Strains Of Salmon Research Articles

Temporal and spatial use of a freshwater lake by upstream and downstream migrating adult Atlantic salmon Salmo salar.

Atlantic salmon Salmo salar typically enter fresh water several months prior to spawning and just as pools can provide areas of refuge in river systems, lakes may also provide important refuge habitat during the spawning migration. Using acoustic telemetry we examined the spatial and temporal movements of wild and a ranched strain of Atlantic salmon in a freshwater lake where the main spawning areas were located upstream of the lake. Over the study period (2011-2014), returning adult wild salmon spent an average of 228 days in fresh water and 90% of that time in the lake. On entering the lake, most wild salmon moved quickly to the northern part of the lake, close to the main inflow, spending an average 76% of the time in this location. The average number of days wild fish were absent from the lake during the main spawning period varied between years, ranging from 10 to 26 days for females and 32 to 35 days for males. Seventy four per cent (17/23) of salmon spawners returned to the lake and two salmon subsequently died in the lake post-spawning. Atypically, two salmon were resident in the lake for the whole period in 2013/14. During the study, wild salmon were detected at depths within the top 5 m for 73% of the time. Median depths post-spawning were greater than in the pre-spawning period, when salmon were found to spend extensive periods at depths in excess of 10 m. In July 2013, when the lake was stratified, thermal regulation behaviour was observed in wild salmon, whereby salmon moved to cooler deeper water when water temperatures at 1 m exceeded 20°C. In contrast to wild salmon, the majority of ranch salmon returned to the traps downstream of the lake prior to the spawning period, which would be expected as they were released as smolts below the freshwater lake. Ranch fish spent an average 80% of the time in the vicinity of receivers in the south of the lake and an average 98% of the time within the top 5 m. However, two ranch females were resident in the lake until the following spring and one ranch female moved upstream into the river during the spawning period. Clearly, in this catchment the lake provides an important habitat for migrating adult salmon. In the context of climate change, where thermal and hydrological regimes in rivers are expected to change in response to changes in air temperature and precipitation patterns, the availability of deep lakes that stratify in the summer and cool water refuges in river systems is likely to play a key role in the sustenance and conservation of salmonid species. Information about the migration patterns of Atlantic salmon in undisturbed freshwater systems may also assist in resolving issues associated with fish passage in impacted rivers and inform management decisions.

Omega‐3 long‐chain polyunsaturated fatty acids in Atlantic salmon: Functions, requirements, sources, de novo biosynthesis and selective breeding strategies

AbstractThe aquaculture industry is a substantial user of wild‐sourced fish oil to supply omega‐3 (n‐3) long‐chain polyunsaturated fatty acids (LC‐PUFAs) in fish diets, which are required by many economically important farmed fish species, particularly Atlantic salmon (Salmo salar L.). Fish oil is commonly replaced with plant‐based oils as more environmentally and economically sustainable substitutes due to concerns regarding over‐fishing of wild stocks and increasing demand. One potential strategy to meet the physiological requirement for n‐3 LC‐PUFA is to improve n‐3 LC‐PUFA biosynthesis in salmon through selective breeding and strain enhancement. The objective of this review is to discuss strategies to supply sufficient levels of n‐3 LC‐PUFA to Atlantic salmon through the diet and de novo biosynthesis through selective breeding and salmon strain enhancement. This review provides an overview on the functions of n‐3 LC‐PUFA in Atlantic salmon, dietary requirements, source and supply of n‐3 LC‐PUFA in aquaculture feeds, and biosynthesis of n‐3 LC‐PUFA in fish. Several relevant studies have revealed the genetic influences on n‐3 LC‐PUFA biosynthesis and storage in Atlantic salmon. The results of the present review show that selective breeding of high n‐3 PUFA‐producing Atlantic salmon could be an effective strategy to improve the amount of EPA and DHA stored in tissues and reduce reliance on dietary sources of n‐3 LC‐PUFA such as fish oil.

