Acute Toxicity of 6PPD-Quinone to Early Life Stage Juvenile Chinook (Oncorhynchus tshawytscha) and Coho (Oncorhynchus kisutch) Salmon.

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.

Effects of fasting and temperature on the biological parameters, proximal composition, and fatty acid profile of Chinook salmon (Oncorhynchus tshawytscha) at different life stages.

We investigated the effects of temperature and fasting on chinook salmon (Oncorhynchus tshawytscha) at different life stages. In the first stage, fish were reared at 13 °C (198.5 ± 34.6 g) or 17 °C (218.3 ± 47.6 g) and fasted for 27 and 26 days, respectively. In the second stage, fish reared at 13 °C (481.8 ± 54.3 g) and 17 °C (597.3 ± 64.3 g) were fasted for 42 and 41 days respectively. At the third stage, fish were reared only at 17 °C (1065.7 ± 190.9 g) and fasted for 42 days. At the end of each fasting period performance, fillet and whole-body proximal composition, and whole-body fatty acid profile were compared among fish before and after fasting. Additionally, fillet fatty acid daily loss was compared in fasted fish from different treatments. The results showed that body weight was not significantly impacted by fasting. However, at 17 °C fasting at all three stages had a negative impact on fillet weight and total fatty acid daily loss. With few exceptions, saturated (SFA), monounsaturated (MUFA) and polyunsaturated fatty acids from n-6 series (n-6 PUFA) were preserved in fillet of fish at 17 °C, while higher daily losses of docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and consequently polyunsaturated from n-3 series (n-3 PUFA) were observed in these same fish and in smaller fish at 13 °C. The results presented in this study provide important information regarding the influence of fasting and temperature on chinook salmon performance and metabolism, providing basis for future nutritional and compositional studies for this important commercial species.

The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle.

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

Biogeochemical processes create distinct isotopic fingerprints to track floodplain rearing of juvenile salmon.

Floodplains represent critical nursery habitats for a variety of fish species due to their highly productive food webs, yet few tools exist to quantify the extent to which these habitats contribute to ecosystem-level production. Here we conducted a large-scale field experiment to characterize differences in food web composition and stable isotopes (δ¹³C, δ¹5N, δ³4S) for salmon rearing on a large floodplain and adjacent river in the Central Valley, California, USA. The study covered variable hydrologic conditions including flooding (1999, 2017), average (2016), and drought (2012-2015). In addition, we determined incorporation rates and tissue fractionation between prey and muscle from fish held in enclosed locations (experimental fields, cages) at weekly intervals. Finally, we measured δ³4S in otoliths to test if these archival biominerals could be used to reconstruct floodplain use. Floodplain-reared salmon had a different diet composition and lower δ13C and δ³4S (δ¹³C = -33.02±2.66‰, δ³4S = -3.47±2.28‰; mean±1SD) compared to fish in the adjacent river (δ¹³C = -28.37±1.84‰, δ³4S = +2.23±2.25‰). These isotopic differences between habitats persisted across years of extreme droughts and floods. Despite the different diet composition, δ¹5N values from prey items on the floodplain (δ¹5N = 7.19±1.22‰) and river (δ¹5N = 7.25±1.46‰) were similar, suggesting similar trophic levels. The food web differences in δ13C and δ³4S between habitats were also reflected in salmon muscle tissue, reaching equilibrium between 24-30 days (2014, δ¹³C = -30.74±0.73‰, δ³4S = -4.6±0.68‰; 2016, δ¹³C = -34.74 ±0.49‰, δ³4S = -5.18±0.46‰). δ³4S measured in sequential growth bands in otoliths recorded a weekly time-series of shifting diet inputs, with the outermost layers recording time spent on the floodplain (δ³4S = -5.60±0.16‰) and river (δ³4S = 3.73±0.98‰). Our results suggest that δ¹³C and δ³4S can be used to differentiate floodplain and river rearing habitats used by native fishes, such as Chinook Salmon, across different hydrologic conditions and tissues. Together these stable isotope analyses provide a toolset to quantify the role of floodplains as fish habitats.

Reconciling fish and farms: Methods for managing California rice fields as salmon habitat.

