Atlantic Salmon Populations Research Articles

The impact of genetic relationship between training and validation populations on genomic prediction accuracy in Atlantic salmon

The potential of genomic selection (GS) to improve production traits has been widely demonstrated in many aquaculture species. Atlantic salmon breeding programmes typically consist of sibling testing schemes, where traits that cannot be measured on the selection candidates are measured on the candidates’ siblings. While annual testing on close relatives is effective, it is expensive due to high genotyping and phenotyping costs. Accurate prediction of breeding values in distant relatives could significantly reduce the cost of GS. This study aimed to evaluate the impact of decreasing the genomic relationship between the training and validation populations on the accuracy of genomic prediction for two key traits; body weight and resistance to sea lice; and to assess the interaction of genetic relationship with SNP density. Phenotype and genotype data from two year classes of a commercial breeding population of Atlantic salmon were used. The accuracy of genomic predictions were close to zero when the prediction was performed across year class, albeit this may reflect a lack of genetic correlation between the same traits measured in the different year classes. Within a year class, systematically reducing the relatedness between the training and validation populations resulted in decreasing accuracy of genomic prediction; when the training and validation populations were set up to contain no relatives with genomic relationships > 0.3, the accuracies decreased by 44% for sea lice count and by 53% for body weight. Less related training and validation populations also tended to result in highly biased predictions. No clear interaction between decreasing SNP density and relatedness between training and validation population was found. These results confirm the importance of close genetic relationships between training and selection populations in salmon breeding programmes, and suggests that prediction across generations using existing approaches would severely compromise the efficacy of GS.

Genetic structure and origin of non-native, free-living Atlantic salmon Salmo salar along a latitudinal gradient in Chile, South America

Limited stocking efforts to introduce Atlantic salmon Salmo salar into Chilean rivers and streams were unsuccessful during the 20th century. Following the arrival of the aquaculture industry during the 1980s, escaped Atlantic salmon have presented an ecological risk to native taxa through predation, competition, and transmission of pathogens or parasites. However, whether commercial aquaculture strains represent the likely source of free-living Atlantic salmon in marine and freshwater environments is unclear. We used 272 single nucleotide polymorphisms to characterize free-living Atlantic salmon (n = 80) captured from 12 marine and freshwater locations in southern Chile. These were compared with 8 reference collections, 6 known commercial strains, and 2 wild populations of Atlantic salmon. We evaluated genetic structure among free-living Atlantic salmon and assessed individual ancestry and origin by assigning mixture samples to reference collections. We found evidence for genetic structure (number of clusters, K = 3) among free-living salmon unexplained by geography, environment, or life stage, but consistent with the number of clusters among commercial aquaculture strains. Most free-living Atlantic salmon had a close ancestry with farmed Norwegian strains, the most widely used by the industry, pointing to recent aquaculture escapes as their origin. Yet recent establishment of self-sustaining populations weakly differentiated from aquaculture broodstock cannot be ruled out. We propose increasing monitoring efforts of free-living Atlantic salmon in remote sites as well as in watersheds located in densely stocked aquaculture areas.

The role played by the Umba fish hatchery in artificial reproduction and conservation of water biological resources in the Murmansk region

The article provides information on the need for artificial reproduction of water biological resources. It is shown that the conservation of biological diversity of fish, maintaining stocks of valuable fish species, preserving the natural habitat is impossible without effective measures in the field of artificial reproduction. A brief description of the activities of the Murmansk branch «Glavrybvod» is given. The greatest attention is paid to the oldest enterprise in the Murmansk region – the Umba fish hatchery. The historical information about the activity of this enterprise is given. An assessment of the current state of the Atlantic salmon stocks in the Umba River basin is given. The main problems of the fish-breeding enterprise are identified and analyzed: a high level of illegal fishing, the consequences of molten timber rafting and the influence of the activities of enterprises of the mining complex. Measures aimed at solving these problems are proposed. It has been proved that thanks to the fish breeders of the Umba fish hatchery, the stocks of the Atlantic salmon population of the Umba River are replenished. It is shown that a promising direction of the plant's activity is the cultivation of other valuable fish species (whitefish, pink salmon, brown trout), which will significantly contribute to the replenishment of valuable fish stocks in the water bodies of the Murmansk region. The role and importance of artificial reproduction and conservation of water biological resources will increase more and more as the anthropogenic impact on the environment intensifies. This type of activity will be the only way to preserve the commercial value of valuable species of fish and other biological resources, which makes artificial reproduction artificial reproduction one of the highest priorities in development of fishery system of the Russian Federation.

