Atlantic Salmon Aquaculture Research Articles

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.

Novel use of nanofiltered hyposaline water to control sea lice (Lepeophtheirus salmonis and Caligus elongatus) and amoebic gill disease, on a commercial Atlantic salmon (Salmo salar) farm

Infestations by the salmon louse (Lepeophtheirus salmonis) and amoebic gill disease (AGD) are currently significant disease concerns facing the Atlantic salmon aquaculture industry in Ireland. Increasing seawater temperatures, and the move away from chemotherapeutants has prompted a new approach to researching areas of host-parasite life histories and using the physiology and behaviour of the parasites to develop novel control methods. Freshwater, with a low ionic concentration can be used to control sea lice and AGD but this may not always be available. Alternative treatments with hydrogen peroxide can prove toxic at the higher summer water temperatures experienced at this latitude. The aim of this study was to determine the efficacy of using nano-filtered hyposaline water as a non-medicinal method to reduce sea lice (L. salmonis and Caligus elongatus) infestation levels and amoebic gill disease under commercial conditions on an Atlantic salmon farm. To achieve this salmon were bathed in a tarpaulin filled with 5 ppt hyposaline water for 4.5 h and a regime of prophylactic bath treatments put in place to follow the production cycle. The nano-filtration unit consistently produced low saline water and resulted in a significant reduction of sea lice levels and AGD following routine 4.5 h baths. A 4.5 h bioassay of detached salmon lice confirmed both hyposaline and freshwater were equally effective against L. salmonis in the absence of the host.

A Novel Marine Pathogen Isolated from Wild Cunners (Tautogolabrus adspersus): Comparative Genomics and Transcriptome Profiling of Pseudomonas sp. Strain J380.

Cunner (Tautogolabrus adspersus) is a cleaner fish being considered for utilized in the North Atlantic salmon (Salmo salar) aquaculture industry to biocontrol sea lice infestations. However, bacterial diseases due to natural infections in wild cunners have yet to be described. This study reports the isolation of Pseudomonas sp. J380 from infected wild cunners and its phenotypic, genomic, and transcriptomic characterization. This Gram-negative motile rod-shaped bacterium showed a mesophilic (4–28 °C) and halotolerant growth. Under iron-limited conditions, Pseudomonas sp. J380 produced pyoverdine-type fluorescent siderophore. Koch’s postulates were verified in wild cunners by intraperitoneally (i.p.) injecting Pseudomonas sp. J380 at 4 × 103, 4 × 105, and 4 × 107 colony forming units (CFU)/dose. Host-range and comparative virulence were also investigated in lumpfish and Atlantic salmon i.p. injected with ~106 CFU/dose. Lumpfish were more susceptible compared to cunners, and Atlantic salmon was resistant to Pseudomonas sp. J380 infection. Cunner tissues were heavily colonized by Pseudomonas sp. J380 compared to lumpfish and Atlantic salmon suggesting that it might be an opportunistic pathogen in cunners. The genome of Pseudomonas sp. J380 was 6.26 megabases (Mb) with a guanine-cytosine (GC) content of 59.7%. Biochemical profiles, as well as comparative and phylogenomic analyses, suggested that Pseudomonas sp. J380 belongs to the P. fluorescens species complex. Transcriptome profiling under iron-limited vs. iron-enriched conditions identified 1159 differentially expressed genes (DEGs). Cellular metabolic processes, such as ribosomal and energy production, and protein synthesis, were impeded by iron limitation. In contrast, genes involved in environmental adaptation mechanisms including two-component systems, histidine catabolism, and redox balance were transcriptionally up-regulated. Furthermore, iron limitation triggered the differential expression of genes encoding proteins associated with iron homeostasis. As the first report on a bacterial infection in cunners, the current study provides an overview of a new marine pathogen, Pseudomonas sp. J380.

What is the limit of sustained swimming in Atlantic salmon post smolts?

