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We present the draft genome sequences of six Flavobacterium psychrophilum isolates recovered from diseased coho salmon ( Oncorhynchus kisutch ) cultured by two farms in Chile. This study provides the first detailed insights into the genomic characteristics of this fish pathogen recovered from a host with limited information and cultured in Chile., Competing Interests: The authors declare no conflict of interest.

The environmental impact of oil spills is a critical concern, particularly pertaining to low sulfur marine diesel (LSMD) and high sulfur fuel oil (HSFO) that are commonly involved in coastal spills. Although transcriptomic biomonitoring of sentinel animals can be a powerful tool for assessing biological effects, conventional methods utilize lethal sampling to examine the liver. As a non-lethal alternative, we have previously shown salmonid caudal fin cyp1a1 is significantly responsive to LSMD-derived toxicants. The present study further investigated the transcriptomic biomonitoring potential of coho salmon smolt caudal fin in comparison to liver tissue in the context of LSMD and HSFO seawater accommodated fraction (seaWAF) exposure in cold-water marine environments. Assessing the toxicity of these seaWAFs involved quantifying polycyclic aromatic hydrocarbon (tPAH50) concentrations and generating gene expression profiles. Initial qPCR analyses revealed significant cyp1a1 response in both liver and caudal fin tissues of both genetic sexes to all seaWAF exposures. RNA-Seq analysis, focusing on the highest LSMD and HSFO seaWAF concentrations (28.4±1.8 and 645.08±146.3 µg/L tPAH50, respectively), revealed distinct tissue-specific and genetic sex-independent transcriptomic responses with an overall enrichment of oxidative stress, cell adhesion, and morphogenesis-related pathways. Remarkably, the caudal fin tissue exhibited transcriptomic response patterns comparable to liver tissue, particularly consistent differential expression of 33 gene transcripts in the liver (independent of sex and oil type) and 44 in the caudal fin. The present work underscores the viability of using the caudal fin as a non-lethal alternative to liver sampling for assessing and tracking oil spill exposure in marine environments., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Female Pacific salmon often experience higher mortality than males during their once-in-a-lifetime up-river spawning migration, particularly when exposed to secondary stressors (e.g. high temperatures). However, the underlying mechanisms remain unknown. One hypothesis is that female Pacific salmon hearts are more oxygen-limited than those of males and are less able to supply oxygen to the body's tissues during this demanding migration. Notably, female hearts have higher coronary blood flow, which could indicate a greater reliance on this oxygen source. Oxygen limitations can develop from naturally occurring coronary blockages (i.e. coronary arteriosclerosis) found in mature salmon hearts. If female hearts rely more heavily on coronary blood flow but experience similar arteriosclerosis levels as males, they will have disproportionately impaired aerobic performance. To test this hypothesis, we measured resting (RMR) and maximum metabolic rate (MMR), aerobic scope (AS) and acute upper thermal tolerance in coho salmon (Oncorhynchus kisutch) with an intact or artificially blocked coronary oxygen supply. We also assessed venous blood oxygen and chemistry (cortisol, ions and metabolite concentrations) at different time intervals during recovery from exhaustive exercise. We found that coronary blockage impaired MMR, AS and the partial pressure of oxygen in venous blood (PvO2) during exercise recovery but did not differ between sexes. Coronary ligation lowered acute upper thermal tolerance by 1.1°C. Although we did not find evidence of enhanced female reliance on coronary supply, our findings highlight the importance of coronary blood supply for mature wild salmon, where migration success may be linked to cardiac performance, particularly during warm water conditions., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2024. Published by The Company of Biologists Ltd.)

The relationship of histopathological changes and the infection of Piscine orthoreovirus 2 (PRV-2) was investigated in coho salmon that were suffering from the erythrocytic inclusion body syndrome (EIBS). Immunohistochemical observations revealed abundant σ1 protein of PRV-2 in the spongy layer of the ventricle of the heart, where severe myocarditis was observed. In the spleen, the virus protein was detected in many erythrocytes, some of which were spherical-shaped and apparently dead. The number of erythrocytes was decreased in the spleen compared to the apparently healthy fish. The virus protein was also detected in some erythrocytes in blood vessels. The viral protein was often detected in many macrophages ingesting erythrocytes or dead cell debris in the spleen or in the kidney sinusoids. Large amounts of the viral genomic segment L2 were also detected in these organs by RT-qPCR. Many necrotic foci were found in the liver, although the virus protein was not detected in the hepatocytes. These results suggest that the primary targets of PRV-2 are myocardial cells and erythrocytes and that clinical symptoms such as anaemia or jaundice and histopathological changes such as myocarditis in EIBS-affected coho salmon are caused by PRV-2 infection., (© 2024 John Wiley & Sons Ltd.)

By the 1980s, after decades of declining numbers in the mid-1900s, Coho salmon ( Oncorhynchus kisutch ) were considered extirpated from the interior Columbia River. In the mid-1990s, the Confederated Tribes of the Umatilla Indian Reservation, the Confederated Tribes and Bands of the Yakama Nation, and the Nez Perce Tribe began successful reintroduction programs of Coho salmon upstream of Bonneville Dam, but which were initially sourced from lower Columbia River hatcheries. Here we present the first Coho salmon parentage-based tagging (PBT) baseline from seven hatchery programs located in the interior Columbia River basin, and two sites at or downstream of Bonneville Dam, composed of over 32,000 broodstock samples. Analyses of baseline collections revealed that genetic structure followed a temporal pattern based on 3-year broodlines rather than geographic location or stocking history. Across hatchery programs, similar levels of genetic diversity was present. The PBT baseline provided multiple direct applications such as identification of origin for Coho salmon collected in a mixed stock at Priest Rapids Dam and the detection of the proportion and distribution of hatchery-origin fish on the spawning grounds in the Methow River basin. The PBT baseline for Coho salmon is freely available for use and can be downloaded from FishGen.net., Competing Interests: The authors have no conflicts of interest to declare., (© 2023 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

The breakdown product of the rubber tire antioxidant N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD)-6-PPD-quinone has been strongly implicated in toxic injury and death in coho salmon (Oncorhynchus kisutch) in urban waterways. Whereas recent studies have reported a wide range of sensitivity to 6PPD-quinone in several fish species, little is known about the risks to Chinook salmon (Oncorhynchus tshawytscha), the primary prey of endangered Southern Resident killer whales (Orcinus orca) and the subject of much concern. Chinook face numerous conservation threats in Canada and the United States, with many populations assessed as either endangered or threatened. We evaluated the acute toxicity of 6PPD-quinone to newly feeding (~3 weeks post swim-up) juvenile Chinook and coho. Juvenile Chinook and coho were exposed for 24 h under static conditions to five concentrations of 6PPD-quinone. Juvenile coho were 3 orders of magnitude more sensitive to 6PPD-quinone compared with juvenile Chinook, with 24-h median lethal concentration (LC50) estimates of 41.0 and more than 67 307 ng/L, respectively. The coho LC50 was 2.3-fold lower than what was previously reported for 1+-year-old coho (95 ng/L), highlighting the value of evaluating age-related differences in sensitivity to this toxic tire-related chemical. Both fish species exhibited typical 6PPD-quinone symptomology (gasping, increased ventilation, loss of equilibrium, erratic swimming), with fish that were symptomatic generally exhibiting mortality. The LC50 values derived from our study for coho are below concentrations that have been measured in salmon-bearing waterways, suggesting the potential for population-level consequences in urban waters. The higher relative LC50 values for Chinook compared with coho merits further investigation, including for the potential for population-relevant sublethal effects. Environ Toxicol Chem 2023;42:815-822. © 2023 His Majesty the King in Right of Canada and The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. Reproduced with the permission of the Minister of Fisheries and Oceans Canada., (© 2023 His Majesty the King in Right of Canada and The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. Reproduced with the permission of the Minister of Fisheries and Oceans Canada.)