Introgression from farmed escapees affects the full life cycle of wild Atlantic salmon.

After a half a century of salmon farming, we have yet to understand how the influx of genes from farmed escapees affects the full life history of Atlantic salmon (Salmo salar L.) in the wild. Using scale samples of over 6900 wild adult salmon from 105 rivers, we document that increased farmed genetic ancestry is associated with increased growth throughout life and a younger age at both seaward migration and sexual maturity. There was large among-population variation in the effects of introgression. Most saliently, the increased growth at sea following introgression declined with the population’s average growth potential. Variation at two major-effect loci associated with age at maturity was little affected by farmed genetic ancestry and could not explain the observed phenotypic effects of introgression. Our study provides knowledge crucial for predicting the ecological and evolutionary consequences of increased aquaculture production worldwide.

Classification of hydropeaking impacts on Atlantic salmon populations in regulated rivers

AbstractThis article proposes and demonstrates a new classification system of fish population level effects of hydropeaking operations in rivers. The classification of impacts is developed along two axes; first, the hydromorphological effect axis assesses the ecohydraulic alterations in rivers introduced by rapid and frequent variations in flow and water level, second the vulnerability axis assesses the site‐specific vulnerability of the fish population. Finally, the population level impact is classified into four classes from small to very large by combining the two axes. The system was tested in four rivers in Norway exposed to hydropeaking, and they displayed a range of outcomes from small to very large impacts on the salmon populations. The river with a relatively high base flow and ramping restrictions scored better than rivers with the lower base flow or limited ramping restrictions, indicating that hydropeaking effects can be mitigated while maintaining high hydropower flexibility. Most effect factors could easily be calculated from timeseries of discharge and water level, whereas the use of hydraulic models to estimate potential stranding areas may require more work. The vulnerability factors are mainly qualitative and depend more heavily on expert judgments and are thus more uncertain. The system was deemed suitable for the purpose of supporting management decisions for rivers exposed to hydropeaking operations. It evaluates the severity of the additional pressures due to hydropeaking operations and proved useful to identify mitigating measures. While the system was developed for Atlantic salmon river systems, it could be adapted to other species or systems.

Using Food Webs and Metabolic Theory to Monitor, Model, and Manage Atlantic Salmon—A Keystone Species Under Threat

Populations of Atlantic salmon are crashing across most of its natural range: understanding the underlying causes and predicting these collapses in time to intervene effectively are urgent ecological and socioeconomic priorities. Current management techniques rely on phenomenological analyses of demographic population time-series and thus lack a mechanistic understanding of how and why populations may be declining. New multidisciplinary approaches are thus needed to capitalize on the long-term, large-scale population data that are currently scattered across various repositories in multiple countries, as well as marshaling additional data to understand the constraints on the life cycle and how salmon operate within the wider food web. Here, we explore how we might combine data and theory to develop the mechanistic models that we need to predict and manage responses to future change. Although we focus on Atlantic salmon—given the huge data resources that already exist for this species—the general principles developed here could be applied and extended to many other species and ecosystems.

The quest for successful Atlantic salmon restoration: perspectives, priorities, and maxims

AbstractAtlantic salmon is often a focal species of restoration efforts throughout the north Atlantic and it is therefore an excellent case study for how best to design programmes to address and mitigate threats and correct population declines. This perspective is written to promote the work that has been accomplished towards restoration of Atlantic salmon populations and synthesize how we believe the lessons can be used effectively to support efforts by management agencies to restore populations. We reviewed where restoration is needed for Atlantic salmon, agreed on definitions for three levels of successful restoration, and then applied these criteria to 49 published papers focused on Atlantic salmon restoration. We identified 16 successful examples of restoration among 49 papers reviewed and discussed what interventions led to success versus failure. We then addressed key questions about when hatchery stocking should be used as part of a restoration measure and whether local restoration efforts are enough when these wide-ranging species encounter broad-scale changes in the north Atlantic, specifically related to issues of climate change and to marine survival. We advise to avoid restoration as much as possible by protecting and managing existing populations and when restoration is necessary, problems should be identified and addressed in partnership with river users. With appropriate resources and research to resolve ongoing mysteries, restoration of lost Atlantic salmon populations is absolutely feasible.

Gut Microbiome of Wild Baltic Salmon (Salmo salar L.) Parr.