A trend in Atlantic salmon aquaculture is to establish new production sites that are susceptible to extreme weather conditions; however, strong and persistent water currents may compromise fish welfare. Defining acceptable current conditions necessitates an assessment of sustained swimming abilities that are fuelled solely by aerobic metabolism and do not result in fatigue. In this study, the limit of sustained swimming was quantified with regards to both speed and time in Atlantic salmon of ~700 g and ~39 cm at 12°C by testing fish in groups of 10 in a large swim tunnel respirometer. First, critical swimming speed (Ucrit) (107 cm s-1) and minimum cost of transport (66 cm s-1) were measured. Sustained swimming trials at constant speeds were then performed based on a percentage of the group mean Ucrit (80, 85, 90, 95, 100 or 105%). Fish were forced to swim until they fatigued or until 72 h had passed. Surprisingly, most fish were able to sustain 80 and 85% Ucrit for 72 consecutive hours. However, at the highest speeds, fatigue was reached within the first 2 h. By categorizing fatigue times of individual fish into <2, 2-72 or >72 h, significant differences in relative swimming speeds were found that corresponded to 2.7, 2.5 and 2.2 body lengths s-1, respectively. These results document impressive sustained swimming capacities in farmed Atlantic salmon and add important temporal insights about ambient current limits with regards to fish welfare at exposed aquaculture sites.

In vivo and in vitro assessment of Atlantic salmon skin exposed to hydrogen peroxide

The salmon louse (Lepeophtheirus salmonis) is a significant problem in Atlantic salmon aquaculture. The industry is forced to use harsh antiparasitic treatments, including hydrogen peroxide (H2O2) baths, to treat the fish. We have utilized in vivo, semi in vivo, and in vitro methods to study the effects of exposures to H2O2. Assessment of external welfare indicators and plasma levels of cortisol, glucose, lactate, and ions did not reveal systemic impacts. Transcriptome analyses showed acute changes in the skin, with transient activation of several transcription factors known as generic stress markers of Atlantic salmon. Post-treatment (24 h), genes involved in the neutralization of free radicals were induced. Expression changes of regulators of cell cycle and cell differentiation were linked to microscopic observations in tissue sections and scale explants cultures. Histology showed adverse effects of H2O2 on skin morphology followed by compensatory recovery, which was not completed after 24 h. Decreased proliferation of cells was observed in keratocyte cultures. Exposure to H2O2, lowered pH (6.8), and elevated temperature (16 °C) markedly decreased the migration of keratocytes, which may indicate a reduced ability to repair skin and compound effects with H2O2. The study adds to the understanding of the adverse effects of hydrogen peroxide and promotes new models in Atlantic salmon skin research.

Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing

BackgroundSalmon Rickettsial Syndrome (SRS), caused by Piscirickettsia salmonis, is one of the primary causes of morbidity and mortality in Atlantic salmon aquaculture, particularly in Chile. Host resistance is a heritable trait, and functional genomic studies have highlighted genes and pathways important in the response of salmon to the bacteria. However, the functional mechanisms underpinning genetic resistance are not yet well understood. In the current study, a large population of salmon pre-smolts were challenged with P. salmonis, with mortality levels recorded and samples taken for genotyping. In parallel, head kidney and liver samples were taken from animals of the same population with high and low genomic breeding values for resistance, and used for RNA-Sequencing to compare their transcriptome profile both pre and post infection.ResultsA significant and moderate heritability (h2 = 0.43) was shown for the trait of binary survival. Genome-wide association analyses using 38 K imputed SNP genotypes across 2265 animals highlighted that resistance is a polygenic trait. Several thousand genes were identified as differentially expressed between controls and infected samples, and enriched pathways related to the host immune response were highlighted. In addition, several networks with significant correlation with SRS resistance breeding values were identified, suggesting their involvement in mediating genetic resistance. These included apoptosis, cytoskeletal organisation, and the inflammasome.ConclusionsWhile resistance to SRS is a polygenic trait, this study has highlighted several relevant networks and genes that are likely to play a role in mediating genetic resistance. These genes may be future targets for functional studies, including genome editing, to further elucidate their role underpinning genetic variation in host resistance.