This study aims to investigate the effects of partial dietary replacement of fish meal with unfermented and/or fermented soybean meal (fermented by Bacillus cereus ) supplemented on the growth performance, whole-body composition, antioxidant and immunity capacity, and their related gene expression of juvenile coho salmon ( Oncorhynchus kisutch ). Four groups of juveniles (initial weight 159.63 ± 9.54 g) at 6 months of age in triplicate were fed for 12 weeks on four different iso-nitrogen (about 41% dietary protein) and iso-lipid (about 15% dietary lipid) experimental diets. The main results were: Compared with the control diet, the diet with replaced 10% fish meal protein with fermented soybean meal protein supplementation can significantly ( p < 0.05) influence the expression of superoxide dismutase, catalase, glutathione peroxidase, glutathione S-transferase, nuclear factor erythroid 2-related factor 2, tumor necrosis factor α and interleukin-6 genes, the growth performance, the serum biochemical indices, and the activity of antioxidant and immunity enzymes. However, there was no significant effect ( p > 0.05) on the survival rate (SR) and whole-body composition in the juveniles among the experimental groups. In conclusion, the diet with replaced 10% fish meal protein with fermented soybean meal protein supplementation could significantly increase the growth performance, antioxidant and immunity capacity, and their related gene expression of juveniles.

Tenacibaculum piscium, a gram-negative bacterium isolated from the skin ulcers of sea-farmed fish, has only been described in Norway. In the present study, we examined 16 Chilean Tenacibaculum isolates recovered from different organs in moribund and dead Atlantic salmon (Salmo salar), Rainbow trout (Oncorhynchus mykiss) and Coho salmon (Oncorhynchus kisutch) cultured at different fish farms between 2014 and 2018. The present study applied biochemical, phenotypic, fatty acid and whole-genome sequence-based analyses to confirm the taxonomic status of the Chilean isolates. The obtained results are the first to confirm the presence of T. piscium in Chile and in Coho salmon, thus extending the recognized geographical and species distribution of this bacterium. Subsequent bath-challenge assays in Atlantic salmon utilizing three T. piscium isolates obtained from different hosts resulted in low cumulative mortality (i.e. 0-35%), even after exposure to an unnaturally high concentration of bacterial cells (i.e. > 10 7 cells/ml). However, scale loss and frayed fins were observed in dead fish. In silico whole-genome analysis detected various genes associated with iron acquisition, encoding of the type IX secretion system and cargo proteins, resistance to tetracycline and fluoroquinolones and stress responses. These data represent an important milestone towards a better understanding on the genomic repertoire of T. piscium., (© 2022 Wiley-VCH GmbH.)

We investigated effect of dietary iron (Fe) on the lipid deposition, nutritional element, and muscle quality in coho salmon. Four level Fe diets at 23.7, 46.4, 77.3, and 127.7 mg/kg were fed to the post-larval coho salmon for 12 weeks. Our results showed that dietary Fe decreased the content of triglyceride and the activity of fatty acid synthetase, ATP-citrate lyase, and acetyl-CoA carboxylase. The content of Fe in muscle was increased with increasing dietary Fe levels, and dietary Fe affected the content of nutritional elements. In addition, dietary Fe levels affected the composition of fatty acids and the content of free amino acids, and increased muscle fiber size. The lower dietary Fe levels also affected the hardness, chewiness, resilience, springiness, cohesiveness, and gumminess of salmon muscle. In all, dietary Fe inhibited the lipid deposition and affected the content of nutritional element and muscle quality in coho salmon., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s).)

The mission of veterinary clinical pathology is to support the diagnostic process by using tests to measure different blood biomarkers to support decision making about farmed fish health and welfare. The objective of this study is to provide reference intervals (RIs) for 44 key hematological, blood biochemistry, blood gasometry and hormones biomarkers for the three most economically important farmed salmonid species in Chile (Atlantic salmon, coho salmon and rainbow trout) during the freshwater (presmolt and smolt age range) and seawater stages (post-smolt and adult age range). Our results confirmed that the concentration or activity of most blood biomarkers depend on the salmonid species, age range and/or the interaction between them, and they are often biologically related to each other. Erythogram and leukogram profiles revealed a similar distribution in rainbow trout and coho salmon, but those in Atlantic salmon were significantly different. While the activity of the most clinically important plasma enzymes demonstrated a similar profile in Atlantic salmon and rainbow trout, coho salmon demonstrated a significantly different distribution. Plasma electrolyte and mineral profiles showed significant differences between salmonid species, especially for rainbow trout, while Atlantic salmon and coho salmon demonstrated a high degree of similarity. Furthermore, electrolytes, minerals and blood gasometry biomarkers were significantly different between age ranges, suggesting a considerably different distribution between freshwater and seawater-farmed fish. The RIs of clinically healthy fish described in this study take into account the high biological variation of farmed fish in Chile, as the 3.059 individuals came from 78 different fish farms, both freshwater and seawater, and blood samples were collected using the same pre-analytical protocol. Likewise, our study provides the Chilean salmon farming industry with standardized protocols that can be used routinely and provides valuable information to improve the preventive vision of aquamedicine through the application of blood biomarkers to support and optimize health, welfare and husbandry management in the salmon farming industry.

Understanding the genetic status of aquaculture strains is essential for developing management guidelines aimed at sustaining the rates of genetic gain for economically important traits, as well as securing populations that will be robust to climate change. Coho salmon was the first salmonid introduced to Chile for commercial purposes and now comprises an essential component of the country's aquaculture industry. Several events, such as admixture, genetic bottlenecks, and rapid domestication, appear to be determinants in shaping the genome of commercial strains representing this species. To determine the impact of such events on the genetic diversity of these strains, we sought to estimate the effective population size (Ne) of several of these strains using genome-wide approaches. We compared these estimates to commercial strains from North America and Japan, as well as a hatchery strain used for supportive breeding of wild populations. The estimates of Ne were based on a method robust to assumptions about changes in population history, and ranged from low (Ne = 34) to relatively high (Ne = 80) in the Chilean strains. These estimates were higher than those obtained from the commercial North American strain but lower than those observed in the hatchery population and the Japanese strain (with Ne over 150). Our results suggest that some populations require measures to control the rates of inbreeding, possibly by using genomic information and incorporating new genetic material to ensure the long-term sustainability of these populations.

Chemical contamination is an increasingly important conservation issue in urban runoff-impacted watersheds. Regulatory and restoration efforts typically evaluate limited conventional parameters and pollutants. However, complex urban chemical mixtures contain hundreds to thousands of organic contaminants that remain unidentified, unregulated, and poorly understood. This study aimed to develop broadly representative metrics of water quality impairment corresponding to previously documented biological degradation along gradients of human impacts. Stream samples ( n = 65, baseflow/rainfall conditions, 2017-2018) were collected from 15 regional watersheds (Puget Sound, WA, USA) across an urbanization gradient defined by landscape characteristics. Surface water chemical composition characterized via non-targeted high-resolution mass spectrometry (7068 detections) was highly correlated with landscape-based urbanization gradient ( p < 0.01) and season ( p < 0.01). Landscape-scale changes in chemical composition closely aligned with two anchors of biological decline: coho salmon ( Oncorhynchus kisutch ) mortality risk ( p < 0.001) and loss of stream macroinvertebrate diversity and abundance ( p < 0.001). We isolated and identified 32 indicators for urban runoff impacts and corresponding receiving water ecological health, including well-known anthropogenic contaminants (e.g., caffeine, organophosphates, vehicle-derived chemicals), two related environmental transformation products, and a novel (methoxymethyl)melamine compound. Outcomes support data-directed selection of next-generation water quality indicators for prioritization and evaluation of watershed management efforts intended to protect aquatic ecosystems.

Piscirickettsiosis is the most important bacterial disease in the Chilean salmon industry, which has sorted several efforts to its control, generating enormous economic losses. Epigenetic alterations, such as DNA methylation, can play a relevant role in the modulation of the metazoans response to pathogens. Bacterial disease may activate global and local immune responses generating intricate responses with significant biological impact in the host. However, it is scarcely understood how bacterial infections influence fish epigenetic alterations. In the present study, we utilized Pacific salmon and Piscirickettsiosis as model, to gain understanding into the dynamics of DNA methylation among fish-bacterial infection interactions. A genome-wide analysis of DNA methylation patterns in female spleen tissue of Pacific salmon was achieved by reduced representation bisulphite sequencing from a time course design. We determined 2,251, 1,918, and 2,516 differentially methylated regions DMRs among infected and control Pacific salmon in 1 dpi, 5 dpi, and 15 dpi, respectively. The mean methylation difference per DMR among control and infected groups was of ~35%, with an oscillatory pattern of hypo, hyper, and hypomethylation across the disease. DMCs, among the control and infected group, showed that they were statistically enriched in intergenic regions and depleted in exons. Functional annotation of the DMR genes demonstrated three KEGG principal categories, associated directly with the host response to pathogens infections. Our results provide the first evidence of epigenetic variation in fish provoked by bacterial infection and demonstrate that this variation can be modulated across the disease.