Assessment of gill microbiome of two strains of Atlantic salmon reared in flowthrough and recirculation hatcheries and following seawater transfer

The gill mucosal microbiome of Atlantic salmon has a significant impact on mucosal health and physiology under homeostatic conditions, but the microbial community may itself be influenced by host genetics, the culture system and seawater transfer. In this study, the impact of two commercial strains of Atlantic salmon, reared in two parallel hatchery systems (flow-through -FT and recirculation -RAS) on the gill microbiome was investigated. Samples of gill mucosal microbiome, tank biofilm and water were collected from the fish cohorts at the hatcheries and following seawater transfer. Though the gill microbiome of fish from the two commercially equivalent FT and RAS hatcheries had similar beta and alpha diversity, the alpha diversity indicators of bacterial communities of gills significantly increased after seawater input. Ultimately, no effect of the genetic strain on the gill microbiome was detected. Our results showed that under commercially equivalent FT or RAS hatchery systems with a common water source, two strains of Atlantic salmon had comparable gill microbiomes.

Size-driven parr-smolt transformation in masu salmon (Oncorhynchus masou)

Anadromous salmonids exhibit partial migration, where some individuals within a population migrate down to the ocean through complex interactions between body size and photoperiod. This study aimed to integrate the ontogenetic and seasonal patterns of smoltification, a series of changes for future marine life, in a strain of masu salmon (Oncorhynchus masou). Spring smoltification, as evidenced by the activation of gill Na+,K+-ATPase (NKA), was induced during winter under an advanced photoperiod. In addition, juveniles showed an additional peak in gill NKA activity in August regardless of the photoperiod. When juvenile masu salmon were subjected to feeding manipulations during the first spring/summer, only fish exceeding a fork length of 12 cm exhibited an increased gill NKA activity. We tested whether size-driven smoltification required a long-day period by exposing juveniles to a constant short-day length (9-h light and 15-h dark) from January to November. Juveniles under short-day conditions exceeded 12 cm in June but showed no signs of smoltification. Thus, masu salmon undergo photoperiod-limited, size-driven smoltification during the first summer and size-limited, photoperiod-driven smoltification the following spring. The findings of the present study provide a framework for further elucidation of the physiological mechanisms underlying partial migration in salmonids.

Identification and Genomic Localization of Autosomal sdY Locus in a Population of Atlantic Salmon (Salmo salar).

The determination of sex in salmonid fishes is controlled by genetic mechanisms, with males being the heterogametic sex. The master sex-determining gene, the sexually dimorphic gene on the Y chromosome (sdY), is a conserved gene across various salmonid species. Nevertheless, variations in the genomic location of sdY have been observed both within and between species. Furthermore, different studies have reported discordances in the association between the sdY and the phenotypic gender. While some males seem to lack this locus, there have been reports of females carrying sdY. Although the exact reasons behind this discordance remain under investigation, some recent studies have proposed the existence of an autosomal, non-functional copy of sdY as a potential cause. In this study, we confirmed the presence of this autosomal sdY in the SalmoBreed strain of Atlantic salmon using a genotyping platform through a novel approach that allows for high-throughput screening of a large number of individuals. We further characterized the segregation profile of this locus across families and found the ratio of genetically assigned female-to-male progeny to be in accordance with the expected profile of a single autosomal sdY locus. Additionally, our mapping efforts localized this locus to chromosome 3 and suggested a putative copy on chromosome 6.

Transcriptomic response to ISAV infection in the gills, head kidney and spleen of resistant and susceptible Atlantic salmon

BackgroundInfectious Salmon Anaemia virus (ISAV) is an orthomyxovirus responsible for large losses in Atlantic salmon (Salmo salar) aquaculture. Current available treatments and vaccines are not fully effective, and therefore selective breeding to produce ISAV-resistant strains of Atlantic salmon is a high priority for the industry. Genomic selection and potentially genome editing can be applied to enhance the disease resistance of aquaculture stocks, and both approaches can benefit from increased knowledge on the genomic mechanisms of resistance to ISAV. To improve our understanding of the mechanisms underlying resistance to ISAV in Atlantic salmon we performed a transcriptomic study in ISAV-infected salmon with contrasting levels of resistance to this virus.ResultsThree different tissues (gills, head kidney and spleen) were collected on 12 resistant and 12 susceptible fish at three timepoints (pre-challenge, 7 and 14 days post challenge) and RNA sequenced. The transcriptomes of infected and non-infected fish and of resistant and susceptible fish were compared at each timepoint. The results show that the responses to ISAV are organ-specific; an important response to the infection was observed in the head kidney, with up-regulation of immune processes such as interferon and NLR pathways, while in gills and spleen the response was more moderate. In addition to immune related genes, our results suggest that other processes such as ubiquitination and ribosomal processing are important during early infection with ISAV. Moreover, the comparison between resistant and susceptible fish has also highlighted some interesting genes related to ubiquitination, intracellular transport and the inflammasome.ConclusionsAtlantic salmon infection by ISAV revealed an organ-specific response, implying differential function during the infection. An immune response was observed in the head kidney in these early timepoints, while gills and spleen showed modest responses in comparison. Comparison between resistance and susceptible samples have highlighted genes of interest for further studies, for instance those related to ubiquitination or the inflammasome.

