HubSmolt: a novel genetic locus defining seawater consequences of freshwater rearing conditions in Atlantic salmon

Atlantic salmon farming depends on freshwater rearing of juvenile fish from egg hatching until they are large enough to undergo transfer to seawater, where they can grow rapidly. Because of the high salt concentrations in seawater, this requires fish to undergo pronounced changes in the gill physiology linked to retention of water and salt excretion. Variability in the success with which this physiological change is achieved is thought to be a major contributor mortality in the seawater phase of salmon production. This variability stems from a combination of how freshwater rearing is conducted and the genetic variation in salmon stocks. In Hubsmolt we will explore the genetic aspect, focussing on a region of salmon chromosome 14, which we call the ´hub locus´. Our interest in this region stems from our recent discovery that genetic variation in this region affects how over 2000 other genes are expressed in the gill prior to transfer to seawater, which makes it particularly promising as a focus for genetic improvement of farmed salmon. HubSmolt aims to understand how variation at the hub locus affects development of juvenile salmon in freshwater and how this links to subsequent performance when the fish are moved to seawater. To achieve this we will conduct experiments in genetically defined fish following a typical commercial rearing protocol. This will include assessment of organ development, immune function, and responses to viral disease and handling stress. In parallel, we will also zoom in on the Hub locus on chromosome 14 to identify at a DNA-level how a single genetic region has such widespread effects on salmon development. To meet these aims we have established strong interdisciplinary partnership between physiologists, geneticists, virologists and aqualculture experts, with backgrounds linking basic science to industry application. This ensures the academic success of the project, facilitates dissemination of practically relevant project findings.

The HubSmolt project focuses on the issue of how to optimise freshwater rearing conditions to maximise welfare and productivity in the seawater phase of salmon production. We recently discovered genetic locus that dramatically affects the light-dependent process of smoltification, affecting molecular reorganisation of the gill, somatic growth in freshwater, and survival in the seawater cage environment. Because of the remarkable extent of the effects on gill gene expression, we call this locus the hub locus. HubSmolt’s objectives are therefore to properly characterise the consequences of variation at this locus for smolt development and seawater performance; additionally it will begin the complex process of defining the mechanisms through the hub locus affects smolt phenotype. To meet the HubSmolt objectives we will conduct a new study in pools of fish, homozygous for either the major or minor allele at the hub locus. Fish will be taken through smoltification protocols using short photoperiod or continuous light, with multi-tissue sampling and endocrine monitoring throughout the freshwater phase. This will allow us to define in what tissues, and at what times the hub locus affects development, and to assess the extent to which such effects interact with rearing conditions. Subsequently, fish will be transferred to seawater cages and monitored to commercial slaughter weight. In parallel, we will conduct controlled handling stresses, and SAV3 virus challenges and assess acute and long term immunological and pathological responses. By combining these analyses with detailed genetic characterisation of the hub locus we will gain a comprehensive picture of how the hub locus affects development prior to seawater transfer and its potential utility in refinement of salmon aquaculture. Through its extensive complementary experience in basic and applied research in salmonid biology, the project consortium is outstandingly qualified to deliver on these objectives.