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the past century. Recently, through cooperative agreements with diverse stakeholders, winter-flooded agricultural rice fields in California's Central Valley have emerged as ecologically functioning floodplain rearing habitat for juvenile Chinook Salmon. From 2013 to 2016, we conducted a series of experiments examining methods to enhance habitat benefits for fall-run Chinook Salmon reared on winter-flooded rice fields in the Yolo Bypass, a modified floodplain managed for flood control, agriculture, and wildlife habitat in the Sacramento River Valley of California. Investigations included studying the effect of 1) post-harvest field substrate; 2) depth refugia; 3) duration of field drainage; and 4) duration of rearing occupancy on in-situ diet, growth and survival of juvenile salmon. Post-harvest substrate treatment had only a small effect on the lower trophic food web and an insignificant effect on growth rates or survival of rearing hatchery-origin, fall-run Chinook Salmon. Similarly, depth refugia, created by trenches dug to various depths, also had an insignificant effect on survival. Rapid field drainage yielded significantly higher survival compared to drainage methods drawn out over longer periods. A mortality of approximately one third was observed in the first week after fish were released in the floodplain. This initial mortality event was followed by high, stable survival rates for the remainder of the 6-week duration of floodplain rearing study. Across years, in-field survival ranged 7.4-61.6% and increased over the course of the experiments. Despite coinciding with the most extreme drought in California's recorded history, which elevated water temperatures and reduced the regional extent of adjacent flooded habitats which concentrated avian predators, the adaptive research framework enabled incremental improvements in design to increase survival. Zooplankton (fish food) in the winter-flooded rice fields were 53-150x more abundant than those sampled concurrently in the adjacent Sacramento River channel. Correspondingly, observed somatic growth rates of juvenile hatchery-sourced fall-run Chinook Salmon stocked in rice fields were two to five times greater than concurrently and previously observed growth rates in the adjacent Sacramento River. The abundance of food resources and exceptionally high growth rates observed during these experiments illustrate the potential benefits of using existing agricultural infrastructure to approximate the floodplain wetland physical conditions and hydrologic patterns (shallow, long-duration inundation of cool floodplain habitats in mid-winter) under which Chinook Salmon evolved and to which they are adapted.

Climate change threatens Chinook salmon throughout their life cycle.

Widespread declines in Atlantic and Pacific salmon (Salmo salar and Oncorhynchus spp.) have tracked recent climate changes, but managers still lack quantitative projections of the viability of any individual population in response to future climate change. To address this gap, we assembled a vast database of survival and other data for eight wild populations of threatened Chinook salmon (O. tshawytscha). For each population, we evaluated climate impacts at all life stages and modeled future trajectories forced by global climate model projections. Populations rapidly declined in response to increasing sea surface temperatures and other factors across diverse model assumptions and climate scenarios. Strong density dependence limited the number of salmon that survived early life stages, suggesting a potentially efficacious target for conservation effort. Other solutions require a better understanding of the factors that limit survival at sea. We conclude that dramatic increases in smolt survival are needed to overcome the negative impacts of climate change for this threatened species.

Can late stage marine mortality explain observed shifts in age structure of Chinook salmon?

Chinook salmon (Oncorhynchus tshawytscha) populations have experienced widespread declines in abundance and abrupt shifts toward younger and smaller adults returning to spawn in rivers. The causal agents underpinning these shifts are largely unknown. Here we investigate the potential role of late-stage marine mortality, defined as occurring after the first winter at sea, in driving this species' changing age structure. Simulations using a stage-based life cycle model that included additional mortality during after the first winter at sea better reflected observed changes in the age structure of a well-studied and representative population of Chinook salmon from the Yukon River drainage, compared with a model estimating environmentally-driven variation in age-specific survival alone. Although the specific agents of late-stage mortality are not known, our finding is consistent with work reporting predation by salmon sharks (Lamna ditropis) and marine mammals including killer whales (Orcinus orca). Taken as a whole, this work suggests that Pacific salmon mortality after the first winter at sea is likely to be higher than previously thought and highlights the need to investigate selective sources of mortality, such as predation, as major contributors to rapidly changing age structure of spawning adult Chinook salmon.

Absolute quantification of priority bacteria in aquaculture using digital PCR.

