Evaluation of Genomic Selection Methods for Wheat Quality Traits in Biparental Populations Indicates Inclination towards Parsimonious Solutions

Breeding for end-use quality traits is often challenging since their assessment requires larger quantities of grain and flour samples, which are usually not available early in the breeding process. Using the mixograph as a fast and effective method of evaluating dough quality together with genomic selection (GS) can help in pre-selecting high-performing progenies earlier in the breeding process and achieve a higher gain per unit of time and cost. In the present study, the potential of GS to predict seven end-use quality traits, including mixograph traits, in two biparental wheat populations was investigated. Field trials with both populations were conducted at two locations in Croatia (Osijek and Slavonski Brod) over three years. Results showed that the size of the training population (TP) plays an important role in achieving higher prediction accuracies, while marker density is not a major limitation. Additionally, results of the present study did not support the optimization of TP based on phenotypic variance as a tool to increase prediction accuracy. The performance of eight prediction models was compared and among them elastic net showed the lowest prediction accuracy for all traits. Bayesian models provided slightly higher prediction accuracy than the ridge regression best linear unbiased prediction (RR-BLUP) model, which is negligible considering the time required to perform an analysis. Although RR-BLUP was not the best performing model in all cases, no advantage of using any other model studied here was observed. Furthermore, strong differences between environments in terms of the prediction accuracy achieved were observed, suggesting that environments that are less predictive should be removed from the dataset used to train the prediction model. The prediction accuracies obtained in this study support implementation of GS in wheat breeding for end-use quality, including some mixograph traits.