Evolution of salmon lice in response to management strategies: a review

AbstractEctoparasitic salmon lice (Lepeophtheirus salmonis) present a major challenge to Atlantic salmon (Salmo salar) aquaculture. The demand for effective louse control has produced diverse management strategies. These strategies essentially impose novel selection pressures on parasite populations, driving the evolution of resistance. Here we assess the potential for salmon lice to adapt to current prevention and control methods. Lice have evolved resistance to at least four of five chemical therapeutants, and use of these chemicals has declined significantly in recent years. The industry has shifted to alternative non‐chemical approaches, yet lice may adapt to these as well. Early research suggests that phenotypic variation exists in the louse population upon which non‐chemical selection pressures could act and that this variation may have a genetic basis. From the existing evidence, as well as an examination of evolutionary processes in other relevant parasite and pest systems, we conclude that the evolution of non‐chemical resistance is an emergent concern that must be considered by the industry. We recommend areas for focused research to better assess this risk. It is also important to determine whether phenotypic shifts in response to non‐chemical selection may shift the ecological niche of the parasite, as this may have cascading effects on wild salmon populations. We also recommend further research to identify strategy combinations that have antagonistic selective effects that slow louse evolution and those with synergistic effects that should be avoided. Greater understanding of evolutionary processes can inform aquaculture policies that counteract the rise of resistant parasite populations.

Wild Atlantic salmon enter aquaculture sea‐cages: A case study

AbstractThere are more than 3,000 Atlantic salmon aquaculture sea‐cages distributed along the coastline of Norway. Many of these sea‐cages are located along the migration routes of wild Atlantic salmon (Salmo salar) postsmolts. This study documents for the first time that wild Atlantic salmon postsmolts can enter sea‐cages stocked with farmed Atlantic salmon. In addition, wild sea trout (Salmo trutta) and salmon/trout hybrid postsmolts were found inside the sea‐cages. The extent of such “bycatch” in commercial aquaculture is vital knowledge for the conservation of Atlantic salmon and sea trout. Further studies are encouraged in order to evaluate the extent of this possible ghost fishing phenomena.

Spatial response of hard- and mixed-bottom benthic epifauna to organic enrichment from salmon aquaculture in northern Norway

Norwegian Atlantic salmon aquaculture is continuing to expand in northern regions dominated by hard- and mixed-bottom substrates. Such habitats contain rich benthic epifaunal communities, including sponges and other sessile invertebrates susceptible to the impacts of particulate material released from finfish farms. Here, conventional soft-sediment sampling techniques are unable to discern the impacts of farm waste, and new monitoring methods and indicator taxa must be identified. This study improves understanding of the impacts of particulate waste released from salmon farms on the density and structure of benthic epifaunal communities on mixed- and hard-bottom substrates. The diversity, density, and composition of epifaunal communities and visually conspicuous benthic infauna were recorded in towed camera transects along the enrichment gradient (~50-800 m) of 3 salmon farms in northern Norway. Elevated fluxes of particulate material in the vicinity of all farms significantly affected epifaunal community composition, as did the coverage of some key substrate types. The defecated mounds of lugworms and the seastar Asterias rubens were notably more abundant near the farms where fluxes were elevated. The sponges Polymastia spp. and Phakellia spp. and the soft coral Duva florida showed significant declines in density with increasing sedimentation and were principal taxa in communities at natural sedimentation levels. Results identify taxa with both positive and negative spatial associations to particulate waste released from finfish farms and the potential for the development of an epifauna indicator-based index for monitoring the environmental impacts of aquaculture in hard- and mixed-bottom dominated substrates.

