Association Mapping for End-Use Quality in Pacific Northwest Soft White Winter Wheat.

Soft white winter wheat is a major export of the Pacific Northwest, and it is used in foreign markets for various end products requiring specific end-use quality profiles. For the Pacific Northwest to maintain or even increase its foreign market share, breeders must continue to develop cultivars with superior end-use quality. Laboratory milling and baking tests can be destructive, costly, and time-consuming, so it is advantageous for wheat breeders to use molecular markers to select experimental lines with superior traits. An association mapping panel of 480 Pacific Northwest soft white cultivars and advanced generation breeding lines was developed from regional breeding programs. This panel was genotyped on a wheat specific 90K iSelect single nucleotide polymorphism (SNP) chip. The raw output of the 90K SNP chip were clustered and filtered prior to any statistical analysis. Lines selected already had a minimum of six location-years of end-use quality data generated from the USDA-ARS Western Wheat Quality Laboratory. Additionally, the panel was grown in Pullman, WA, in 2014 and was subjected to further laboratory milling and baking tests. The genotypic data was combined with best linear unbiased predictions (BLUPs) from historical phenotypic data of the breeding lines in the panel. Genome-wide association mapping using mixed linear models in the GAPIT R package enabled associations to be made between the SNP markers and favorable end-use quality traits. Significant markers for multiple end-use quality traits were found on chromosomes 1B, 1D, 3B and 6A. If breeding lines with desirable alleles for end-use quality traits can be selected in earlier generations, then cultivar development may be expedited.