Alecia M Kiszonas

doi:10.1186/s12864-022-08676-5

Genetic architecture of end-use quality traits in soft white winter wheat

BMC Genomics. 2022 Jun 14;23(1):440. doi: 10.1186/s12864-022-08676-5.

Authors

Meriem Aoun^{1

2}, Arron H Carter¹, Craig F Morris³, Alecia M Kiszonas⁴

Affiliations

¹ Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
² Currently Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA.
³ USDA-ARS Western Wheat & Pulse Quality Laboratory, Washington State University, E-202 Food Quality Building, Pullman, WA, 99164, USA.
⁴ USDA-ARS Western Wheat & Pulse Quality Laboratory, Washington State University, E-202 Food Quality Building, Pullman, WA, 99164, USA. alecia.kiszonas@usda.gov.

Abstract

Background: Genetic improvement of end-use quality is an important objective in wheat breeding programs to meet the requirements of grain markets, millers, and bakers. However, end-use quality phenotyping is expensive and laborious thus, testing is often delayed until advanced generations. To better understand the underlying genetic architecture of end-use quality traits, we investigated the phenotypic and genotypic structure of 14 end-use quality traits in 672 advanced soft white winter wheat breeding lines and cultivars adapted to the Pacific Northwest region of the United States.

Results: This collection of germplasm had continuous distributions for the 14 end-use quality traits with industrially significant differences for all traits. The breeding lines and cultivars were genotyped using genotyping-by-sequencing and 40,518 SNP markers were used for association mapping (GWAS). The GWAS identified 178 marker-trait associations (MTAs) distributed across all wheat chromosomes. A total of 40 MTAs were positioned within genomic regions of previously discovered end-use quality genes/QTL. Among the identified MTAs, 12 markers had large effects and thus could be considered in the larger scheme of selecting and fixing favorable alleles in breeding for end-use quality in soft white wheat germplasm. We also identified 15 loci (two of them with large effects) that can be used for simultaneous breeding of more than a single end-use quality trait. The results highlight the complex nature of the genetic architecture of end-use quality, and the challenges of simultaneously selecting favorable genotypes for a large number of traits. This study also illustrates that some end-use quality traits were mainly controlled by a larger number of small-effect loci and may be more amenable to alternate selection strategies such as genomic selection.

Conclusions: In conclusion, a breeder may be faced with the dilemma of balancing genotypic selection in early generation(s) versus costly phenotyping later on.

Keywords: Association mapping; End-use quality; Molecular markers; Soft white winter wheat.

MeSH terms

Genome-Wide Association Study
Phenotype
Plant Breeding
Quantitative Trait Loci*
Triticum* / genetics

Abstract

MeSH terms

Grants and funding