Dynamics of BK channel expression in gills during smoltification of Atlantic Salmon under farm conditions

Smoltification is a crucial step in the aquaculture of Atlantic salmon. Currently, the Na+/K+ ATPase (NKA) test is used to determine whether fish have adapted to seawater when moved from freshwater. The mortality rate of unadapted fish in Chile is ~10% after smoltification. During this period, BK channel expression decreases in gills after two weeks in saline water under laboratory conditions. However, these findings have not yet been tested on an industrial scale. We characterized the changes in mRNA levels of BK channels in gills from Salmo salar during smoltification using salmon farming protocols and compare these results against gill NKA activity and found a significant decrease in expression of BK channel transcripts during the smolt stage. We also characterized the dynamic of the BK channel expression (mRNA) versus NKA activity by using transcriptomic and RT-PCR analyses under an industrial setting. BK channels are involved in a variety of physiological processes, and our results indicate that BK potassium channel expression in gills could form the basis of a new complementary test to determine the level of smoltification more precisely.

Comparative Genomics Analysis of Vibrio anguillarum Isolated from Lumpfish (Cyclopterus lumpus) in Newfoundland Reveal Novel Chromosomal Organizations.

Vibrio anguillarum is a Gram-negative marine pathogen causative agent of vibriosis in a wide range of hosts, including invertebrates and teleosts. Lumpfish (Cyclopterus lumpus), a native fish of the North Atlantic Ocean, is utilized as cleaner fish to control sea lice (Lepeophtheirus salmonis) infestations in the Atlantic salmon (Salmo salar) aquaculture industry. V. anguillarum is one of the most frequent bacterial pathogens affecting lumpfish. Here, we described the phenotype and genomic characteristics of V. anguillarum strain J360 isolated from infected cultured lumpfish in Newfoundland, Canada. Koch’s postulates determined in naïve lumpfish showed lethal acute vibriosis in lumpfish. The V. anguillarum J360 genome was shown to be composed of two chromosomes and two plasmids with a total genome size of 4.56 Mb with 44.85% G + C content. Phylogenetic and comparative analyses showed that V. anguillarum J360 is closely related to V. anguillarum strain VIB43, isolated in Scotland, with a 99.8% genome identity. Differences in the genomic organization were identified and associated with insertion sequence elements (ISs). Additionally, V. anguillarum J360 does not possess a pJM1-like plasmid, typically present in virulent isolates from the Pacific Ocean, suggesting that acquisition of this extrachromosomal element and the virulence of V. anguillarum J360 or other Atlantic isolates could increase.

Screening of Fish Cell Lines for Piscine Orthoreovirus-1 (PRV-1) Amplification: Identification of the Non-Supportive PRV-1 Invitrome.

Piscine reovirus (PRV) is the causative agent of heart and skeletal muscle inflammation (HSMI), which is detrimental to Atlantic Salmon (AS) aquaculture, but so far has not been cultivatable, which impedes studying the disease and developing a vaccine. Homogenates of head kidney and red blood cells (RBC) from AS in which PRV-1 had been detected were applied to fish cell lines. The cell lines were from embryos, and from brain, blood, fin, gill, gonads, gut, heart, kidney, liver, skin, and spleen, and had the shapes of endothelial, epithelial, fibroblast, and macrophage cells. Most cell lines were derived from the Neopterygii subclass of fish, but one was from subclass Chondrostei. Cultures were examined by phase contrast microscopy for appearance, and by quantitative polymerase chain reaction (qPCR) for PRV-1 RNA amplification and for the capacity to transfer any changes to new cultures. No changes in appearance and Ct values were observed consistently or transferable to new cultures. Therefore, 31 cell lines examined were unable to support PRV-1 amplification and are described as belonging to the non-supportive PRV-1 invitrome. However, these investigations and cell lines can contribute to understanding PRV-1 cellular and host tropism, and the interactions between virus-infected and bystander cells.

