Strategies to improve the accuracy and reduce costs of genomic prediction in aquaculture species

Genomic selection (GS) has great potential to increase genetic gain in aquaculture breeding; however, its implementation is hindered owing to high genotyping cost and the large number of individuals to genotype. This study investigated the efficiency of genomic prediction in four aquaculture species. In total, 749 to 1481 individuals with records for disease resistance and growth traits were genotyped using SNP arrays ranging from 12K to 40K. We compared the prediction accuracies and bias of breeding values obtained from BLUP, genomic BLUP (GBLUP), Bayesian mixture (BayesR), weighted GBLUP (WGBLUP), and genomic feature BLUP (GFBLUP). For GFBLUP, the genomic feature matrix was constructed based on prior information from genome‐wide association studies. Fivefold cross‐validation was performed with 20 replicates. Moreover, to reduce the cost of GS, we reduced the SNP density based on linkage disequilibrium as well as the reference population size. The results showed that the methods with marker information produced more accurate predictions than the pedigree‐based BLUP method. For the genomic model, BayesR performed prediction with a similar or higher accuracy compared to GBLUP. For the four traits, WGBLUP yielded an average of 1.5% higher accuracy than GBLUP. However, the accuracy of genomic prediction decreased by an average of 6.2% for GFBLUP compared to GBLUP. When the density of SNP panels was reduced to 3K, which was sufficient to obtain accuracies similar to those using the whole dataset in the four species, the cost of GS was estimated to be 50% lower than that of genotyping all animals with high‐density panels. In addition, when the reference population size was reduced by 10%, evenly from full‐sib family, the accuracy of genomic prediction was almost unchanged, and the cost reduction was 8% in the four populations. Our results have important implications for translating the benefits of GS to most aquaculture species.