Prevalence of epitheliocystis in freshwater Atlantic salmon reared in flow-through and recirculation aquaculture systems.

Epitheliocystis, an intracellular bacterial infection in the gills and skin epithelium, has been frequently reported in Atlantic salmon (Salmo salar) during freshwater production in a number of countries. This study describes the prevalence and intensity of a natural epitheliocystis infection present in the gills of two strains of Atlantic salmon reared in either a flow-through (FT) or a recirculation aquaculture system (RAS) in Ireland. Repeated sampling of gills prior to and throughout seawater transfer, histology and quantitative real-time PCR were used to determine infection prevalence and intensity. Despite no clinical gill disease, and minor histopathological changes, epitheliocystis lesions were identified in histology at all time points. Specific PCR confirmed the presence of Candidatus Clavichlamydia salmonicola in both strains and its number of copies was correlated with intensity of epitheliocystis lesions. A significant interaction between hatchery system and fish strain on the prevalence and intensity of gill epitheliocystis was found both using histological and molecular methods. Specifically, fish from FT had higher prevalence and intensity than RAS reared fish and within FT, the Irish cohort were more affected than Icelandic.

Variation in volatile organic compounds in Atlantic salmon mucus is associated with resistance to salmon lice infection

Salmon lice are ectoparasites that threaten wild and farmed salmonids. Artificial selection of salmon for resistance to the infectious copepodid lice stage currently relies on in vivo challenge trials on thousands of salmon a year. We challenged 5750 salmon with salmon lice (Lepeophtheirus salmonis) from two distinct farmed strains of salmon in two separate trials. We found that volatile organic compounds (VOC), 1-penten-3-ol, 1-octen-3-ol and 6-methyl-5-hepten-2-one in the mucus of the salmon host after salmon lice infection, were significantly associated with lice infection numbers across a range of water temperatures (5 °C, 10 °C, 17 °C). Some VOCs (benzene, 1-octen-3-ol and 3,5,5-trimethyl-2-hexene) were significantly different between lines divergently selected for salmon lice resistance. In a combined population assessment, selected VOCs varied between families in the range of 47- 59% indicating a genetic component and were positively correlated to the salmon hosts estimated breeding values 0.59–0.74. Mucosal VOC phenotypes could supplement current breeding practices and have the potential to be a more direct and ethical proxy for salmon lice resistance provided they can be measured prior to lice infestation.

The endangered freshwater pearl mussel Margaritifera margaritifera shows adaptation to a local salmonid host in Finland

Abstract The freshwater pearl mussel Margaritifera margaritifera (FPM) is an endangered unionid which has a glochidium larva that attaches to the gills of Atlantic salmon Salmo salar or brown trout S. trutta, although some FPM populations have been shown to exclusively attach to only one of these species. The origin of host fish populations may be crucial for conservation actions for this mussel species, but the relative suitability of local (sympatric) and non‐local (allopatric) salmonid populations as the hosts for FPM has been studied only rarely. We hypothesised that FPM glochidia would show adaptation to local salmonid strains and, therefore, that they would be more successful (abundant, larger) attached to sympatric than to allopatric fish. Here, we investigated the infection success (abundance and growth of encysted larvae in fish) of FPM in local versus non‐local fish by caging different strains of brown trout and Atlantic salmon in rivers where FPM populations are present. Higher abundances of glochidia in local fish were observed in three brown trout streams, and larger glochidia were found in sympatric hosts in one brown trout stream and in one salmon river. Furthermore, non‐local allopatric fish were not better hosts than local fish in any of the FPM populations tested, neither in brown trout or salmon rivers and neither in abundance nor size of larvae. Therefore, the results supported the hypothesis that glochidia show local adaptation by being more successful when attached to local fish strains. Thus, the local, sympatric fish strain should be preferred in FPM conservation programmes that involve captive breeding of juvenile mussels and introduction of host fish, but the regional assessment of local host dependency of FPM also would be important outside the current study area. The results also indicate the importance of restoration of original salmonid populations in FPM rivers to enable the natural, effective reproduction cycle of FPM in their original, sympatric hosts, and thus to promote the recovery of endangered FPM populations.