Fish welfare in offshore salmon aquaculture

AbstractTo accommodate further growth in the Atlantic salmon aquaculture industry, new production sites may well be established at more exposed locations along the coast or even offshore. Here, fish will encounter strong currents and powerful waves, which are avoided at traditional sheltered locations. Exposed locations offer several advantages and necessitate new technological advancements. However, the most crucial question is whether Atlantic salmon are able to thrive in these more extreme environments. In this review, we describe how strong water currents affect the physiology, behaviour and ultimately the welfare of the fish. If ambient current speeds exceed swimming capacities, fish become fatigued and get stuck on the cage wall leading to unacceptable welfare. The swimming capacity will depend on both the magnitude and duration of the current speeds encountered. Moreover, several environmental and biological factors modulate swimming capabilities, where temperature, body size and health status are particularly important to consider. A series of empirical studies are subsequently used to formulate welfare guidelines with regard to biological limits in exposed aquaculture. In addition, owing to the growing popularity of cleaner fish in salmon aquaculture, we also evaluate their usefulness at exposed sites. Overall, Atlantic salmon is a powerful sustained swimmer, and based on available site surveys of ocean currents, we conclude that the prospects for responsible farming at exposed sites looks promising. However, cleaner fish species such as lumpfish and ballan wrasse are poor swimmers and are therefore not recommended for deployment at exposed sites.

Evaluation of sodium percarbonate as a bath treatment for amoebic gill disease in Atlantic salmon

Amoebic gill disease (AGD), caused by Neoparamoeba perurans, is a major health challenge for Atlantic salmon aquaculture globally. While freshwater bathing for 2 hr is effective in reducing infection severity, there is need for more rapid and lower cost alternatives. To this end, a combination of sodium percarbonate (SPC) in freshwater was examined for its treatment efficacy. Initial in vitro studies showed a reduction in amoeba viability when exposed for 30 min to freshwater containing >500 mg/L SPC. Subsequently, AGD-affected salmon were bathed for 30 min in 16°C freshwater containing 100, 500 or 1,000 mg/L SPC, or for 2 hr in 16°C freshwater to mimic industry practice. Treatment at the highest SPC concentration caused extensive gill damage and substantial mortality. Neither occurred to a significant extent at lower SPC concentrations. Gill pathology of surviving fish 10 days post-treatment (dpt) was comparable to or more severe than pre-treatment, and significantly (p < .001) more severe than in 2 hr freshwater bathed fish. N. perurans DNA was confirmed by qPCR in all treatment groups at 10 dpt. The data indicate that a 30-min exposure to SPC in freshwater is not a suitable alternative to existing freshwater treatment of AGD.

The metabolic rate response to feed withdrawal in Atlantic salmon post-smolts

Feed withdrawal is a widespread practice in Atlantic salmon (Salmo salar) aquaculture to empty the gut prior to major farming operations, while certain pathogens and suboptimal environmental conditions in production cages are known to induce prolonged fasting. However, these fasting periods may be in conflict with ethical and legal obligations to farm animals. Presently, science-based recommendations on responsible fasting times that consider fish welfare are lacking. In this study, we measured the standard metabolic rate (SMR) and metabolic rate following acute handling and confinement stress in Atlantic salmon post smolts (~575 g, ~38 cm) following 1, 2, 3 and 4 weeks of feed withdrawal and 1 week of subsequent refeeding at 12 °C. The purpose was to identify when changes in metabolic mode occurred and assess whether the capacity to respond to stress eventually was compromised, since such observations could serve as potential welfare indicators. The SMR decreased significantly from 84.4 ± 4.7 mg O2 kg h−1 in control fish to 71.0 ± 1.8 mg O2 kg h−1 following 1 week of fasting. A further significant decrease to 65.0 ± 3.7 mg O2 kg h−1 was measured after 3 weeks, while refeeding returned SMR to control levels. The increase in MO2 following acute stress was unaffected for the first three weeks of fasting. However, the 4 week group showed a reduced peak response compared to the preceding weeks (278 ± 13 vs. 310 ± 7 mg O2 kg h−1). Weight, fork length and condition factor did not change significantly during the fasting period, and the fish immediately resumed eating upon refeeding. We conclude that up to 4 weeks of feed withdrawal had negligible effects on fish welfare. Moreover, an improved aerobic scope owing to a reduced SMR may be advantageous prior to certain farm operations.

