Genomic selection in a commercial winter wheat population

Genomic selection models can be trained using historical data and filtering genotypes based on phenotyping intensity and reliability criterion are able to increase the prediction ability. We implemented genomic selection based on a large commercial population incorporating 2325 European winter wheat lines. Our objectives were (1) to study whether modeling epistasis besides additive genetic effects results in enhancement on prediction ability of genomic selection, (2) to assess prediction ability when training population comprised historical or less-intensively phenotyped lines, and (3) to explore the prediction ability in subpopulations selected based on the reliability criterion. We found a 5 % increase in prediction ability when shifting from additive to additive plus epistatic effects models. In addition, only a marginal loss from 0.65 to 0.50 in accuracy was observed using the data collected from 1 year to predict genotypes of the following year, revealing that stable genomic selection models can be accurately calibrated to predict subsequent breeding stages. Moreover, prediction ability was maximized when the genotypes evaluated in a single location were excluded from the training set but subsequently decreased again when the phenotyping intensity was increased above two locations, suggesting that the update of the training population should be performed considering all the selected genotypes but excluding those evaluated in a single location. The genomic prediction ability was substantially higher in subpopulations selected based on the reliability criterion, indicating that phenotypic selection for highly reliable individuals could be directly replaced by applying genomic selection to them. We empirically conclude that there is a high potential to assist commercial wheat breeding programs employing genomic selection approaches.