Piscirickettsiosis is the most important bacterial disease in the Chilean salmon industry, which has borne major economic losses due to failure to control it. Cells use extracellular vesicles (EVs) as an inter-cellular communicators to deliver several factors (e.g., microRNAs) that may regulate the responses of other cells. However, there is limited knowledge about the identification and characterization of EV-miRNAs in salmonids or the effect of infections on these. In this study, Illumina sequencing technology was used to identify Coho salmon plasma EV-miRNAs upon Piscirickettsia salmonis infection at four different time points. A total of 118 novels and 188 known EV-miRNAs, including key immune teleost miRNAs families (e.g., miR-146, miR-122), were identified. A total of 245 EV-miRNAs were detected as differentially expressed (FDR < 5%) in terms of control, with a clear down-regulation pattern throughout the disease. KEGG enrichment results of EV-miRNAs target genes showed that they were grouped mainly in cellular, stress, inflammation and immune responses. Therefore, it is hypothesized that P. salmonis could potentially benefit from unbalanced modulation response of Coho salmon EV-miRNAs in order to promote a hyper-inflammatory and compromised immune response through the suppression of different key immune host miRNAs during the course of the infection, as indicated by the results of this study., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Flavobacterium psychrophilum causes bacterial coldwater disease (BCWD) in salmonids, resulting in significant losses worldwide. Several serotyping and genetic studies of F. psychrophilum have suggested some geno-/serotypes may be either host-specific or generalistic in nature; however, this association has not been adequately explored in vivo using more natural exposure routes. Herein, F. psychrophilum isolate US19-COS, originally recovered from coho salmon (Oncorhynchus kisutch) and belonging to multilocus sequence typing clonal complex (CC) CC-ST9, and isolate US53-RBT, recovered from rainbow trout (Oncorhynchus mykiss) and belonging to CC-ST10, were serotyped via PCR, evaluated for proteolytic activity and utilized to determine their median lethal dose in immersion-challenged coho salmon fingerlings. US19-COS belonged to serotype 0, hydrolysed casein and gelatin but not elastin, led to fulminant multiorgan infections and elicited severe gross and microscopic pathology. In contrast, US53-RBT, belonging to serotype 2, hydrolysed all three substrates, but did not lead to detectable infections, disease signs or mortality in any exposed coho salmon despite proving virulent to rainbow trout in previous experiments. This study provides in vivo evidence for potential host specificity of some F. psychrophilum genotypes that can also be serologically distinct, a matter of importance towards better understanding F. psychrophilum disease ecology and epidemiology., (© 2021 John Wiley & Sons Ltd.)

Coho Salmon Oncorhynchus kisutch show fidelity to natal spawning watersheds. Fine-scale homing, however, within rivers is not well understood. Interior Fraser Coho (IFC) salmon eggs were incubated at known spawning locations in the Coldwater River, two main stem sites and one-off channel pond site, providing otolith reference data for comparison to otolith signatures for returning adults using laser ablation inductively coupled plasma mass spectrometry. Elemental ratios for Ba:Ca and Sr:Ca in otoliths of juvenile O. kisutch differed significantly among the spawning locations examined. Juvenile otolith data were used to conduct a linear discriminant analysis to assess fine-scale homing in adults. Juvenile data were all assigned to the location where they had been incubated, producing a robust data set used to compare adult otoliths and define natal locations based on elemental signatures in otoliths of adult spawners. Homing and straying were apparent at the reach level; 57.1% of adults returned to their natal spawning locations, while 42.9% strayed to other spawning sites within the Coldwater River. Straying to novel incubation sites at the reach scale demonstrated plasticity in homing within a watershed., (© 2020 Fisheries Society of the British Isles.)

Multiple Pleistocene glaciations significantly affected the gene pool of many species inhabiting the Northern part of the Pacific Rim, an area with a rich glacial history. This paper is devoted to the study of intraspecific polymorphism of the coho salmon and the routes of its settlement throughout the Asian part of its range. Such problems are traditionally solved by comparing parts of the mitochondrial genome. Here, two fragments of mtDNA, the control region (D-loop) and the cytochrome b gene (cytb), were investigated. It was shown that the settlement of the Asian Pacific coast by the coho salmon was preceded by a chain of successive migration events from the refugium located on the North American continent to the South of the ice sheet covering the area of modern Canada and southern Alaska. The low level of genetic polymorphism in Asian coho populations seems to be a result of a pronounced founder effect, rather than being characteristic of the species as a whole.

The success and sustainability of Chilean aquaculture largely depends on the control of endemic and emerging pathogens, including several species of the genus Tenacibaculum. Tenacibaculum dicentrarchi and "Tenacibaculum finnmarkense" have been detected and confirmed in Chilean Atlantic salmon (Salmo salar). However, no outbreaks of tenacibaculosis in rainbow trout (Oncorhynchus mykiss) or coho salmon (Oncorhynchus kisutch) have been reported, either in Chile or globally. The aims of this study were to determine whether the mortalities recorded for rainbow trout and coho salmon from five marine fish farms located in the Los Lagos, Aysén, and Magallanes Regions could be caused by Tenacibaculum spp. The diseased fish exhibited cutaneous haemorrhages, tail and peduncle rots, and damage on the mouth and tongue. Microbiological analysis of infected external tissues yielded 13 bacterial isolates. The isolates were identified as members of the genus Tenacibaculum through biochemical analysis (e.g. Gram-stain negative, straight rods, filamentous cells and motile by gliding), but differences existed in biochemical results, making species-level identification through biomolecular tools essential. The 16S rRNA analysis found that the majority of isolates were more closely related to "T. finnmarkense" than T. dicentrarchi, while the phylogenetic trees resulting from multilocus sequence data recovered the four main clades (clades I to IV) identified by Olsen et al. (2017, Veterinary Microbiology, 205, 39). This is the first documented occurrence of clinical tenacibaculosis in farmed rainbow trout and coho salmon globally, and it extends the known host distribution of this pathogen in Chile. Moreover, we confirm the presence of Tenacibaculum species in the Chilean Patagonia. These findings highlight the importance of establishing preventative measures to minimize the spread of this disease within the Chilean marine aquaculture industry, as well as the need for monitoring initiatives worldwide in these farmed fish species., (© 2020 John Wiley & Sons Ltd.)

Piscine orthoreovirus genotype 1 (PRV-1) is the causative agent of heart and skeletal muscle inflammation (HSMI) in farmed Atlantic salmon (Salmo salar L.). The virus has also been found in Pacific salmonids in western North America, raising concerns about the risk to native salmon and trout. Here, we report the results of laboratory challenges using juvenile Chinook salmon, coho salmon and rainbow trout injected with tissue homogenates from Atlantic salmon testing positive for PRV-1 or with control material. Fish were sampled at intervals to assess viral RNA transcript levels, haematocrit, erythrocytic inclusions and histopathology. While PRV-1 replicated in all species, there was negligible mortality in any group. We observed a few erythrocytic inclusion bodies in fish from the PRV-1-infected groups. At a few time points, haematocrits were significantly lower in the PRV-1-infected groups relative to controls, but in no case was anaemia noted. The most common histopathological finding was mild, focal myocarditis in both the non-infected controls and PRV-1-infected fish. All cardiac lesions were judged mild, and none were consistent with those of HSMI. Together, these results suggest all three species are susceptible to PRV-1 infection, but in no case did infection cause notable disease in these experiments., (© Published 2020. This article is a U.S. Government work and is in the public domain in the USA. Journal of Fish Diseases published by John Wiley & Sons Ltd.)