Comparative transcriptome analysis of pilchard orthomyxovirus (POMV) and infectious salmon anaemia virus (ISAV)

The Tasmanian Atlantic salmon (Salmo salar) aquaculture industry had remained relatively free of major viral diseases until the recent emergence of pilchard orthomyxovirus (POMV). The virus originally isolated from wild pilchards in Southern Australia is of great concern to the industry as it can cause high mortality. Despite its classification in the Orthomyxoviridae family, POMV is genetically divergent from infectious salmon anaemia virus (ISAV) and potentially represents a new genus within the family. Previous research has produced a formal case definition for clinical POMV, but the molecular events that underpin viral infection have not been characterized. Here we have undertaken a comparative transcriptome analysis of the response of Atlantic salmon kidney cells (ASK) in vitro to both POMV and ISAV using RNA sequencing, by harvesting cells at 6 and 24 h post infection (hpi). Despite their genomic differences, both orthomyxoviruses induced significant, and in some cases similar, innate antiviral responses. Early up-regulation of pathogen recognition receptor genes, RIG-I and TLR3, was observed in response to both viruses and triggered downstream interferon (IFN) responses. Interferon transcripts (IFN-alpha1 and INF-alpha2) were only induced in POMV infected cells at 24 hpi, but IFN-alpha3 was up-regulated in all time points and with both viruses. In addition, a strong induction of antiviral response genes (Mx and ISG15) was observed during the early infection with both viruses. Analysis of transcription factor binding sites in the up-regulated gene sets indicated that the host response to both viruses was largely driven by interferon regulatory factors (IRF) 1 and 2. Only three genes (slc35f2, odf2, LOC106608698) were differentially expressed in opposite directions, up-regulated with POMV and strongly down-regulated with ISAV at 24 hpi. Differential expression of these transcripts is possibly a consequence of virus divergence, but could also be associated to higher viral loads observed in the infection with POMV. Results from this study improve our understanding of the innate immune responses and host-pathogen interactions between POMV and Atlantic salmon. Early host response genes could potentially be exploited as subclinical biomarkers specific to POMV, and improved the development of tools for disease surveillance.

Potential for offshore aquaculture development in North Korea: Focusing on Atlantic salmon farming

This study investigated the potential for Atlantic salmon farming in North Korea. Farmed Atlantic salmon (Salmo salar) are aquaculture products commonly consumed in East Asia, but they are not commercially produced in large quantities. One barrier to Atlantic salmon farming is that the marine environmental conditions (i.e., water temperatures) in much of East Asia are unsuitable. North Korea has recently initiated Atlantic salmon farming assuming it has appropriate locations for it. If North Korea indeed has suitable locations for successful Atlantic salmon aquaculture and the United Nations' sanctions were lifted, the country's Atlantic salmon farming project might have potential for successful inter-Korean economic collaborations. The current study analyzed North Korea's possible farming sites using remote sensing data, and it used those findings to evaluate the feasibility of inter-Korean Atlantic salmon fishery collaborations and to propose policy implications. Remote sensing information estimated sea surface temperatures and hydrodynamic modeling extended that to estimate the sea temperatures at various depths to precisely propose appropriate farming locations in North Korea. The results indicated that most of North Korea's sea surface temperatures were below 20 °C in January through June. However, the surface temperatures in July and August exceeded 20 °C, indicating unsuitability for Atlantic salmon farming during that period. The water temperatures at the 25-m depth were below 20 °C year round, and Atlantic salmon farming would be possible there using submersible farming technologies, such as plant-type offshore fish farming systems.