Comparison between genome sequences of Chilean Tenacibaculum dicentrarchi isolated from red conger eel (Genypterus chilensis) and Atlantic salmon (Salmo salar) focusing on bacterial virulence determinants.

Tenacibaculum dicentrarchi is an emerging pathogen for salmonid cultures and red conger eel (Genypterus chilensis) in Chile, causing high economic losses not only in Chile but also to the global salmon industry. Infected fish show severe gross skin lesions that are sometimes accompanied by bone exposure. Despite pathogenicity demonstrated by Koch's postulates, no knowledge is currently available regarding the virulence machinery of T.dicentrarchi strains. Comparisons between the genome sequences of the eight T.dicentrarchi strains obtained from G.chilensis and Atlantic salmon (Salmo salar) provide insights on the existence of genomic diversity within this bacterium. The T.dicentrarchi type strain 3509T was used as a reference genome. Depending on the T.dicentrarchi strain, the discovered diversity included genes associated with iron acquisition mechanisms, copper homeostasis encoding, resistance to tetracycline and fluoroquinolones, pathogenic genomic islands and phages. Interestingly, genes encoding the T9SS membrane protein PorP/SprF were retrieved in all of the analysed T.dicentrarchi strains, regardless of the host fish (i.e. red conger eel or Atlantic salmon). However, the T6SS core component protein VgrG was identified in only one Atlantic salmon strain. Three types of peptidase genes and proteins associated with quorum sensing were detected in all of the T.dicentrarchi strains. In turn, all eight strains presented a total of 17 proteins associated with biofilm formation, which was previously confirmed through physiological studies. This comparative analysis will help elucidate and describe the genes and pathways that are likely involved in the virulence process of T.dicentrarchi. All or part of these predicted genes could aid the pathogen during the infective process in fish, making further physiological research necessary for clarification.

Freshwater, Landlocked Grand Lake Strain of Atlantic Salmon (Salmo salar L.) as a Potential Genetic Source of Long Chain Polyunsaturated Fatty Acids Synthesis

Selection efforts focused on adaptation to plant-based diets, particularly the ability to synthesize polyunsaturated fatty acids (PUFA), are now emerging in aquaculture. Landlocked salmon (Grand Lake population; GL) may differ from the commercial Saint John River (SJR) strain in terms of PUFA metabolism. The objective of this study was to determine if GL salmon can contribute toward broodstock selection for enhanced PUFA synthesis. Two diets containing either fish oil (FO) or plant-based oil (FO-free) were fed to the SJR and GL strains (∼58 g/fish) for 16 weeks. Growth, liver, and muscle fatty acid (FA) content, and transcript expression of lipid metabolism and inflammation-related genes were evaluated. GL salmon fed the FO diet showed reduced growth compared to SJR salmon (fed either diet); however, GL salmon fed the FO-free diet, growth was not significantly different compared to any group. In liver, SJR salmon fed the FO-free diet had higher levels of n-6 PUFAs (21.9%) compared to GL fed the same diet (15.9%); while GL salmon fed the FO-free diet had higher levels of monounsaturated FAs (48.9%) compared with SJR salmon fed the same diet (35.7%). 20:5n-3 and 22:6n-3 were the same in GL and SJR salmon liver and muscle, respectively, fed the FO-free diet. In liver, GL salmon fed the FO-free diet had higher acac and acly compared to all treatments and had higher fasb compared to both strains fed the FO-diet. GL salmon fed the FO-free diet had higher cd36c and fabp3b in liver compared to GL salmon fed the FO diet and SJR salmon fed either diet. GL salmon fed the FO-free diet had higher lect2a and pgds in liver compared to SJR salmon fed the FO-free diet. In muscle, GL salmon fed the FO-free diet had higher fadsd5 and fadsd6b compared with both strains fed the FO diet. These results suggest there is a genetic basis behind the potential for GL salmon to utilize FO-free diets more efficiently than SJR salmon, with regards to FA metabolism.