This paper describes the first case of bacterial kidney disease (BKD) to be identified in coho salmon Oncorhynchus kisutch in Russia. The fish in question was caught in Lake Bolshoi Vilyui on the Kamchatka Peninsula. The diseased fish had foci of granulomatous inflammation in the kidneys. The diagnosis was confirmed by isolating the bacterium Renibacterium salmoninarum from kidney tissue in pure culture, and by determining the partial 16S RNA gene sequence of the isolate. This is the first detection of this pathogen in the genus Oncorhynchus in Russia, and detection of BKD in coho salmon indicates that the pathogen is present in the natural fish populations of Kamchatka. Therefore, it will be necessary to conduct screening studies of mature salmon selected for artificial reproduction, for the presence of BKD signs and asymptomatic infection with R. salmoninarum, which will allow us to estimate the prevalence of the pathogen.

For Pacific salmon, the key fisheries management goal in British Columbia (BC) is to maintain and restore healthy and diverse Pacific salmon populations, making conservation of salmon biodiversity the highest priority for resource management decision-making. Salmon status assessments are often conducted on coded-wire-tagged subsets of indicator populations based on assumptions of little differentiation within or among proximal populations. In the current study of southern BC coho salmon ( Oncorhynchus kisutch ) populations, parentage-based tagging (PBT) analysis provided novel information on migration and life-history patterns to test the assumptions of biological homogeneity over limited (generally < 100 km) geographic distances and, potentially, to inform management of fisheries and hatchery broodstocks. Heterogeneity for location and timing of fishery captures, family productivity, and exploitation rate was observed over small geographic scales, within regions that are, or might be expected to be, within the area encompassed by a single-tagged indicator population. These results provide little support for the suggestion that information gained from tagged indicator populations is representative of marine distribution, productivity, and exploitation patterns of proximal populations., Competing Interests: None declared., (© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

This study focused on applying different high hydrostatic pressure + carbon dioxide (HHP + CO 2 ) processing conditions on refrigerated (4 °C, 25 days) farmed coho salmon ( Oncorhynchus kisutch ) to inactivate endogenous enzymes (protease, lipase, collagenase), physicochemical properties (texture, color, lipid oxidation), and microbial shelf life. Salmon fillets were subjected to combined HHP (150 MPa/5 min) and CO 2 (50%, 70%, 100%). Protease and lipase inactivation was achieved with combined HHP + CO 2 treatments in which lipase activity remained low as opposed to protease activity during storage. Collagenase activity decreased approximately 90% during storage when applying HHP + CO 2 . Combined treatments limited the increase in spoilage indicators, such as total volatile amines and trimethylamine. The 150 MPa + 100% CO 2 treatment was the most effective at maintaining hardness after 10 days of storage. Combined treatments limited HHP-induced color change and reduced the extent of changes caused by storage compared with the untreated sample. Microbial shelf life was extended by the CO 2 content and not by the HHP treatments; this result was related to an increased lag phase and decreased growth rate. It can be concluded that combining HHP and CO 2 could be an effective method of inactivating endogenous enzymes and extend salmon shelf life.

Background: Growth regulation is a complex process influenced by genetic and environmental factors. We examined differences between growth hormone (GH) transgenic (T) and non-transgenic (NT) coho salmon to elucidate whether the same loci were involved in controlling body size and gene expression phenotypes, and to assess whether physiological transformations occurring from GH transgenesis were under the influence of alternative pathways. The following genomic techniques were used to explore differences between size classes within and between transgenotypes (T vs. NT): RNA-Seq/Differentially Expressed Gene (DEG) analysis, quantitative PCR (qPCR) and OpenArray analysis, Genotyping-by-Sequencing, and Genome-Wide Association Study (GWAS)., Results: DEGs identified in comparisons between the large and small tails of the size distributions of T and NT salmon (NT Large , NT Small , T Large and T Small ) spanned a broad range of biological processes, indicating wide-spread influence of the transgene on gene expression. Overexpression of growth hormone led to differences in regulatory loci between transgenotypes and size classes. Expression levels were significantly greater in T fish at 16 of 31 loci and in NT fish for 10 loci. Eleven genes exhibited different mRNA levels when the interaction of size and transgenotype was considered (IGF1, IGFBP1, GH, C3-4, FAS, FAD6, GLUT1, G6PASE1, GOGAT, MID1IP1). In the GWAS, 649 unique SNPs were significantly associated with at least one study trait, with most SNPs associated with one of the following traits: C3&#95;4, ELA1, GLK, IGF1, IGFBP1, IGFII, or LEPTIN. Only 1 phenotype-associated SNP was found in common between T and NT fish, and there were no SNPs in common between transgenotypes when size was considered., Conclusions: Multiple regulatory loci affecting gene expression were shared between fast-growing and slow-growing fish within T or NT groups, but no such regulatory loci were found to be shared between NT and T groups. These data reveal how GH overexpression affects the regulatory responses of the genome resulting in differences in growth, physiological pathways, and gene expression in T fish compared with the wild type. Understanding the complexity of regulatory gene interactions to generate phenotypes has importance in multiple fields ranging from applications in selective breeding to quantifying influences on evolutionary processes.

Hemoglobin derivatives are often quantified in blood to establish cardio-respiratory status and possible causes of impaired oxygen transport. The derivative known as methemoglobin results from oxidation of hemoglobin and is pathologically relevant because it cannot transport oxygen. In species and individuals possessing unstable methemoglobin, methemoglobin formation leads to rapid hemichrome formation and precipitation. Oxidizing reagents in standard methemoglobin analysis techniques therefore prevent accurate quantification of hemoglobin oxidative degradation products in species possessing unstable hemoglobin. In this study, we demonstrated that individual coho salmon ( Oncorhynchus kisutch ) possess unstable methemoglobin. Because molar absorptivities of coho methemoglobin, hemichrome and carboxyhemoglobin were significantly different from humans, the use of previous standard methods leads to an overestimation of methemoglobin in coho. Spontaneous conversion of methemoglobin to hemichrome was also demonstrated in Chinook ( O. tshawytscha ), pink ( O. gorbuscha ) and chum salmon ( O. keta ), but not steelhead ( O. mykiss ), indicating there may be a frequent need to account for unstable hemoglobin when quantifying methemoglobin in salmonids.•Our method builds upon multi-component analysis (MCA) by using a multivariate modeling technique to derive the coho-specific molar absorptivities of major hemoglobin derivatives•This approach fills a current need for the accurate quantification of methemoglobin in fishes possessing unstable hemoglobin., (© 2020 The Authors. Published by Elsevier B.V.)

Background: Transcriptomic responses to immune stimulation were investigated in coho salmon (Oncorhynchus kisutch) with distinct growth phenotypes. Wild-type fish were contrasted to strains with accelerated growth arising either from selective breeding (i.e. domestication) or genetic modification. Such distinct routes to accelerated growth may have unique implications for relationships and/or trade-offs between growth and immune function., Results: RNA-Seq was performed on liver and head kidney in four 'growth response groups' injected with polyinosinic-polycytidylic acid (Poly I:C; viral mimic), peptidoglycan (PGN; bacterial mimic) or PBS (control). These groups were: 1) 'W': wild-type, 2) 'TF': growth hormone (GH) transgenic salmon with ~ 3-fold higher growth-rate than W, 3) 'TR': GH transgenic fish ration restricted to possess a growth-rate equal to W, and 4) 'D': domesticated non-transgenic fish showing growth-rate intermediate to W and TF. D and TF showed a higher similarity in transcriptomic response compared to W and TR. Several immune genes showed constitutive expression differences among growth response groups, including perforin 1 and C-C motif chemokine 19-like. Among the affected immune pathways, most were up-regulated by Poly I:C and PGN. In response to PGN, the c-type lectin receptor signalling pathway responded uniquely in TF and TR. In response to stimulation with both immune mimics, TR responded more strongly than other groups. Further, group-specific pathway responses to PGN stimulation included NOD-like receptor signalling in W and platelet activation in TR. TF consistently showed the most attenuated immune response relative to W, and more DEGs were apparent in TR than TF and D relative to W, suggesting that a non-satiating ration coupled with elevated circulating GH levels may cause TR to possess enhanced immune capabilities. Alternatively, TF and D salmon are prevented from acquiring the same level of immune response as TR due to direction of energy to high overall somatic growth. Further study of the effects of ration restriction in growth-modified fishes is warranted., Conclusions: These findings improve our understanding of the pleiotropic effects of growth modification on the immunological responses of fish, revealing unique immune pathway responses depending on the mechanism of growth acceleration and nutritional availability.