Gut microbiota of wild Baltic salmon (a sub-population of Atlantic salmon Salmo salar L.) parr was first analyzed using microbial profiling of the 16S rRNA gene (V3-V4 region) and high taxonomic richness was revealed. At the phylum level, the gut microbiota was dominated by Firmicutes, Actinobacteria, and Proteobacteria, the most numerous of which were Firmicutes. The phylum Tenericutes (mainly assigned to Mycoplasmataceae), which is common both in wild North- and East- Atlantic salmon parr, was not detected in Baltic salmon parr. Across all samples, unique amplicon sequence variants (ASVs) belonging to the unclassified Bacilli, Actinomycetales, and Rhizobiales were identified as the major taxa. Fifteen ASVs at the family level were found in all gut samples of Baltic salmon parr, the majority of which were Mycobacteriaceae, Cryptosporangiaceae, Microbacteriaceae, and Planctomycetaceae. At the genus level, Mycobacterium, Clostridium sensu stricto, and Hyphomicrobium were dominant but at low levels in all gut samples. Our study has revealed that the gut microbial community of wild Baltic salmon parr differs from those of wild North- and East-Atlantic salmon parr. This can be due to biogeographical differences or host-selective pressures, as the Baltic salmon population is believed to have split from the Atlantic salmon population in the Ancylian period.

Genotype-by-environment interaction for growth in seawater and freshwater in Atlantic salmon (Salmo salar)

A severe outbreak of infectious salmon anemia (ISA) virus in Chile in 2007 led to considerable changes in breeding practices and regulations for the salmon industry. The Atlantic salmon (Salmo salar) broodstock reproductive cycle, from birth to maturity, is now wholly carried out in freshwater in some companies while commercial salmon are finished in saltwater. The genetic differences pertaining to growth between fish reared in freshwater and seawater are unknown. The objective of this work was to evaluate the genotype by environment interaction for body weight in two independent Atlantic salmon populations (year class 2012 and 2014), both reared in seawater and freshwater. Heritability estimates and genetic correlations for body weight in both environments were estimated through a linear bivariate animal model. Estimated heritabilities were moderate to high (0.23 ± 0.04 to 0.46 ± 0.08); indicating that body weight improvement is feasible through genetic selection. The genetic correlations for body weight between freshwater and saltwater rearing were low: 0.31 ± 0.13 for year class 2012 and 0.26 ± 0.14 for year class 2014; indicating a considerable genotype by environment interaction for growth in Atlantic salmon. The genotype by environment interaction causes a re-ranking of selection candidates, reducing the potential to maximize genetic gain for growth when broodstock is reared in freshwater and production is done in seawater.

Taking full advantage of the diverse assemblage of data at hand to produce time series of abundance: a case study on Atlantic salmon populations of Brittany

Estimation of abundance with wide spatiotemporal coverage is essential to the assessment and management of wild populations. But, in many cases, data available to estimate abundance time series have diverse forms, variable quality over space and time and they stem from multiple data collection procedures. We developed a hierarchical Bayesian modelling (HBM) approach that take full advantage of the diverse assemblage of data at hand to estimate homogeneous time series of abundances irrespective of the data collection procedure. We apply our approach to the estimation of adult abundances of 18 Atlantic salmon (Salmo salar) populations of Brittany (France) from 1987 to 2017 using catch statistics, environmental covariates, and fishing effort. Additional data of total or partial abundance collected in four closely monitored populations are also integrated into the analysis. The HBM framework allows the transfer of information from the closely monitored populations to the others. Our results reveal no clear trend in the abundance of adult returns in Brittany over the period studied.

Commercial implementation of genomic selection in Tasmanian Atlantic salmon: Scheme evolution and validation.

Genomic information was included for the first time in the prediction of breeding values for Atlantic salmon within the Australian Salmon Enterprises of Tasmania Pty Ltd selective breeding program in 2016. The process to realize genomic selection in the breeding program begun in 2014 with the scheme finalized and fully implemented for the first time in 2018. The high potential of within family selection to accelerate genetic gain, something not possible using the traditional pedigree‐based approach, provided the impetus for implementation. Efficient and effective genotyping platforms are essential for genomic selection. Genotype data from high density arrays revealed extensive persistence of linkage disequilibrium in the Tasmania Atlantic salmon population, resulting in high accuracies of both imputation and genomic breeding values when using imputed data. Consequently, a low‐density novel genotype‐by‐sequence assay was designed and incorporated into the scheme. Through the use of a static high‐ and dynamic low‐density genotyping platforms, an optimized genotyping scheme was devised and implemented such that all individuals in every year class are genotyped efficiently while maximizing the genetic gains and minimizing costs. The increase in the rates of genetic gain attributed to the implementation of genomic selection is significant across both the breeding programs primary and secondary traits. Substantial improvement in the ability to select parents prior to progeny testing is observed across multiple years. The resultant economic impacts for the industry are considerable based on the increases in genetic gain for traits achieved within the breeding program and the use of genomic selection for commercial production.