Summer Is Coming! Tackling Ocean Warming in Atlantic Salmon Cage Farming.

Simple SummaryAtlantic salmon (Salmo salar) has become a commodity worldwide. The culture of Atlantic salmon is by far the most well-developed branch of marine finfish aquaculture, with this species ranking among the top ten most highly produced in global aquaculture. While Atlantic salmon has been commonly farmed in sea cages located in colder waters (e.g., in Norway, Chile and Tasmania), these regions can experience the negative impacts of heat waves that push seawater temperature above values tolerated by this species. These climate-change-driven shifts in water temperature can be associated with mass mortality events and urgent actions are needed to cope with a changing ocean. This paper reviews the thermal limits of adult Atlantic salmon and lists the negative effects driven by heat stress. We highlight how biotechnology and the genetic diversity of wild populations may help producers to tackle this challenge. Selective breeding programs and other more advanced biotechnological solutions (e.g., gene editing) may play a key role in this quest to produce new strains of Atlantic salmon that more readily tolerate higher water temperatures, without compromising productivity and profitability.Atlantic salmon (Salmo salar) cage farming has traditionally been located at higher latitudes where cold seawater temperatures favor this practice. However, these regions can be impacted by ocean warming and heat waves that push seawater temperature beyond the thermo-tolerance limits of this species. As more mass mortality events are reported every year due to abnormal sea temperatures, the Atlantic salmon cage aquaculture industry acknowledges the need to adapt to a changing ocean. This paper reviews adult Atlantic salmon thermal tolerance limits, as well as the deleterious eco-physiological consequences of heat stress, with emphasis on how it negatively affects sea cage aquaculture production cycles. Biotechnological solutions targeting the phenotypic plasticity of Atlantic salmon and its genetic diversity, particularly that of its southernmost populations at the limit of its natural zoogeographic distribution, are discussed. Some of these solutions include selective breeding programs, which may play a key role in this quest for a more thermo-tolerant strain of Atlantic salmon that may help the cage aquaculture industry to adapt to climate uncertainties more rapidly, without compromising profitability. Omics technologies and precision breeding, along with cryopreservation breakthroughs, are also part of the available toolbox that includes other solutions that can allow cage farmers to continue to produce Atlantic salmon in the warmer waters of the oceans of tomorrow.

Sexually Dimorphic Growth Stimulation in a Strain of Growth Hormone Transgenic Coho Salmon (Oncorhynchus kisutch)

Growth hormone (GH) transgenic fish often exhibit remarkable transformations in growth rate and other phenotypes relative to wild-type. The 5750A transgenic coho salmon strain exhibits strong sexually dimorphic growth, with females possessing growth stimulation at a level typical of that seen for both sexes in other strains harbouring the same gene construct (e.g. M77), while males display a modest level of growth stimulation. GH mRNA levels were significantly higher in females than in males of the 5750A strain but equivalent in the M77 strain, indicating sex and transgene insertion locus altered transgene expression. We found that acute estradiol treatments did not influence GH expression in either strain (5750A and M77) or the transgene promoter (metallothionein-B), suggesting that estradiol level was not a significant factor influencing transgene activity. The feminization of XX and XY fish of the 5750A and M77 strains generated all-female groups and resulted in equalized growth of the two genetic sexes, suggesting that the presence of the Y chromosome was not directly capable of influencing the GH transgene–mediated growth in a physiological female conditions. These data suggest that the difference in growth rate seen between the sexes in the 5750A strain arises from non-estradiol-mediated sex influences on gene regulation at the transgene locus. This study shows how genetic factors and transgene insertion sites can influence transgene expression with significant consequent effects on phenotype.

