Genetics, Epigenetics, and Genotype-Environment Interaction in RAS-Reared Atlantic Salmon, Salmo salar

Abstract

While use of freshwater net-pens is widespread in Scotland, employment of recirculating aquaculture systems (RAS) for Atlantic salmon aquaculture is increasing. These husbandry environments differ which, due to environmental influences on salmons’ life cycle, may impact their commercial production. This study aimed to understand the environmental, genetic and epigenetic factors influencing salmon performance under varied culture systems by: (1) estimating phenotypic and genetic parameters, as well as genotype-environment interactions (GxE) of a population reared in RAS or ambient loch system, (2) studying if manipulation of environmental parameters impacted DNA methylation and gene expression, and (3) assessing whether the freshwater environment impacted salmon performance in saltwater. Results indicated that RAS-reared smolts were smaller, had lower trait variance, and greater heritability estimates compared to loch counterparts. Moderate GxE were identified for weight, as well as differing genomic associations with phenotypic expression depending on rearing environment. However, environmental manipulation was not observed to impact DNA methylation in a meaningful way, despite clear gene expression changes. In saltwater, despite their smaller size on transfer, RAS-reared post-smolts appeared to grow at a faster rate than loch-reared counterparts while maintaining greater trait heterogeneity. This difference was reflected in low-to-moderate estimates of GxE for growth rate. Temporal patterns in trait heritability also differed with freshwater-rearing environment. This suggested that although differences in phenotypic performance were observed at the end of freshwater-rearing, these did not negatively impact the RAS population after saltwater transfer. Such conclusions could benefit from further investigation into the genetic regulation of environment-specific traits, economic viability of potential management decisions, and further GxE studies, for example. Furthermore, although differences were observed in phenotypic performance at both freshwater and saltwater phases, this did not appear to result from methylation changes despite gene expression differences, suggesting a possible role of alternative epigenetic mechanisms.