Impact of phenotypic information and composition of reference population on genomic prediction in fish under the presence of genotype by environment interaction

Abstract

The difficulty or high cost to register pedigree and the presence of genotype by environment interaction (G×E) are the factors limiting conventional selective breeding in aquaculture. The limitation could be overcome by genomic selection. The objective of this study was to investigate the impact of phenotypic information and composition of reference population on genomic prediction in aquaculture under the presence of G×E, and the impact of genotyping strategy for selection candidates on genetic progress. The study was based on simulated data mimicking a rainbow trout population under G×E where genetic correlation between breeding environment and commercial production environment was 0.8, 0.5 or 0.2. Different scenarios of reference population were investigated, with regard to reference individuals from breeding population or production population, reference individuals were a random sample or a selected sample of top fish, and the phenotypic performance of the reference individuals were measured in breeding environment or in production environment. These scenarios were assessed on accuracy and unbiasedness of predicted breeding value for performance in commercial production environment. The results showed that genomic prediction greatly increased accuracy of selection, compared with conventional pedigree-based selection. Reference population comprising top individuals led to low accuracy and serious bias of genomic prediction. Accuracies of breeding values for performance in production environment predicted based on phenotypic information from breeding farm were low when genetic correlation between breeding and production environments was less than 0.8. With records of performance measured in production farm, reference population comprising individuals from breeding population gave higher prediction accuracy than the reference individuals from production population did. In addition, preselecting candidates from the breeding population for genotyping led to larger selection response than randomly genotyping candidates. These results indicate that genomic selection is feasible and promising in fish breeding under the presence of G×E. It is a good strategy to use a reference population comprising individuals randomly sampled from breeding population but reared in commercial production farm to get phenotypic records (RanBC in the context). Such a reference population is representative of the whole population, have a close relationship with candidates, and lead to a direct selection for performance in commercial production environment. In the situation of limited cost for genotyping selection candidates, genotyping top selection candidates is a good strategy since it can realize high selection intensity.