Impact of freshwater rearing on saltwater performance: A genotype-environment interaction study in Atlantic Salmon (Salmo salar)

Atlantic salmon, Salmo salar, have traditionally been reared in net-pens in freshwater (FW) lochs up to smoltification, with subsequent transfer to saltwater (SW) cages for grow-out. Recently, interest in recirculating aquaculture systems (RAS) has grown due to environmental and husbandry benefits. To investigate the impact of RAS on their production cycle, we conducted an experiment under commercial conditions, raising a group of salmon in either a FW-RAS or -loch system. The study evaluated the effects of FW-rearing on SW performance by investigating phenotypic performance, genetic architecture, and genotype-environment interactions (GxE), which describe how the effects of different genotypes on traits change with environmental variation, potentially impacting performance across systems. We co-reared salmon for approximately nine-months before splitting them: half remained in FW-RAS and half transferred to FW-loch, where they were separated for about eight weeks. Both groups were then transferred to a SW cage-site. We sampled fish at the end of FW-rearing as smolts and three-months post-SW transfer as post-smolts, taking fin clips for genotyping. Results indicate that RAS-reared smolts were smaller in FW but demonstrated enhanced growth and lower trait variance post-transfer. Sexually dimorphic growth was observed in the loch population. Heritability of morphological traits increased post-SW transfer in the loch population but decreased in RAS. GxE for SW morphological traits were minimal, though significant genotype re-ranking was observed for SW growth. Genetic correlations between FW and SW morphological traits were high, except for whole-body weight in the loch population. These findings indicate that RAS-origin post-smolts, despite smaller FW size, showed faster growth and reduced phenotypic variance in SW compared to loch-origin fish. Differences in heritability estimates and genotype re-ranking for SW growth suggest that breeding programs may need to refine selection strategies for varied rearing environments.