Modern aquaculture systems are designed for intensive rearing of fish or other species. Both land-based and offshore systems typically contain high loads of biomass and the water quality in these systems is of paramount importance for fish health and production. Microorganisms play a crucial role in removal of organic matter and nitrogen-recycling, production of toxic hydrogen sulfide (H2S), and can affect fish health directly if pathogenic for fish or exerting probiotic properties. Methods currently used in aquaculture for monitoring certain bacteria species numbers still have typically low precision, specificity, sensitivity and are time-consuming. Here, we demonstrate the use of Digital PCR as a powerful tool for absolute quantification of sulfate-reducing bacteria (SRB) and major pathogens in salmon aquaculture, Moritella viscosa, Yersinia ruckeri and Flavobacterium psychrophilum. In addition, an assay for quantification of Listeria monocytogenes, which is a human pathogen bacterium and relevant target associated with salmonid cultivation in recirculating systems and salmon processing, has been assessed. Sudden mass mortality incidents caused by H2S produced by SRB have become of major concern in closed aquaculture systems. An ultra-sensitive assay for quantification of SRB has been established using Desulfovibrio desulfuricans as reference strain. The use of TaqMan® probe technology allowed for the development of multi-plex assays capable of simultaneous quantification of these aquaculture priority bacteria. In single-plex assays, limit of detection was found to be at around 20 fg DNA for M. viscosa, Y. ruckeri and F. psychrophilum, and as low as 2 fg DNA for L. monocytogenes and D. desulfuricans.

Differential impacts of freshwater and marine covariates on wild and hatchery Chinook salmon marine survival.

Large-scale atmospheric conditions in the Northeast Pacific Ocean affect both the freshwater environment in the Columbia River Basin and marine conditions along the coasts of Oregon, Washington, and British Columbia, resulting in correlated conditions in the two environments. For migrating species, such as salmonids that move through multiple habitats, these correlations can amplify the impact of good or poor physical conditions on growth and survival, as movements among habitats may not alleviate effects of anomalous conditions. Unfortunately, identifying the mechanistic drivers of salmon survival in space and time is hindered by these cross-habitat correlations. To address this issue, we modeled the marine survival of Snake River spring/summer Chinook salmon with multiple indices of the marine environment and an explicit treatment of the effect of arrival timing from freshwater to the ocean, and found that both habitats contribute to marine survival rates. We show how this particular carryover effect of freshwater conditions on marine survival varies by year and rearing type (hatchery or wild), with a larger effect for wild fish. As environmental conditions change, incorporating effects from both freshwater and marine habitats into salmon survival models will become more important, and has the additional benefit of highlighting how management actions that affect arrival timing may improve marine survival.

Genetic Engineering of Livestock: The Opportunity Cost of Regulatory Delay.

Genetically engineered (GE) livestock were first reported in 1985, and yet only a single GE food animal, the fast-growing AquAdvantage salmon, has been commercialized. There are myriad interconnected reasons for the slow progress in this once-promising field, including technical issues, the structure of livestock industries, lack of public research funding and investment, regulatory obstacles, and concern about public opinion. This review focuses on GE livestock that have been produced and documents the difficulties that researchers and developers have encountered en route. Additionally, the costs associated with delayed commercialization of GE livestock were modeled using three case studies: GE mastitis-resistant dairy cattle, genome-edited porcine reproductive and respiratory syndrome virus-resistant pigs, and the AquAdvantage salmon. Delays of 5 or 10 years in the commercialization of GE livestock beyond the normative 10-year GE product evaluation period were associated with billions of dollars in opportunity costs and reduced global food security.

Can the creation of new freshwater habitat demographically offset losses of Pacific salmon from chronic anthropogenic mortality?

Over 1 billion USD are devoted annually to rehabilitating freshwater habitats to improve survival for the recovery of endangered salmon populations. Mitigation often requires the creation of new habitat (e.g. habitat offsetting) to compensate population losses from human activities, however offsetting schemes are rarely evaluated. Anadromous Pacific salmon are ecologically, culturally, and economically important in the US and Canada, and face numerous threats from degradation of freshwater habitats. Here we used a matrix population model of coho salmon (Oncorhynchus kisutch) to determine the amount of habitat offsetting needed to compensate mortality (2-20% per year) caused by a range of development activities. We simulated chronic mortality to three different life stages (egg, parr, smolt/adult), individually and simultaneously, to mimic impacts from development, and evaluated if the number of smolts produced from constructed side-channels demographically offset losses. We show that under ideal conditions, the typical size of a constructed side-channel in the Pacific Northwest (PNW) (3405 m2) is sufficient to compensate for only relatively low levels of chronic mortality to either the parr or smolt/adult stages (2-7% per year), but populations do not recover if mortality is >10% per year. When we assumed lower productivity (e.g.; 25th percentile), we found that constructed channels would need to be 2.5-4.5 fold larger as compared to the typical size built in the PNW, respectively, to maintain population sizes. Moreover, when we imposed mortality to parr and smolt/adult stages simultaneously, we found that constructed side-channels would need to be between 1.8- and 2.3- fold larger that if the extra chronic mortality was imposed to one life stage only. We conclude that habitat offsetting has the potential to mitigate chronic mortality to early life stages, but that realistic assumptions about productivity of constructed side-channels and cumulative effects of anthropogenic disturbances on multiple life stages need to be considered.

