Multi-trait genomic selection improves the prediction accuracy of end-use quality traits in hard winter wheat

Improvement of end-use quality remains one of the most important goals in hard winter wheat (HWW) breeding. Nevertheless, the evaluation of end-use quality traits is confined to later development generations owing to resource-intensive phenotyping. Genomic selection (GS) has shown promise in facilitating selection for end-use quality; however, lower prediction accuracy (PA) for complex traits remains a challenge in GS implementation. Multi-trait genomic prediction (MTGP) models can improve PA for complex traits by incorporating information on correlated secondary traits, but these models remain to be optimized in HWW. A set of advanced breeding lines from 2015 to 2021 were genotyped with 8725 single-nucleotide polymorphisms and was used to evaluate MTGP to predict various end-use quality traits that are otherwise difficult to phenotype in earlier generations. The MTGP model outperformed the ST model with up to a twofold increase in PA. For instance, PA was improved from 0.38 to 0.75 for bake absorption and from 0.32 to 0.52 for loaf volume. Further, we compared MTGP models by including different combinations of easy-to-score traits as covariates to predict end-use quality traits. Incorporation of simple traits, such as flour protein (FLRPRO) and sedimentation weight value (FLRSDS), substantially improved the PA of MT models. Thus, the rapid low-cost measurement of traits like FLRPRO and FLRSDS can facilitate the use of GP to predict mixograph and baking traits in earlier generations and provide breeders an opportunity for selection on end-use quality traits by culling inferior lines to increase selection accuracy and genetic gains.