Quantitative trait loci and genes associated with salmonid alphavirus load in Atlantic salmon: implications for pancreas disease resistance and tolerance

Salmonid alphavirus infection results in pancreas disease causing severe economic losses for Atlantic salmon aquaculture. Knowledge about genes and pathways contributing to resistance is limited. A 54 K SNP panel was used to genotype 10 full-sibling families each consisting of ~ 110 offspring challenged with salmonid alphavirus subtype 3. Relative heart viral load was assessed at 4- and 10-weeks post-infection using quantitative PCR. A moderate genomic heritability of viral load at 4 weeks (0.15–0.21) and a high positive correlation with survival (0.91–0.98) were detected. Positions of QTL detected on chromosome 3 matched those for survival detected by other studies. The SNP of highest significance occurred in the 3′ untranslated region of gig1, a fish-specific antiviral effector. Locus B of immunoglobulin heavy chain mapped to an area containing multiple SNPs with genome-wide association. Heart mRNA-seq comparing parr from families with high- versus low-genomic breeding value, and matching sample genotypes for SNPs, identified two eQTL for salmonid alphavirus load. Immune genes associated with trans-eQTL were numerous and spread throughout the genome. QTL regions contained several genes with known or predicted immune functions, some differentially expressed. The putative functional genes and variants identified could help improve marker-based selection for pancreas disease resistance.

Cleaner fish growth, welfare and survival in Atlantic salmon sea cages during an autumn-winter production

Cleaner fish used as a biological control agent against salmon lice is rapidly increasing in Atlantic salmon aquaculture. However, concerns have been raised about the welfare and mortality of cleaner fish in salmon cage systems, which could in turn affect their performance in controlling salmon lice. In a 4-month autumn-winter study, we monitored growth, welfare, mortality and daytime depth distribution of the most commonly used cleaner fish, farmed ballan wrasse and lumpfish, in six salmon production sea cages where thermo- and haloclines were present. Ballan wrasse did not grow (SGR: small: −0.01% day−1, large: −0.06% day−1), while lumpfish significantly doubled in size (SGR: 0.87% day−1) during the study. High losses (registered mortality + unregistered loss) were observed in both species (57 and 27% of ballan wrasse and lumpfish, respectively). The welfare status of remaining individuals generally improved over the study period, regardless of species. Brief daytime camera observations at hides found ballan wrasse were typically deeper at warmer (median 12.4 °C) more saline (median 31.7 ppt) depths, where salmon were expected to reside during day periods, compared to lumpfish generally occupying colder (median 7.3 °C), brackish (median 18.9 ppt) water in surface layers. Considerable mortalities, minimal feeding (inferred from ceased growth) by ballan wrasse and a possible mismatch in lumpfish and salmon depths (inferred from limited daytime camera observations) suggest that cleaner fish may have low long-term effectiveness against salmon lice in stratified salmon sea cages over autumn-winter. Similar studies across seasons, locations and cage types (e.g. depth-based cage technologies) are vital to understand the extent of these issues in salmon aquaculture more broadly.

Prevention not cure: a review of methods to avoid sea lice infestations in salmon aquaculture

AbstractThe Atlantic salmon aquaculture industry still struggles with ectoparasitic sea lice despite decades of research and development invested into louse removal methods. In contrast, methods to prevent infestations before they occur have received relatively little research effort, yet may offer key benefits over treatment‐focused methods. Here, we summarise the range of potential and existing preventative methods, conduct a meta‐analysis of studies trialling the efficacy of existing preventative methods and discuss the rationale for a shift to the prevention‐focused louse management paradigm. Barrier technologies that minimise host–parasite encounter rates provide the greatest protection against lice, with a weighted median 76% reduction in infestation density in cages with plankton mesh ‘snorkels’ or ‘skirts’, and up to a 100% reduction for fully enclosed cages. Other methods such as geographic spatiotemporal management, manipulation of swimming depth, functional feeds, repellents and host cue masking can drive smaller reductions that may be additive when used in combination with barrier technologies. Finally, ongoing development of louse‐resistant salmon lineages may lead to long‐term improvements if genetic gain is maintained, while the development of an effective vaccine remains a key target. Preventative methods emphasise host resistance traits while simultaneously reducing host–parasite encounters. Effective implementation has the potential to dramatically reduce the need for delousing and thus improve fish welfare, productivity and sustainability in louse‐prone salmon farming regions.