Recent declines in salmon body size impact ecosystems and fisheries.

Declines in animal body sizes are widely reported and likely impact ecological interactions and ecosystem services. For harvested species subject to multiple stressors, limited understanding of the causes and consequences of size declines impedes prediction, prevention, and mitigation. We highlight widespread declines in Pacific salmon size based on 60 years of measurements from 12.5 million fish across Alaska, the last largely pristine North American salmon-producing region. Declines in salmon size, primarily resulting from shifting age structure, are associated with climate and competition at sea. Compared to salmon maturing before 1990, the reduced size of adult salmon after 2010 has potentially resulted in substantial losses to ecosystems and people; for Chinook salmon we estimated average per-fish reductions in egg production (-16%), nutrient transport (-28%), fisheries value (-21%), and meals for rural people (-26%). Downsizing of organisms is a global concern, and current trends may pose substantial risks for nature and people.

Use of a mechanistic growth model in evaluating post-restoration habitat quality for juvenile salmonids.

Individual growth data are useful in assessing relative habitat quality, but this approach is less common when evaluating the efficacy of habitat restoration. Furthermore, available models describing growth are infrequently combined with computational approaches capable of handling large data sets. We apply a mechanistic model to evaluate whether selection of restored habitat can affect individual growth. We used mark-recapture to collect size and growth data on sub-yearling Chinook salmon and steelhead in restored and unrestored habitat in five sampling years (2009, 2010, 2012, 2013, 2016). Modeling strategies differed for the two species: For Chinook, we compared growth patterns of individuals recaptured in restored habitat over 15-60 d with those not recaptured regardless of initial habitat at marking. For steelhead, we had enough recaptured fish in each habitat type to use the model to directly compare habitats. The model generated spatially explicit growth parameters describing size of fish over the growing season in restored vs. unrestored habitat. Model parameters showed benefits of restoration for both species, but that varied by year and time of season, consistent with known patterns of habitat partitioning among them. The model was also supported by direct measurement of growth rates in steelhead and by known patterns of spatio-temporal partitioning of habitat between these two species. Model parameters described not only the rate of growth, but the timing of size increases, and is spatially explicit, accounting for habitat differences, making it widely applicable across taxa. The model usually supported data on density differences among habitat types in Chinook, but only in a couple of cases in steelhead. Modeling growth can thus prevent overconfidence in distributional data, which are commonly used as the metric of restoration success.

Enhanced marine monitoring and toxicity study of oil spill dispersants including Corexit EC9500A in the presence of diluted bitumen.

Observations made for the analysis of the oil spill dispersant tracer dioctyl sulfosuccinate (DOSS) during LC50 toxicity testing, highlighted a stability issue for this tracer compound in seawater. A liquid chromatography high-resolution quadrupole time-of-flight mass spectrometry (LC/QToF) was used to confirm monooctyl sulfosuccinate (MOSS) as the only significant DOSS breakdown product, and not the related isomer, 4-(2-ethylhexyl) 2-sulfobutanedioate. Combined analysis of DOSS and MOSS was shown to be applicable to monitoring of spill dispersants Corexit® EC9500A, Finasol OSR52, Slickgone NS, and Slickgone EW. The unassisted conversion of DOSS to MOSS occurred in all four oil spill dispersants solubilized in seawater, although differences were noted in the rate of MOSS formation. A marine microcosm study of Corexit EC9500A, the formulation most rapid to form MOSS, provided further evidence of the stoichiometric conversion of DOSS to MOSS under conditions relevant to real world dilbit spill. Results supported combined DOSS and MOSS analysis for the monitoring of spill dispersant in a marine environment, with a significant extension of sample collection time by 10 days or longer in cooler conditions. Implications of the unassisted formation of MOSS and combined DOSS:MOSS analysis are discussed in relation to improving dispersant LC50 toxicity studies.

