Genomic selection uses marker-based predictions to improve and accelerate the breeding process. Numerous studies have investigated the accuracy of genomic predictions; however, few studies have directly compared genomic and phenotypic selection. We compared genomic and phenotypic selection in five sets of selection candidates from a barley breeding program. In each set, about 96 breeding lines were genotyped with 1536 single nucleotide polymorphism (SNP) markers and phenotyped for yield, Fusarium head blight (FHB) severity, and deoxynivalenol (DON) concentration. A set of 168 lines and the same set of SNP markers were used to train a prediction model and predict the performance of the selection candidates using ridge regression best linear unbiased prediction. The best-performing 10% of the breeding lines in each selection candidate set were selected using both methods and revaluated in several trials. We found similar significant response to selection using genomic and phenotypic selection for FHB severity and DON concentration, and no significant response for yield using either method. For all traits, genomic selection significantly increased genetic similarity compared with the selection candidates. In addition, genomic selection, compared with phenotypic selection, resulted in an increase in the frequency of favorable alleles. Three indirect selection methods for DON concentration, (predicted FHB severity, empirical FHB severity, and predicted DON concentration) performed similarly to direct phenotypic selection for DON, but differed considerably in cost. We conclude that the use of genomic selection for yield and FHB breeding in barley should result in gains from response to selection that are similar to the gains obtained using phenotypic selection, but with a shorter breeding cycle time and lower cost.
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