Genome-wide association improves genomic selection for ammonia tolerance in the orange-spotted grouper (Epinephelus coioides)

Abstract

A high concentration of ammonia is toxic to intensively cultured groupers, with a potential to affect their survival and production. It is therefore useful to select groupers with a high tolerance to ammonia. Based on genome-wide loci, to predict the genomic estimated breeding value (GEBV) of individuals, genomic selection (GS) can expedite genetic improvement over traditional pedigree-based approaches. However, GS has not previously been applied in grouper breeding. In this study, 600 orange-spotted groupers (Epinephelus coioides) were genotyped by whole-genome resequencing and over 3 million single nucleotide polymorphisms (SNPs) were identified. A moderate heritability of 0.36 ± 0.12 was estimated using these SNPs. Four methods, i.e. BayesA, BayesB, BayesC, and rrBLUP, were used for GS, and the average AUC (Area under receiver operating characteristic) values of these methods were 0.641, 0.643, 0.642, and 0.640, respectively. The predictive accuracies of a genome-wide association study (GWAS) informative SNPs and those of the randomly selected SNPs were compared. The accuracy of GWAS-informative SNPs reached 100%, which was higher than that of the random SNPs. These results suggest that GWAS can be used to improve the cost-efficiency of GS, due to a substantial reduction in genotyping cost and time. GS is therefore suitable for improving the ammonia tolerance of groupers.