Phenotypic stress response does not influence the upper thermal tolerance of male Atlantic salmon (Salmo salar).

Fish can be identified as either low responders (LR) or high responders (HR) based on post-stress cortisol levels and whether they exhibit a proactive or reactive stress coping style, respectively. In this study, male Atlantic salmon (Salmo salar) from 17 families reared at 9°C were repeatedly exposed to an acute handling stress over a period of four months, with plasma cortisol levels measured at 1h post-stress. Fish were identified as either LR or HR if the total Z-score calculated from their cortisol responses fell into the lower or upper quartile ranges, respectively; with intermediate responders (IR) classified as the remainder. Salmon characterized as LR, IR or HR were then subjected to an incremental thermal challenge, where temperature was raised at 0.2°C day-1 from their acclimation temperature (12°C) to mimic natural sea-cage farming conditions during the summer in Newfoundland. Interestingly, feed intake remained high up to 22°C, while previous studies have shown a decrease in salmon appetite after ∼16-18°C. After the first three mortalities were recorded at elevated temperature, a subset of LR and HR salmon were exposed to another acute handling stress event at 23.6°C. Basal and post-stress measurements of plasma cortisol, glucose and lactate did not differ between stress response phenotypes at this temperature. In the end, the average incremental thermal maximum (ITMax) of LR and HR fish was not different (25.1°C). In comparison, the critical thermal maximum (CTMax; temperature increased at 2°C h-1) of the remaining IR fish that had been held at 12°C was 28.5°C. Collectively, these results: 1) show that this population of Atlantic salmon is very thermally tolerant, and further question the relevance of CTMax in assessing responses to real-world temperature changes; and 2) indicate that characterization of stress phenotype at 9°C is not predictive of their stress response or survival at high temperatures. Therefore, selection of fish based on phenotypic stress response at low temperatures may not be beneficial to incorporate into Atlantic salmon breeding programs, especially if the goal is to improve growth performance and survival at high temperatures in sea-cages.

Serial sampling reveals temperature associated response in transcription profiles and shifts in condition and infectious agent communities in wild Atlantic salmon

Abstract Anadromous Atlantic salmon (Salmo salar) populations have declined across their Southern distributions in North America. While river temperature has been identified as a central factor influencing migration behavior and over‐winter survival, little research has addressed the prevalence of infectious agents in wild Atlantic salmon populations. Further, current understanding of how temperature may interact with fish condition to influence infection outcomes in the wild is limited. The objective of this research was to characterize the change in individual condition and pathogen dynamics as salmon acclimatized to the freshwater environment during the spawning migration. Serial individual sampling (non‐lethal gill biopsy and microwave fatmeter readings) was accomplished by repeated capture and release of 27 marked individuals, which revealed how lipid content, infectious agent prevalence and relative loads, and stress and osmoregulatory transcripts changed during the initial month of their annual spawning migration. Relative infection burden (a composite metric representing the overall pathogen profile) and transcription profiles were modeled with freshwater residency, river temperature, and lipid content. Infectious agents Tetracapsuloides bryosalmonae, Candidatus Branchiomonas cysticola, Flavobacterium psychrophilum, Paranucleospora theridion, and Piscichylamidia salmonis were detected in the population. Relative infection burden and microbial pathogen species richness increased over the course of the study. Water temperature and time since fresh water entry were related to salmon transcriptional response, but not relative infection burden, highlighting the metabolic cost associated with warming temperatures and dynamic nature of pathogen infection profiles in migratory fish species. This work is the first to provide a comprehensive screening of microbial pathogen species in wild Atlantic salmon in the region, and the first to employ a unique study design that facilitates serial sampling without imposing holding stress. The high prevalence and relative load of T. bryosalmonae observed may demonstrate increased exposure to transmission pathways as a result of migratory barriers or elevated susceptibility to infection during spawning migrations in anadromous species.