Monitoring the growth of salmon during their early marine phase provides insights into prey availability, and growth rates may be linked to risks of size-dependent mortality. However, the measurement of growth rate is challenging for free-living salmon in the ocean. Insulin-like growth factor (IGF)-I is a growth-promoting hormone that is emerging as a useful index of growth in salmon. In addition, laboratory-based studies using coho salmon have shown that one of circulating IGF-binding proteins (IGFBPs), IGFBP-1b, is induced by fasting and thus could be used as an inverse index of growth and/or catabolic state in salmon. However, few studies have measured plasma levels of IGFBP-1b in salmon in the wild. We measured plasma IGFBP-1b levels for postsmolt coho salmon collected in the Strait of Georgia and surrounding waters, British Columbia, Canada, and compared regional differences in IGFBP-1b to ecological information such as seawater temperature and stomach fullness. Plasma IGFBP-1b levels were the highest in fish from Eastern Johnstone Strait and relatively high in Queen Charlotte Strait and Western Johnstone Strait, which was in good agreement with the poor ocean conditions for salmon hypothesized to occur in that region. The molar ratio of plasma IGF-I to IGFBP-1b, a theoretical parameter of IGF-I availability to the receptor, discriminated differences among regions better than IGF-I or IGFBP-1b alone. Our data suggest that plasma IGFBP-1b reflects catabolic status in postsmolt coho salmon, as highlighted in fish in Eastern Johnston Strait, and is a useful tool to monitor negative aspects of salmon growth in the ocean.

Behavioural changes that occur during the parr-smolt transformation were investigated in juvenile coho salmon Oncorhynchus kisutch. Fish from two populations were examined from the Fraser River catchment in British Columbia, Canada; a short and a long-distance migrating population. Fish showed a significant decrease in condition factor and significant increase in gill Na + K + -ATPase activity during the spring indicating that they became competent smolts, but no difference between populations. Temperature preference trials were conducted using a shuttlebox system throughout the spring. Mean temperature preference did not differ between the two populations, but preferred temperature decreased with development from 16.5 ± 0.3°C for parr to 15.5 ± 0.4°C for smolts. Mean swimming velocity was also greater in smolts than parr, but there was no difference between the two populations. The preference for warmer water temperature observed for parr in early spring may be advantageous for stimulating smolt development. Preference for slightly cooler temperatures observed for smolts would sustain elevated seawater tolerance during the smolt window by a short time and may ensure successful transition to the marine environment., (© 2019 The Fisheries Society of the British Isles.)

In salmonid parentage-based tagging (PBT) applications, entire hatchery broodstocks are genotyped, and subsequently, progeny can be nonlethally sampled and assigned back to their parents using parentage analysis, thus identifying their hatchery of origin and brood year (i.e., age). Inter- and intrapopulation variability in migration patterns, life history traits, and fishery contributions can be determined from PBT analysis of samples derived from both fisheries and escapements (portion of a salmon population that does not get caught in fisheries and returns to its natal river to spawn). In the current study of southern British Columbia coho salmon ( Oncorhynchus kisutch ) populations, PBT analysis provided novel information on intrapopulation heterogeneity among males in the total number of progeny identified in fisheries and escapements, the proportion of progeny sampled from fisheries versus escapement, the proportion of two-year-old progeny (jacks) produced, and the within-season return time of progeny. Fishery recoveries of coho salmon revealed heterogeneity in migration patterns among and within populations, with recoveries from north and central coast fisheries distinguishing "northern migrating" from "resident" populations. In northern migrating populations, the mean distance between fishery captures of sibs (brothers and sisters) was significantly less than the mean distance between nonsibs, indicating the possible presence of intrapopulation genetic heterogeneity for migration pattern. Variation among populations in productivity and within populations in fish catchability indicated that population selection and broodstock management can be implemented to optimize harvest benefits from hatcheries. Application of PBT provided valuable information for assessment and management of hatchery-origin coho salmon in British Columbia., Competing Interests: None declared.

Piscirickettsia salmonis is the etiologic agent of salmon rickettsial syndrome (SRS) and is responsible for considerable economic losses in salmon aquaculture. The bacterium affects coho salmon (CS; Oncorhynchus kisutch ), Atlantic salmon (AS; Salmo salar ), and rainbow trout (RT; Oncorhynchus mykiss ) in several countries, including Norway, Canada, Scotland, Ireland, and Chile. We used Bayesian genome-wide association study analyses to investigate the genetic architecture of resistance to P. salmonis in farmed populations of these species. Resistance to SRS was defined as the number of days to death and as binary survival (BS). A total of 828 CS, 2130 RT, and 2601 AS individuals were phenotyped and then genotyped using double-digest restriction site-associated DNA sequencing and 57K and 50K Affymetrix® Axiom® single nucleotide polymorphism (SNP) panels, respectively. Both traits of SRS resistance in CS and RT appeared to be under oligogenic control. In AS, there was evidence of polygenic control of SRS resistance. To identify candidate genes associated with resistance, we applied a comparative genomics approach in which we systematically explored the complete set of genes adjacent to SNPs, which explained more than 1% of the genetic variance of resistance in each salmonid species (533 genes in total). Thus, genes were classified based on the following criteria: i) shared function of their protein domains among species, ii) shared orthology among species, iii) proximity to the SNP explaining the highest proportion of the genetic variance, and iv) presence in more than one genomic region explaining more than 1% of the genetic variance within species. Our results allowed us to identify 120 candidate genes belonging to at least one of the four criteria described above. Of these, 21 of them were part of at least two of the criteria defined above and are suggested to be strong functional candidates influencing P. salmonis resistance. These genes are related to diverse biological processes, such as kinase activity, GTP hydrolysis, helicase activity, lipid metabolism, cytoskeletal dynamics, inflammation, and innate immune response, which seem essential in the host response against P. salmonis infection. These results provide fundamental knowledge on the potential functional genes underpinning resistance against P. salmonis in three salmonid species.

Land-based recirculating aquaculture systems (RAS) have been used to rear salmon from smolt to market-sized adults, but high operating costs have limited their wide spread adoption. One clear advantage of using RAS for salmon aquaculture over open net pens is that fish can be reared under optimal conditions in an attempt to maximize growth and physiological performance and reduce overall production costs. However, few studies have attempted to define the optimal conditions for the long-term rearing of salmon. Thus, the goal of this study is to determine the effects of salinity and photoperiod, two factors that can be easily manipulated in RAS, on the physiological performance of coho salmon (Oncorhynchus kisutch) during long-term rearing. To address this goal, post-smolt coho salmon were reared for 150 days in replicate RAS at 2.5, 5, 10 and 30 ppt under either 12:12 and 24:0 (light:dark) photoperiods. Routine metabolic rate, maximum metabolic rate, aerobic scope and hypoxia tolerance were measured at 60 and 120 days of rearing, while swimming performance was assessed at 60 and 150 days of rearing. There were no effects of salinity or photoperiod on metabolic rate measurements, hypoxia tolerance or swimming performance at any sampling time. There were, however, significant effects of salinity and photoperiod on post-swimming hematology. The results suggest that physiological disturbances continue to manifest due to different environmental conditions, despite acclimation, but do not hinder the animal's ability to cope with physiological stressors. Overall, rearing salinity and photoperiod had very few measurable effects on the physiology and performance of coho salmon except the ionoregulatory disturbances following swimming at salinities of 2.5 and 30 ppt., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Land-based, closed containment salmon aquaculture involves rearing salmon from smolt to adult in recirculating aquaculture systems (RAS). Unlike in open-net pen aquaculture, rearing conditions can be specified in RAS in order to optimize growth and physiological stress tolerance. The environmental conditions that yield optimal stress tolerance in salmon are, however, unknown. To address this knowledge gap, we reared Atlantic (Salmo salar) and coho (Oncorhynchus kisutch) salmon in 7 separate RASs for 400 days post-smoltification under 2 photoperiods (24:0 or 12:12, light:dark) and 4 salinities (2.5, 5, 10 or 30 ppt.) and assessed the effects of these conditions on thermal tolerance. We found that over the first 120 days post-smoltification, rearing coho under a 24:0 photoperiod resulted in a ~2 °C lower critical thermal maxima (CT max ) than in coho reared under a 12:12 photoperiod. This photoperiod effect did not persist at 200 and 400 days, which was coincident with an overall decrease in CTmax in coho. Finally, Atlantic salmon had a higher CT max (~28 °C) compared to coho (~26 °C) at 400 days post-smoltification. Overall, these findings are important for the future implications of RAS and for the aquaculture industry to help identify physiologically sensitive time stages., (Copyright © 2018 Elsevier Inc. All rights reserved.)