Targeted mutagenesis of \u22065 and \u22066 fatty acyl desaturases induce dysregulation of lipid metabolism in Atlantic salmon (Salmo salar)

BackgroundWith declining wild fish populations, farmed salmon has gained popularity as a source for healthy long-chain highly unsaturated fatty acids (LC-HUFA). However, the introduction of plant oil in farmed salmon feeds has reduced the content of these beneficial LC-HUFA. The synthetic capability for LC-HUFAs depends upon the dietary precursor fatty acids and the genetic potential, thus there is a need for in-depth understanding of LC-HUFA synthetic genes and their interactions with other genes involved in lipid metabolism. Several key genes of LC-HUFA synthesis in salmon belong to the fatty acid desaturases 2 (fads2) family. The present study applied whole transcriptome analysis on two CRISPR-mutated salmon strains (crispants), 1) Δ6abc/5Mt with mutations in Δ5fads2, Δ6fads2-a, Δ6fads2-b and Δ6fads2-c genes, and 2) Δ6bcMt with mutations in Δ6fads2-b and Δ6fads2-c genes. Our purpose is to evaluate the genetic effect fads2 mutations have on other lipid metabolism pathways in fish, as well as to investigate mosaicism in a commercial species with a very long embryonal period.ResultsBoth Δ6abc/5Mt and Δ6bcMt crispants demonstrated high percentage of indels within all intended target genes, though different indel types and percentage were observed between individuals. The Δ6abc/5Mt fish displayed several disruptive indels which resulted in over 100 differentially expressed genes (DEGs) enriched in lipid metabolism pathways in liver. This includes up-regulation of srebp1 genes which are known key transcription regulators of lipid metabolism as well as a number of down-stream genes involved in fatty acid de-novo synthesis, fatty acid β-oxidation and lipogenesis. Both elovl5 and elovl2 genes were not changed, suggesting that the genes were not targeted by Srebp1. The mutation of Δ6bcMt surprisingly resulted in over 3000 DEGs which were enriched in factors encoding genes involved in mRNA regulation and stability.ConclusionsCRISPR-Cas9 can efficiently mutate multiple fads2 genes simultaneously in salmon. The results of the present study have provided new information on the transcriptional regulations of lipid metabolism genes after reduction of LC-HUFA synthesis pathways in salmon.

Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere.

Most Atlantic salmon (Salmo salar L.) populations follow an anadromous life cycle, spending early life in freshwater, migrating to the sea for feeding, and returning to rivers to spawn. At the end of the last ice age ~10,000 years ago, several populations of Atlantic salmon became landlocked. Comparing their genomes to their anadromous counterparts can help identify genetic variation related to either freshwater residency or anadromy. The objective of this study was to identify consistently divergent loci between anadromous and landlocked Atlantic salmon strains throughout their geographical distribution, with the long‐term aim of identifying traits relevant for salmon aquaculture, including fresh and seawater growth, omega‐3 metabolism, smoltification, and disease resistance. We used a Pool‐seq approach (n = 10–40 individuals per population) to sequence the genomes of twelve anadromous and six landlocked Atlantic salmon populations covering a large part of the Northern Hemisphere and conducted a genomewide association study to identify genomic regions having been under different selection pressure in landlocked and anadromous strains. A total of 28 genomic regions were identified and included cadm1 on Chr 13 and ppargc1a on Chr 18. Seven of the regions additionally displayed consistently reduced heterozygosity in fish obtained from landlocked populations, including the genes gpr132, cdca4, and sertad2 on Chr 15. We also found 16 regions, including igf1 on Chr 17, which consistently display reduced heterozygosity in the anadromous populations compared to the freshwater populations, indicating relaxed selection on traits associated with anadromy in landlocked salmon. In conclusion, we have identified 37 regions which may harbor genetic variation relevant for improving fish welfare and quality in the salmon farming industry and for understanding life‐history traits in fish.

