SNP Markers Linked to Wheat Pre-Harvest Sprouting Resistance Identified in an Association Study Can Significantly Improve Selection Efficiency

Wheat pre-harvest sprouting (PHS), germination of physiologically matured grains in a spike before harvesting, can cause significant reduction in wheat end-use quality and thus in grain sale price. Evaluation of a large number of wheat lines for PHS resistance in wheat breeding is time and effort consuming, and genetic markers can provide prediction by taking advantages of linkage disequilibrium. In this study, genome-wide association study (GWAS) was conducted using a panel of 185 U.S. wheat lines that were genotyped with the 9K iSelect single nucleotide polymorphism (SNP) assay to identify SNP markers closely related to PHS resistance. The identified markers closely linked to quantitative trait loci (QTL) for PHS resistance were used to predict PHS resistance for each wheat line. The predicted result was compared with that from genomic prediction. The panel was evaluated for PHS resistance in Manhattan and Hays in both 2013 and 2014. GWAS identified 6 QTLs on chromosomes 3A, 4A, 6A, 7A, 1B and 3B, and these QTLs showed varied effects under different environments. Thirteen SNPs identified in 3 QTL regions were used to predict PHS resistance, and the prediction accuracies were compared with those of different genomic prediction methods (ridge regression BLUP and the Bayesian methods). The set of significant SNPs identified in association study made the best prediction among all the prediction methods used. Therefore, for those quantitative traits that are mainly controlled by a few major QTL, marker-assisted selection can be more effective than genomic selection.