In fish used for food production and scientific research, fast growth can be achieved via selective breeding or induced instantaneously via growth hormone (GH) transgenesis (GHT). The proteomic basis for these distinct routes towards a similar higher phenotype remains uncharacterized, as are associated implications for health parameters. We addressed this knowledge gap using skeletal muscle proteomics in coho salmon (Oncorhynchus kisutch), hypothesising that i) selective breeding and GHT are underpinned by both parallel and unique changes in growth systems, and ii) rapidly-growing fish strains have lowered scope to allocate resources towards immune function. Quantitative profiling of GHT and growth-selected strains was done in comparison to wild-type after injection with PBS (control) or Poly I:C (to mimic infection). We identified remodelling of the muscle proteome in each growth-enhanced strain that was strikingly non-overlapping. GHT was characterized by focal upregulation of systems driving protein synthesis, while the growth-selected fish presented a larger and more diverse set of changes, consistent with complex alterations to many metabolic and cellular pathways. Poly I:C had little detectable effect on the muscle proteome. This study demonstrates that distinct proteome profiles can explain outwardly similar enhanced growth phenotypes, improving our understanding of growth mechanisms in anthropogenic animal strains. SIGNIFICANCE: This work provides the first proteomic insights into mechanisms underpinning different anthropogenic routes to rapid growth in salmon. High-throughput proteomic profiling was used to reveal changes supporting enhanced growth, comparing skeletal muscle of growth hormone transgenic (GHT) and selectively-bred salmon strains with their wild-type counterparts. Contrasting past mRNA-level comparisons of the same fish strains, our data reveals a surprisingly substantial proteomic divergence between the GHT and selectively bred strains. The findings demonstrate that many unique molecular mechanisms underlie growth-enhanced phenotypes in different types of fish strain used for food production and scientific research., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

Wild Pacific salmon, including Coho salmon Onchorynchus kisutch , have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage-based tagging (PBT) may overcome problems associated with coded-wire tag-based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded-wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774-individual, 267-population baseline available for assignment. Coho salmon from un-CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT-GSI system of identification to individuals in 2017 fisheries and escapements provided high-resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian-origin coho salmon relative to CWTs, and an opportunity for a genetic-based system to replace the current CWT system for coho salmon assessment.

The increasing capacity of transcriptomic analysis by high throughput sequencing has highlighted the presence of a large proportion of transcripts that do not encode proteins. In particular, long non-coding RNAs (lncRNAs) are sequences with low coding potential and conservation among species. Moreover, cumulative evidence has revealed important roles in post-transcriptional gene modulation in several taxa. In fish, the role of lncRNAs has been scarcely studied and even less so during the immune response against sea lice. In the present study we mined for lncRNAs in Atlantic salmon (Salmo salar) and Coho salmon (Oncorhynkus kisutch), which are affected by the sea louse Caligus rogercresseyi, evaluating the degree of sequence conservation between these two fish species and their putative roles during the infection process. Herein, Atlantic and Coho salmon were infected with 35 lice/fish and evaluated after 7 and 14 days post-infestation (dpi). For RNA sequencing, samples from skin and head kidney were collected. A total of 5658/4140 and 3678/2123 lncRNAs were identified in uninfected/infected Atlantic and Coho salmon transcriptomes, respectively. Species-specific transcription patterns were observed in exclusive lncRNAs according to the tissue analyzed. Furthermore, neighbor gene GO enrichment analysis of the top 100 highly regulated lncRNAs in Atlantic salmon showed that lncRNAs were localized near genes related to the immune response. On the other hand, in Coho salmon the highly regulated lncRNAs were localized near genes involved in tissue repair processes. This study revealed high regulation of lncRNAs closely localized to immune and tissue repair-related genes in Atlantic and Coho salmon, respectively, suggesting putative roles for lncRNAs in salmon against sea lice infestation., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Physiological changes during the parr-smolt transformation were investigated in short distance (Chilliwack River) and long-distance (Salmon River) migrating coho salmon Oncorhynchus kisutch populations in British Columbia, Canada. Biochemical and molecular indicators were used to monitor smolt development for fish reared at 10 °C throughout the spring. Fish grew well and developed the physical appearance of competent smolts. Both populations exhibited increases in gill Na + -K + -ATPase activity (NKA; an important indicator of seawater tolerance) at the same date and the duration of the increase in enzyme activity did not differ between populations. Gill messenger (m)RNA copies for two isoforms of the NKA α subunit, α1a and α1b, showed significant changes and the pattern was similar between populations. Growth hormone receptor and prolactin receptor mRNA from the gill showed modest changes associated with smolting in the spring for both populations, suggesting that these may not be useful indicators of smolt development in hatchery-reared O. kisutch. Consequently, the duration of the smolt window was not based on the region of origin in the present study., (© 2018 The Fisheries Society of the British Isles.)

Growth hormone (GH) transgenic (T) coho salmon consistently show remarkably enhanced growth associated with increased appetite and food consumption compared to non-transgenic wild-type (NT) coho salmon. To improve understanding of the mechanism by which GH overexpression mediates food intake and digestion in T fish, feed intake and gastric evacuation rate (over 7 days) were measured in size-matched T and NT coho salmon. T fish displayed greatly enhanced feed intake levels (~ 2.5-fold), and more than 3-fold increase in gastric evacuation rates relative to NT coho salmon. Despite the differences in feed intake, no differences were noted in the time taken from first ingestion of food to stomach evacuation between genotypes. These results indicate that enhanced feed intake is coupled with an overall increased processing rate to enhance energy intake by T fish. To further investigate the molecular basis of these responses, we examined the messenger RNA (mRNA) levels of several genes in appetite- and gastric-regulation pathways (Agrp1, Bbs, Cart, Cck, Glp, Ghrelin, Grp, Leptin, Mc4r, Npy, and Pomc) by qPCR analyses in the brain (hypothalamus, preoptic area) and pituitary, and in peripheral tissues associated with digestion (liver, stomach, intestine, and adipose tissue). Significant increases in mRNA levels were found for Agrp1 in the preoptic area (POA) of the brain, and Grp and Pomc in pituitary for T coho salmon relative to NT. Mch and Npy showed significantly lower mRNA levels than NT fish in all brain tissues examined across all time-points after feeding. Mc4r and Cart for T showed significantly lower mRNA levels than NT in the POA and hypothalamus, respectively. In the case of peripheral tissues, T fish had lower mRNA levels of Glp and Leptin than NT fish in the intestine and adipose tissue, respectively. Grp, Cck, Bbs, Glp, and Leptin in stomach, adipose tissue, and/or intestine showed significant differences across the time-points after feeding, but Ghrelin showed no significant difference between T and NT fish in all tested tissues.

A tension between cooperation and conflict characterizes the behavioral dynamics of many social species. The foraging benefits of group living include increased efficiency and reduced need for vigilance, but social foraging can also encourage theft of captured prey from conspecifics. The payoffs of stealing prey from others (scrounging) versus capturing prey (producing) may depend not only on the frequency of each foraging strategy in the group but also on an individual's ability to steal. By observing the foraging behavior of juvenile coho salmon ( Oncorhynchus kisutch ), we found that, within a group, relatively smaller coho acted primarily as producers and took longer to handle prey, and were therefore more likely to be targeted by scroungers than relatively larger coho. Further, our observations suggest that the frequency of scrounging may be higher when groups contained individuals of different sizes. Based on these observations, we developed a model of phenotype-limited producer-scrounger dynamics, in which rates of stealing were structured by the relative size of producers and scroungers within the foraging group. Model simulations show that when the success of stealing is positively related to body size, relatively large predators should tend to be scroungers while smaller predators should be producers. Contrary to previous models, we also found that, under certain conditions, producer and scrounger strategies could coexist for both large and small phenotypes. Large scroungers tended to receive the highest payoff, suggesting that producer-scrounger dynamics may result in an uneven distribution of benefits among group members that-under the right conditions-could entrench social positions of dominance.