Transcriptomic comparison of communally reared wild, domesticated and hybrid Atlantic salmon fry under stress and control conditions

BackgroundDomestication is the process by which organisms become adapted to the human-controlled environment. Since the selection pressures that act upon cultured and natural populations differ, adaptations that favour life in the domesticated environment are unlikely to be advantageous in the wild. Elucidation of the differences between wild and domesticated Atlantic salmon may provide insights into some of the genomic changes occurring during domestication, and, help to predict the evolutionary consequences of farmed salmon escapees interbreeding with wild conspecifics. In this study the transcriptome of the offspring of wild and domesticated Atlantic salmon were compared using a common-garden experiment under standard hatchery conditions and in response to an applied crowding stressor.ResultsTranscriptomic differences between wild and domesticated crosses were largely consistent between the control and stress conditions, and included down-regulation of environmental information processing, immune and nervous system pathways and up-regulation of genetic information processing, carbohydrate metabolism, lipid metabolism and digestive and endocrine system pathways in the domesticated fish relative to their wild counterparts, likely reflective of different selection pressures acting in wild and cultured populations. Many stress responsive functions were also shared between crosses and included down-regulation of cellular processes and genetic information processing and up-regulation of some metabolic pathways, lipid and energy in particular. The latter may be indicative of mobilization and reallocation of energy resources in response to stress. However, functional analysis indicated that a number of pathways behave differently between domesticated and wild salmon in response to stress. Reciprocal F1 hybrids permitted investigation of inheritance patterns that govern transcriptomic differences between these genetically divergent crosses. Additivity and maternal dominance accounted for approximately 42 and 25% of all differences under control conditions for both hybrids respectively. However, the inheritance of genes differentially expressed between crosses under stress was less consistent between reciprocal hybrids, potentially reflecting maternal environmental effects.ConclusionWe conclude that there are transcriptomic differences between the domesticated and wild salmon strains studied here, reflecting the different selection pressures operating on them. Our results indicate that stress may affect certain biological functions differently in wild, domesticated and hybrid crosses and these should be further investigated.

Comparison of growth rates between growth hormone transgenic and selectively-bred domesticated strains of coho salmon (Oncorhynchus kisutch) assessed under different culture conditions

Aquaculture continues to be the fastest-growing animal food sector and accounts for over 50% of the world's fish consumption. This trend is projected to continue, highlighting the role that the aquaculture industry will play in ensuring future global food security. Enhancement of growth rates of fish can optimize aquaculture production and has been achieved through selective breeding programs producing fast-growing domesticated strains, or the development of growth hormone (GH) transgenic strains. Although the ability of selectively-bred domesticated and GH transgenic salmon to outgrow wild-type salmon is well documented, very little research has been reported that directly compares the growth rates of domesticated and GH transgenic strains. The aim of the present study was to compare the growth and survival of selectively-bred domesticated and GH transgenic coho salmon across a range of experimental conditions. We performed four experiments investigating the growth rates of domesticated and GH transgenic salmon by comparing these strains at different developmental stages and under different experimental rearing conditions, as well as under conditions when strains were competing and when they were reared separately. Results from all experiments showed that GH transgenic coho salmon grew faster and to a larger size than the selectively-bred domesticated coho salmon. This was true whether fish groups were reared post-smolt in freshwater or seawater, whether reared together or separately, and whether manipulated to be size-matched at early stages. Thus, GH transgenesis could become a viable complement to selective breeding to produce fast-growing salmon for aquaculture systems. While further research can continue to optimize the development and use of transgenic strains, the data presented here also are important for environmental risk assessments by providing data on the relative fitness and ecological consequences of selectively-bred domesticated and GH transgenic fish should they enter nature.

Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires.

In teleost fish as in mammals, humoral adaptive immunity is based on B lymphocytes expressing highly diverse immunoglobulins (IG). During B cell differentiation, IG loci are subjected to genomic rearrangements of V, D, and J genes, producing a unique antigen receptor expressed on the surface of each lymphocyte. During the course of an immune response to infections or immunizations, B cell clones specific of epitopes from the immunogen are expanded and activated, leading to production of specific antibodies. Among teleost fish, salmonids comprise key species for aquaculture. Rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) are especially important from a commercial point of view and have emerged as critical models for fish immunology. The growing interest to capture accurate and comprehensive antibody responses against common pathogens and vaccines has resulted in recent efforts to sequence the IG repertoire in these species. In this context, a unified and standardized nomenclature of salmonid IG heavy chain (IGH) genes is urgently required, to improve accuracy of annotation of adaptive immune receptor repertoire dataset generated by high-throughput sequencing (AIRRseq) and facilitate comparisons between studies and species. Interestingly, the assembly of salmonids IGH genomic sequences is challenging due to the presence of two large size duplicated IGH loci and high numbers of IG genes and pseudogenes. We used data available for Atlantic salmon to establish an IMGT standardized nomenclature of IGH genes in this species and then applied the IMGT rules to the rainbow trout IGH loci to set up a nomenclature, which takes into account the specificities of Salmonid loci. This unique, consistent nomenclature for Salmonid IGH genes was then used to construct IMGT sequence reference directories allowing accurate annotation of AIRRseq data. The complex issues raised by the genetic diversity of salmon and trout strains are discussed in the context of IG repertoire annotation.