Poor feeding opportunities and reduced condition factor for salmon post-smolts in the Northeast Atlantic Ocean

AbstractDuring the last few decades, many wild Atlantic salmon populations have declined dramatically. One possible contributing factor for the decline is reduced prey availability at sea. Here, we examine post-smolt diet and investigate if post-smolts show signs of selective feeding based on 2546 post-smolts sampled from west of Ireland to the northern Norwegian Sea over a 25-year period. We also test for changes over time in stomach fullness, diet, condition factor and body length. There was a clear reduction in condition factor for post-smolts sampled in the Norwegian Sea in the period 2003–2012. The post-smolt stomach fullness was also reduced in the same period. The reduction in condition factor is partly explained by reduced stomach fullness, including a reduction of highly energetic fish larvae and Amphipoda in the diet. Feeding on other prey, such as meso-zooplankton and insects, cannot substitute the high-quality fish larvae and Amphipoda in the post-smolt diet. This is the first study to document how salmon post-smolts feeding in the Norwegian Sea are affected by reduced feeding conditions. Possible causes for the observed changes in post-smolt feeding are ocean warming, decreased primary productivity, and reduced recruitment of important fish larvae.

Factors affecting Atlantic Salmon Populations Adversely; Using the River Dee, Scotland, as an Example

The stocks of the Atlantic salmon (Salmo salar) have declined in the sea and in many rivers in North America and Europe in recent years and are experiencing a crisis. Despite their high degree of legal protection, the quality of their aquatic environments within rivers and in the sea, including local coastal waters, appears to be deteriorating. Salmon survival, has declined both within the sea and within rivers. The status of the Atlantic salmon stocks is considered here, together with the adverse effects of different sources, and those steps that may need to be taken to improve the condition of the salmon. This paper is intended to assist management bodies in taking steps to resolve the problems that exist for salmon, both within rivers and in the sea. It makes particular use of information available from the River Dee in Scotland.

Factors Affecting Atlantic Salmon Populations Adversely; Using the River Dee, Scotland, as an Example

The stocks of the Atlantic salmon (Salmo salar) in many rivers in North America and Europe have declined in recent years and are experiencing a crisis. Despite their high degree of legal protection, the quality of their aquatic environments within rivers and in the sea, including local coastal waters, appears to be deteriorating. Salmon survival, has declined both within the sea and within rivers. The status of the Atlantic salmon stocks is considered here, together with the adverse effects of different sources, and those steps that may need to be taken to improve the condition of the salmon. This paper is intended to assist management bodies in taking steps to resolve the problems that exist for salmon, both within rivers and in the sea. It makes particular use of information available on the River Dee in Scotland.

Genotypic female Atlantic salmon (Salmo salar) immersed in an exogenous androgen overexpress testicular-related genes and develop as phenotypic males

In Atlantic salmon (Salmo salar) aquaculture, it can be more profitable to produce all-female populations. For this species, all-female populations can be created by crossing normal female broodstock (XX) with masculinised female broodstock (XX, known as neomales). Neo-males are typically produced via the application of an exogenous androgen treatment during the labile period (developmental window where phenotypic sex can be easily reversed). The present study determined the masculinisation rate (at 81 and 240–241 days after treatment, dat) following a single 2-h immersion in 17α-methyldihydrotestosterone (MDHT, 400 μg/L) applied at 19 days post hatch (dph) to an all-female Atlantic salmon population with and without dimethyl sulfoxide (DMSO, 300 ppm) as an adjuvant. The expression of several sex differentiation-related genes was also determined in the control and MDHT groups at 0, 1, 3, 7, 16, 33 and 56 dat. Survival and growth were not significantly different between treatment groups. At 81 dat, the proportion of males in the control, DMSO, MDHT and MDHT+DMSO groups was 5%, 5%, 100% and 100%, respectively. At 240–241 dat, the proportion of males in these groups was 6%, 0%, 82% and 88%, respectively. A small proportion of intersex fish were also observed in the control, MDHT and MDHT+DMSO groups at this time, as were sterile fish in the MDHT and MDHT+DMSO groups. When compared to the control group, significant effects of MDHT on gene expression were not detected before 16 dat. Cytochrome P450, family 19, subfamily A, polypeptide 1a (cyp19a1a) expression was downregulated from 33 dat, whereas anti-müllerian hormone (amh) and gonadal soma-derived factor (gsdf) expression was upregulated from 56 dat in the MDHT group. Forkhead box L2a (foxl2a), r-spondin 1 (rspo1) and sexually dimorphic on the Y chromosome (sdY) expression was unaffected by MDHT treatment during the experimental period. This study provides new insights into the changes in gene expression and gonadal morphology induced in genotypic female Atlantic salmon following an immersion in MDHT. The changes in gene expression observed could be involved in mediating morphological sex reversal, and the temporal scale at which they occurred may have implications for refining the age at which sex reversal treatments should be applied in this species. The findings also showed that similar rates of masculinisation are achieved with MDHT alone or in combination with DMSO.