Wild stocks of Pacific salmonids have experienced sharp declines in abundance over the past century. Consequently, billions of fish are released each year for enhancing abundance and sustaining fisheries. However, the beneficial role of this widely used management practice is highly debated since fitness decrease of hatchery-origin fish in the wild has been documented. Artificial selection in hatcheries has often been invoked as the most likely explanation for reduced fitness, and most studies to date have focused on finding signatures of hatchery-induced selection at the DNA level. We tested an alternative hypothesis, that captive rearing induces epigenetic reprogramming, by comparing genome-wide patterns of methylation and variation at the DNA level in hatchery-reared coho salmon ( Oncorhynchus kisutch ) with those of their wild counterparts in two geographically distant rivers. We found a highly significant proportion of epigenetic variation explained by the rearing environment that was as high as the one explained by the river of origin. The differentially methylated regions show enrichment for biological functions that may affect the capacity of hatchery-born smolts to migrate successfully in the ocean. Shared epigenetic variation between hatchery-reared salmon provides evidence for parallel epigenetic modifications induced by hatchery rearing in the absence of genetic differentiation between hatchery and natural-origin fish for each river. This study highlights epigenetic modifications induced by captive rearing as a potential explanatory mechanism for reduced fitness in hatchery-reared salmon., Competing Interests: The authors declare no conflict of interest.

Coho salmon were extirpated in the mid-20th century from the interior reaches of the Columbia River but were reintroduced with relatively abundant source stocks from the lower Columbia River near the Pacific coast. Reintroduction of Coho salmon to the interior Columbia River (Wenatchee River) using lower river stocks placed selective pressures on the new colonizers due to substantial differences with their original habitat such as migration distance and navigation of six additional hydropower dams. We used restriction site-associated DNA sequencing (RAD-seq) to genotype 5,392 SNPs in reintroduced Coho salmon in the Wenatchee River over four generations to test for signals of temporal structure and adaptive variation. Temporal genetic structure among the three broodlines of reintroduced fish was evident among the initial return years (2000, 2001, and 2002) and their descendants, which indicated levels of reproductive isolation among broodlines. Signals of adaptive variation were detected from multiple outlier tests and identified candidate genes for further study. This study illustrated that genetic variation and structure of reintroduced populations are likely to reflect source stocks for multiple generations but may shift over time once established in nature.

Salmon species cultured in Chile evidence different levels of susceptibility to the sea louse Caligus rogercresseyi. These differences have mainly been associated with specific immune responses. Moreover, iron regulation seems to be an important mechanism to confer immunity during the host infestation. This response called nutritional immunity has been described in bacterial infections, despite that no comprehensive studies involving in marine ectoparasites infestation have been reported. With this aim, we analysed the transcriptome profiles of Atlantic and coho salmon infected with C. rogercresseyi to evidence modulation of the iron metabolism as a proxy of nutritional immune responses. Whole transcriptome sequencing was performed in samples of skin and head kidney from Atlantic and coho salmon infected with sea lice. RNA-seq analyses revealed significant upregulation of transcripts in both salmon species at 7 and 14 dpi in skin and head kidney, respectively. However, iron regulation transcripts were differentially modulated, evidencing species-specific expression profiles. Genes related to heme degradation and iron transport such as hepcidin, transferrin and haptoglobin were primary upregulated in Atlantic salmon; meanwhile, in coho salmon, genes associated with heme biosynthesis were strongly transcribed. In summary, Atlantic salmon, which are more susceptible to infestation, presented molecular mechanisms to deplete cellular iron availability, suggesting putative mechanisms of nutritional immunity. In contrast, resistant coho salmon were less affected by sea lice, mainly activating pro-inflammatory mechanisms to cope with infestation., (© 2017 John Wiley & Sons Ltd.)

Although Caligus rogercresseyi negatively impacts Chilean salmon farming, the metabolic effects of infection by this sea louse have never been completely characterized. Therefore, this study analyzed lactate responses in the plasma, as well as the liver/muscle lactate dehydrogenase (LDH) activity and gene expression, in Salmo salar and Oncorhynchus kisutch infested by C. rogercresseyi. The lactate responses of Atlantic and Coho salmon were modified by the ectoparasite. Both salmon species showed increasing in plasma levels, whereas enzymatic activity increased in the muscle but decreased in the liver. Gene expression was overexpressed in both Coho salmon tissues but only in the liver for Atlantic salmon. These results suggest that salmonids need more energy to adapt to infection, resulting in increased gene expression, plasma levels, and enzyme activity in the muscles. The responses differed between both salmon species and over the course of infection, suggesting potential species-specific responses to sea-lice infection., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Measures of genetic diversity within and among populations and historical geomorphological data on stream landscapes were used in model simulations based on approximate Bayesian computation (ABC) to examine hypotheses of the relative importance of stream features (geomorphology and age) associated with colonization events and gene flow for coho salmon Oncorhynchus kisutch breeding in recently deglaciated streams (50-240 years b.p.) in Glacier Bay National Park (GBNP), Alaska. Population estimates of genetic diversity including heterozygosity and allelic richness declined significantly and monotonically from the oldest and largest to youngest and smallest GBNP streams. Interpopulation variance in allele frequency increased with increasing distance between streams (r = 0·435, P < 0·01) and was inversely related to stream age (r = -0·281, P < 0·01). The most supported model of colonization involved ongoing or recent (<10 generations before sampling) colonization originating from large populations outside Glacier Bay proper into all other GBNP streams sampled. Results here show that sustained gene flow from large source populations is important to recently established O. kisutch metapopulations. Studies that document how genetic and demographic characteristics of newly founded populations vary associated with successional changes in stream habitat are of particular importance to and have significant implications for, restoration of declining or repatriation of extirpated populations in other regions of the species' native range., (© 2017 The Fisheries Society of the British Isles.)

Salmon exposed to waterborne metals can experience olfactory impairment leading to disrupted chemosensation. In the current study, we investigated the effects of cadmium (Cd) on salmon olfactory function by modeling an exposure scenario where juvenile salmon transiently migrate through a polluted waterway. Coho were exposed to environmentally relevant concentrations of waterborne Cd (2 and 30 µg/L) for 48 h and (0.3 and 2 μg/L) for 16 days, followed by a 16-day depuration associated with outmigration. Cadmium exposures inhibited behavioral responses towards L-cysteine and conspecific odorants, with effects persisting following the depuration. Behavioral alterations following the 30 µg/L exposure were associated with increased olfactory epithelial gene expression of metallothionein (mt1a) and heme oxygenase (hmox1); reduced expression of olfactory signal transduction (OST) molecules; and reduced expression of mRNAs encoding major coho odorant receptors (ORs). Salmon OR array analysis indicated that Cd preferentially impacted expression of OST and OR markers for ciliated olfactory sensory neurons (OSNs) relative to microvillus OSNs, suggesting a differential sensitivity of these two major OSN populations. Behavioral alterations on exposure to 0.3 and 2 µg/L Cd were associated with increased mt1a, but not with major histological or OR molecular changes, likely indicating disrupted OST as a major mechanism underlying the behavioral dysfunction at the low-level Cd exposures. Laser-ablation mass spectrometry analysis revealed that the OSN injury and behavioral dysfunction was associated with significant Cd bioaccumulation within the olfactory sensory epithelium. In summary, low-level Cd exposures associated with polluted waterways can induce differential and persistent olfactory dysfunction in juvenile coho salmon., (© The Author 2016. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Caligus rogercresseyi, an ectoparasite affecting the Chilean salmon industry, can cause immunosuppression and physiological stress in farmed fish. Interestingly, coho salmon (Oncorhynchus kisutch) are notably resistant to infestation, whereas Atlantic salmon (Salmo salar) are phenotypically more susceptible to sea lice. However, comparative studies on immune responses to C. rogercresseyi have not been conducted. In this study, Illumina sequencing was conducted to evaluate head kidney and skin samples taken 7 and 14 days post-infestation, yielding a total of 1492 and 1522 contigs annotated to immune-related genes for Atlantic and coho salmon, respectively. Both species evidenced an upregulation of inflammatory genes. Atlantic salmon had highly upregulated TLR22 and MHCII at 14 days post-infestation, while coho salmon had highly upregulated stat5 and il1r transcripts. Fourteen transcripts related to T H 1, T H 2, TLR, and macrophage responses were corroborated via RT-qPCR. Statistical analyses indicated an upregulation of mmp13, cox2, il10, ccr3, tlr22a2, and tlr21 in Atlantic salmon and of ifnγ, cd83, T-bet, tlr13, and tlr19 in coho salmon. These results suggest strong differences between the Atlantic and coho salmon immune responses, where coho salmon, the more resistant species, presented a primary T H 1 response. Additionally, putative roles of TLRs in salmonids against sea lice were evidenced. This study is the first comparative transcriptome analysis that reveals species-specific immune responses in salmons infected with C. rogercresseyi., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