Growth hormone regulates opsin expression in the retina of a salmonid fish.

Colour vision relies on retinal photoreceptors that express a different predominant visual pigment protein (opsin). In several vertebrates, the primary opsin expressed by a photoreceptor can change throughout ontogeny, although the molecular factors that influence such regulation are poorly understood. One of these factors is thyroid hormone which, together with its receptors, modulates opsin expression in the retinas of multiple vertebrates including rodents and salmonid fishes. In the latter, thyroid hormone induces a switch in opsin expression from SWS1 (ultraviolet light sensitive) to SWS2 (short wavelength or blue light sensitive) in the single cone photoreceptors of the retina. The actions of other hormones on opsin expression have not been investigated. In the present study, we used a transgenic strain of coho salmon (Oncorhynchus kitsutch) with enhanced levels of circulating growth hormone compared to that of wild siblings to assess the effects of this hormone on the SWS1 to SWS2 opsin switch. Transgenic fish showed a developmentally accelerated opsin switch compared to size-matched controls as assessed by immunohistological and in situ hybridisation labelling of photoreceptors and by quantification of transcripts using quantitative polymerase chain reaction. This accelerated switch led to a different spectral sensitivity maximum, under a middle to long wavelength adapting background, from ultraviolet (λmax ~380nm) in controls to short wavelengths (λmax ~430nm) in transgenics, demonstrating altered colour vision. The effects of growth hormone over-expression were independent of circulating levels of thyroid hormone (triiodothyronine), the hormone typically associated with opsin switches in vertebrates.

Characterization of smoltification in the Tasmanian strain of Atlantic salmon (Salmo salar) in recirculation and flow-through systems

This study examined morphological, physiological and molecular indicators of smoltification in Atlantic salmon (Salmo salar) juveniles in a flow-through (FT) and recirculating aquaculture system (RAS). Fish were exposed to 24-h light to initiate smoltification, for 5 (FT) and 7 (RAS) weeks prior to transfer from freshwater (FW) to seawater (SW) and were sampled weekly preceding and following SW transfer. Mass, length, condition factor, plasma chloride, gill Na+/K+-ATPase (NKA) activity and expression of salinity-specific isoforms of NKA mRNA transcripts were monitored. Fish raised in FT had significantly lower specific growth rate (SGR) in FW than in SW and showed a significant 5-6-fold increase in gill NKA activity, and high plasma chloride levels after transfer to SW. These fish also exhibited no significant reduction in relative mRNA expression of NKAα1a in FW but a sharp significant downregulation post-SW transfer. No significant increase in NKAα1b was seen until week 8 (3 weeks post-SW transfer). The log2 ratio of NKAα1b to NKAα1a showed a significant 8-fold increase throughout the study. Fish raised in the RAS had significantly higher SGR in FW than SW, and showed significantly higher plasma chloride in saltwater challenged fish compared to the freshwater control at all weeks during the FW phase. Fish had a 50% higher initial NKA activity than in FT, increasing significantly 2-3-fold and showed an immediate down-regulation of NKAα1a after exposure to 24-hr light in FW, and a further reduction after SW-transfer. There was no significant increase in NKAα1b in the RAS-raised fish for the duration of the study, and there was a significant 8-fold increase in log2 ratio of NKAα1b to NKAα1a. Whilst there were too many varying factors to statistically compare hatchery type in this study, it's evident that there are potentially system-related effects worthy of future investigation.