Identification of genotyping-by-sequencing sequence tags associated with milling performance and end-use quality traits in hard red spring wheat (Triticum aestivum L.)

Authors: BOEHM, JEFFREY - Washington State University; IBBA, MARIA ITRIA - Washington State University; Kiszonas, Alecia; See, Deven; Skinner, Daniel; Morris, Craig

Submitted to: Journal of Cereal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/14/2017
Publication Date: 8/1/2017
Publication URL: http://handle.nal.usda.gov/10113/5801805
Citation: Boehm, J.D., Ibba, M., Kiszonas, A., See, D.R., Skinner, D.Z., Morris, C.F. 2017. Identification of genotyping-by-sequencing sequence tags associated with milling performance and end-use quality traits in hard red spring wheat (Triticum aestivum L.). Journal of Cereal Science. 77:73-83.

Interpretive Summary: Wheat breeders are constantly aiming to develop cultivars with higher yields while maintaining desirable end-use quality traits and processing characteristics. By dissecting the genetic complexity of quantitatively controlled end-use quality traits and identifying QTLs and new markers that may be used for MAS, breeders can more efficiently develop cultivars with superior agronomic and end-use quality traits. To achieve that goal, a GBS approach was used to obtain genotyping data for a set of 139 recombinant inbred lines (RILs) that were developed from a hard red spring wheat ‘ND2603’ x ‘Butte86’ bi-parental mapping population, segregating for Puroindoline alleles at the Hardness locus, and high and low molecular weight glutenin alleles at the Glu-A1, Glu-B1, Glu-A3, Glu-B3 and Glu-D3 loci. A linkage map was developed for the population using the genotyping data and subsequent multiple QTL mapping identified 99 significant QTLs with LOD scores greater than 3.0 that located QTL for the sixteen end-use quality traits on 15 different wheat chromosomes. The reporting and validation of these QTLs will enhance the breeding process for these end-use quality traits and will assist wheat breeders in developing cultivars with favorable alleles through the use of marker assisted selection.

Technical Abstract: Wheat quality is defined by culinary end-uses and processing characteristics. Wheat breeders are interested to identify quantitative trait loci for grain, milling, and end-use quality traits because it is imperative to understand the genetic complexity underlying quantitatively inherited traits to develop cultivars with desirable alleles. A set of 139 recombinant inbred lines (RILs) developed from a hard red spring wheat ‘ND2603’ x ‘Butte86’ bi-parental mapping population, segregating for Puroindoline alleles at the Hardness locus, and high and low molecular weight glutenin alleles at the Glu-A1, Glu-B1, Glu-A3, Glu-B3 and Glu-D3 loci were grown in a randomized complete block design in two replications at Bozeman, MT and Pullman, WA, USA. Grain was evaluated for sixteen grain, milling and end-use quality parameters. The RILs were genotyped using a combination of GBS, SSR and allele-specific sequence tagged site markers. In total, 696 polymorphic markers were identified and used to develop a linkage map which covered every wheat chromosome except 4D. Multiple QTL mapping identified 29 significant major QTLs explaining greater than 15% of the phenotype variance each with LOD scores between 5.2 – 18.6 for 11 different end-use quality traits on chromosomes 1A, 1B, 3B, 5A, 7A, and 7B. Transgressive segregates were observed for all phenotypes, and co-locating QTLs controlling multiple end-use quality traits were confirmed on chromosomes 1BL, 5AS, 7AS, 7AL, and 7BS. The reporting and validation of these QTL will enhance the breeding process for these end-use quality traits and will assist wheat breeders in developing cultivars with favorable alleles through the use of marker assisted selection.