The transcription factor NFE2L2 (Nuclear Factor, Erythroid 2-Like 2, or NRF2) plays a key role in maintaining the redox state within cells. Characterization of this pathway has extended to fish, most notably zebrafish (Danio rerio), in which two paralogs of the transcription factor exist: Nrf2a, an activator, and Nrf2b, a negative regulator during embryogenesis. Only one ARE target has been thoroughly delineated in zebrafish, and this deviated from the canonical sequence derived from studies in mammals. In general, the mechanistic pathway has not been characterized in non-model aquatic organisms that are commonly exposed to environmental pollutants. The current study compares the zebrafish paralogs to those found in a non-model teleost, the ecologically important salmonid, Oncorhnychus kisutch (coho salmon). Two salmon paralogs, Nrf2A and -2B, described here were found to possess only slightly greater identity between one another (84% of amino acids) than to the singleton ortholog of the esocid Esox lucius (80-82%), the nearest non-salmonid outgroup. Unlike one of the zebrafish forms, each is a strong activating factor based on sequence homology and in vitro testing. To uncover functional target AREs in coho, promoter flanking sequences were isolated for five genes that protect cells against oxidative stress: heme oxygenase 1, peroxiredoxin 1, glutamate-cysteine ligase, and the glutathione S-transferases pi and rho (hmox1, prdx1, gclc, gstp, and gstr). All except gstr had functional elements and all fit the standard mammalian-derived canonical sequence, unlike the motif found in zebrafish gstp. Expression studies demonstrate the presence of both Nrf2 paralogs in multiple organs, although in differing ratios. Collectively, our findings extend the conservation of Nrf2 and the ARE to salmonids, and should help inform future work in teleosts on mechanisms of redox control, as well as responsiveness of this pathway and its downstream antioxidant gene targets to chemical exposures in the environment., (Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.)

Survival, competition, growth and reproductive success in fishes are highly dependent on food intake, food availability and feeding behavior and are all influenced by a complex set of metabolic and neuroendocrine mechanisms. Overexpression of growth hormone (GH) in transgenic fish can result in greatly enhanced growth rates, feed conversion, feeding motivation and food intake. The objectives of this study were to compare seasonal feeding behavior of non-transgenic wild-type (NT) and GH-transgenic (T) coho salmon (Oncorhynchus kisutch), and to examine the effects of intraperitoneal injections of the appetite-regulating peptides cholecystokinin (CCK-8), bombesin (BBS), glucagon-like peptide-1 (GLP-1), and alpha-melanocyte-stimulating hormone (α-MSH) on feeding behavior. T salmon fed consistently across all seasons, whereas NT dramatically reduced their food intake in winter, indicating the seasonal regulation of appetite can be altered by overexpression of GH in T fish. Intraperitoneal injections of CCK-8 and BBS caused a significant and rapid decrease in food intake for both genotypes. Treatment with either GLP-1 or α-MSH resulted in a significant suppression of food intake for NT but had no effect in T coho salmon. The differential response of T and NT fish to α-MSH is consistent with the melanocortin-4 receptor system being a significant pathway by which GH acts to stimulate appetite. Taken together, these results suggest that chronically increased levels of GH alter feeding regulatory pathways to different extents for individual peptides, and that altered feeding behavior in transgenic coho salmon may arise, in part, from changes in sensitivity to peripheral appetite-regulating signals., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Background: Heart and skeletal muscle inflammation (HSMI) is an emerging disease of marine-farmed Atlantic salmon Salmo salar, first recognized in 1999 in Norway, and recently associated with piscine orthoreovirus (PRV) infection. To date, HSMI lesions with presence of PRV have only been described in marine-farmed Atlantic salmon in Norway. A new HSMI-like disease in rainbow trout Oncorhynchus mykiss associated with a PRV-related virus has also been reported in Norway., Methods: Sampling of Atlantic salmon and coho salmon was done during potential disease outbreaks, targeting lethargic/moribund fish. Fish were necropsied and tissues were taken for histopathologic analysis and testing for PRV by RT-qPCR assay for segment L1 and conventional RT-PCR for PRV segment S1. The PCR products were sequenced and their relationship to PRV strains in GenBank was determined using phylogenetic analysis and nucleotide and amino acid homology comparisons., Results: The Atlantic salmon manifested the classical presentation of HSMI with high PRV virus loads (low Ct values) as described in Norway. The coho salmon with low Ct values had myocarditis but only in the spongy layer, the myositis of red muscle in general was mild, and the hepatic necrosis was severe. Upon phylogenetic analysis of PRV segment S1 sequences, all the Chilean PRV strains from Atlantic salmon grouped as sub-genotype Ib, whereas the Chilean PRV strains from coho salmon were more diversified, grouping in both sub-genotypes Ia and Ib and others forming a distinct new phylogenetic cluster, designated Genotype II that included the Norwegian PRV-related virus., Conclusions: To our knowledge the present work constitutes the first published report of HSMI lesions with presence of PRV in farmed Atlantic salmon outside of Europe, and the first report of HSMI-like lesions with presence of PRV in coho salmon in Chile. The Chilean PRV strains from coho salmon are more genetically diversified than those from Atlantic salmon, and some form a distinct new phylogenetic cluster, designated Genotype II.

In this study, we isolated, identified and characterized isolates of Tenacibaculum dicentrarchi in Atlantic salmon (Salmo salar) farmed in Chile for the first time. In 2010 and 2014, mortalities were observed in Atlantic salmon (average weight 25-30 and 480-520 g, respectively) at an aquaculture centre in Puerto Montt, Chile. Severe tail rots, frayed fins and, in some cases, damaged gills were detected. Wet smear analyses of these lesions revealed a high occurrence of Gram-negative, filamentous bacteria. Microbiological analysis of infected gill and tail tissues yielded six bacterial isolates. All were identified as T. dicentrarchi through polyphasic taxonomy, which included phenotypic characterization, 16S rRNA sequencing and multilocus sequence typing. The latter method revealed a close relationship of the Chilean genotype with the T. dicentrarchi type strain and two Norwegian Atlantic cod (Gadus morhua) isolates. The pathogenic potential of the TdChD05 isolate was assessed by challenging Atlantic salmon and rainbow trout (Oncorhynchus mykiss) for one hour, which resulted in mean cumulative mortality rates of 65% and 93%, respectively, as well as clinical signs 14 days post-challenge. However, challenged Coho salmon (Oncorhynchus kisutch) presented no mortalities or clinical signs of infection. These findings indicate that the geographical and host distribution of T. dicentrarchi is wider than previously established and that this bacterium may have negative impacts on salmonid cultures., (© 2016 Blackwell Verlag GmbH.)

Salmonids are an important family of fish both from economic and basic research perspectives, and have been subjected to extensive research at whole-animal and molecular levels. Most research to date has been conducted on Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), but more recently other salmonids have become a focus of study due to their interesting life histories and because of their potential for use in commercial aquaculture. However, molecular biology and genetic analyses for these emerging species are currently hampered due to the lack of extensive genomic resources. To overcome some of these limitations, we have constructed a 43,228 sequence transcriptome from 13 tissues from coho salmon, Oncorhynchus kisutch using de novo transcriptome assembly methods. The transcriptome profiling analysis has provided data distinguishing allelic variation from paralogues that arose during the recent whole-genome duplication event in this family, thus allowing simplified analysis of gene-specific expression. Additionally, 1599 novel coho sequences have been identified through comparison with transcriptomes from two other salmonids species (Atlantic salmon and rainbow trout), and with northern pike. The transcriptome presented here will be useful for genomic analysis of coho salmon and other closely related salmonid species., (Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.)