Genome-Assisted Gene-Flow Rescued Genetic Diversity Without Hindering Growth Performance in an Inbred Coho Salmon (Oncorhynchus kisutch) Population Selected for High Growth Phenotype

Abstract

Selective breeding is a powerful tool for improving aquaculture production. A well-managed breeding program is essential, as populations can otherwise lose genetic diversity, leading to reduced selection response and inbreeding excesses. In such cases, genetic diversity in broodstock must be restored by introducing individuals from external populations. However, this can reduce the accumulated genetic gains from selective breeding. However, the selective introduction of individuals with superior phenotypes will allow the restoration of genetic diversity without sacrificing these gains. In this study, we demonstrated this possibility using a selectively bred (SB) and a randomly bred (RB) population of coho salmon (Oncorhynchus kisutch). Forty males with superior growth were selected from the RB population using genomic selection and crossed with 127 randomly collected females from the SB population, producing a newly bred (NB) population. Genetic diversity, assessed from population statistics such as effective number of alleles, allele richness, and observed heterozygosity of 11 microsatellite markers, was higher in NB than in SB and RB. Additionally, fork length and body weight were compared among the three populations after 12 months of growth post-fertilization in common tanks. The least-squares means of fork length and body weight were similar between NB (164.9 mm and 57.9 g) and SB (161.1 mm and 53.7 g), while both were significantly greater than RB (150.4 mm and 43.0 g). Our results highlight the effectiveness of genome-assisted gene flow in restoring the genetic diversity of a population without compromising accumulated genetic gain in growth.