Trends in marine survival of Atlantic salmon populations in eastern Canada

Abstract Declines in wild Atlantic salmon (Salmo salar) abundance throughout the north Atlantic are primarily attributed to decreases in survival at sea. However, comparing trends in marine survival among populations is challenging as data on both migrating smolts and returning adults are sparse and models are difficult to parameterize due to their varied life histories. We fit a hierarchical Bayesian maturity schedule model to data from seven populations in eastern Canada to estimate numbers of out-migrating smolts, survival in the first and second year at sea, and the proportion returning after 1 year. Trends in survival at sea were not consistent among populations; we observe positive, negative, and no correlations in these, suggesting that large-scale patterns of changes in marine survival are not necessarily representative for individual populations. Variation in return abundances was mostly explained by marine survival in the first winter at sea in all but one population. However, variation in the other components were not negligible and their relative importance differed among populations. If salmon populations do not respond in a uniform manner to changing environmental conditions throughout their range, future research initiatives should explore why.

Redefining the oceanic distribution of Atlantic salmon

Determining the mechanisms driving range-wide reductions in Atlantic salmon marine survival is hindered by an insufficient understanding of their oceanic ecology and distribution. We attached 204 pop-up satellite archival tags to post-spawned salmon when they migrated to the ocean from seven European areas and maiden North American salmon captured at sea at West Greenland. Individuals migrated further north and east than previously reported and displayed increased diving activity near oceanographic fronts, emphasizing the importance of these regions as feeding areas. The oceanic distribution differed among individuals and populations, but overlapped more between geographically proximate than distant populations. Dissimilarities in distribution likely contribute to variation in growth and survival within and among populations due to spatio-temporal differences in environmental conditions. Climate-induced changes in oceanographic conditions will alter the location of frontal areas and may have stock-specific effects on Atlantic salmon population dynamics, likely having the largest impacts on southern populations.

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

BackgroundInfectious Salmonid Anaemia Virus (ISAV) causes a notifiable disease that poses a large threat for Atlantic salmon (Salmo salar) aquaculture worldwide. There is no fully effective treatment or vaccine, and therefore selective breeding to increase resistance to ISAV is a promising avenue for disease prevention. Genomic selection and potentially genome editing can be applied to enhance host resistance, and these approaches benefit from improved knowledge of the genetic and functional basis of the target trait. The aim of this study was to characterise the genetic architecture of resistance to ISAV in a commercial Atlantic salmon population and study its underlying functional genomic basis using RNA Sequencing.ResultsA total of 2833 Atlantic salmon parr belonging to 194 families were exposed to ISAV in a cohabitation challenge in which cumulative mortality reached 63% over 55 days. A total of 1353 animals were genotyped using a 55 K SNP array, and the estimate of heritability for the trait of binary survival was 0.13–0.33 (pedigree-genomic). A genome-wide association analysis confirmed that resistance to ISAV was a polygenic trait, albeit a genomic region in chromosome Ssa13 was significantly associated with resistance and explained 3% of the genetic variance. RNA sequencing of the heart of 16 infected (7 and 14 days post infection) and 8 control fish highlighted 4927 and 2437 differentially expressed genes at 7 and 14 days post infection respectively. The complement and coagulation pathway was down-regulated in infected fish, while several metabolic pathways were up-regulated. The interferon pathway showed little evidence of up-regulation at 7 days post infection but was mildly activated at 14 days, suggesting a potential crosstalk between host and virus. Comparison of the transcriptomic response of fish with high and low breeding values for resistance highlighted TRIM25 as being up-regulated in resistant fish.ConclusionsISAV resistance shows moderate heritability with a polygenic architecture, but a significant QTL was detected on chromosome 13. A mild up-regulation of the interferon pathway characterises the response to the virus in heart samples from this population of Atlantic salmon, and candidate genes showing differential expression between samples with high and low breeding values for resistance were identified.