Multiscale modelling of cage effects on the transport of effluents from open aquaculture systems.

Most Atlantic salmon mariculture operations use open sea cages for the grow out phase. The ultimate fate and effects of the effluents and the possibilities of disease transfer between fish farms are major concerns for farmers, governance and the general public alike. Numerical model systems applied to studying and managing effluents and disease transfer in mariculture must realistically resolve the hydrodynamics in the vicinity of the fish farms. In the present study, the effects of the aquaculture structures on the current patterns were introduced in the ocean model system SINMOD. The drag parameters for the ocean model were determined by comparing the simulation results from the ANSYS Fluent ® software suite and SINMOD in an idealized channel setting with uniform currents. The model was run for a number of realistic scenarios in high horizontal resolution (∼30 m) with sea cages influencing the flow field. Comparisons between extensive current measurements and the simulation results showed that the model system reproduced the current local current field well. By running simulation scenarios with and without the effects of the sea cages on the flow field, it was possible to assess the importance of such effects for numerical dispersal models and aquaculture environment interactions simulations and hence for assessment of environmental impacts.

Effects of exposing shrimp larvae (Pandalus borealis) to aquaculture pesticides at field relevant concentrations, with and without food limitation.

Anti-parasitic drugs used in the aquaculture industry are discharged to the sea after treatment of salmon. In this study, the effects of azamethiphos (AZA) in the Salmosan® formulation and deltamethrin (DEL) in the Alpha Max® formulation, have been assessed in Northern shrimp larvae (Pandalus borealis) when administered both separately and in combination. The exposure concentrations were 100 ng/L for AZA and 2 ng/L for DEL, each representing a 1000-fold dilution of the prescribed concentrations for salmon. These two chemicals were combined at these concentrations to give a third treatment (AZA + DEL). When larvae were exposed for two hours on the first, second and third days post hatch (dph), significantly increased mortality and reduced swimming activity were observed for larvae from the DEL and combined AZA + DEL treatments 4 dph, though not in larvae from the AZA treatment. A single pulse exposure, delivered on the first day post hatch, caused similar effects on mortality and swimming activity 4 dph as the three-pulse exposure. Mortality was driven by the presence of DEL in both experiments, with no amplification or reduction of effects observed when DEL and AZA were combined. Larvae were observed for 13 days following the single pulse exposure, with food limitation introduced as an additional stressor on day 4. In the DEL and AZA + DEL treatments mortality continued to increase regardless of food level, with no larvae completing development to stage II. The overriding toxicity of DEL masked any potential effects the reduced food ration may have exerted. Swimming activity was lower for AZA treated larvae than Control larvae 13 dph, when both groups were fed daily, though no other significant changes to mortality, development to stage II, feeding rate or gene expression were observed. Food limited Control and AZA larvae had lower swimming activity and feeding rate than daily fed Control larvae, with expression of pyruvate kinase and myosin genes also downregulated. However, there was no negative effect on survival or successful development to stage II in these treatments. In addition, mesencephalic astrocyte-derived neurotropic factor was downregulated in food limited Control larvae when compared with the daily fed Controls. Results from this study together with reported estimates of dispersion plume concentrations of discharged pesticides indicate that toxic concentrations of deltamethrin could reach shrimp larvae several kilometers from a treated salmon farm.

Loci associated with variation in gene expression and growth in juvenile salmon are influenced by the presence of a growth hormone transgene.

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 (NTLarge, NTSmall, TLarge and TSmall) 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_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.

Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon.

Genomic approaches permit direct estimation of inbreeding and its effect on fitness. We used genomic-based estimates of inbreeding to investigate their relationship with eight adult traits in a captive-reared Pacific salmonid that is released into the wild. Estimates were also used to determine whether alternative broodstock management approaches reduced risks of inbreeding. Specifically, 1,100 unlinked restriction-site associated (RAD) loci were used to compare pairwise relatedness, derived from a relationship matrix, and individual inbreeding, estimated by comparing observed and expected homozygosity, across four generations in two hatchery lines of Chinook salmon that were derived from the same source. The lines are managed as "integrated" with the founding wild stock, with ongoing gene flow, and as "segregated" with no gene flow. While relatedness and inbreeding increased in the first generation of both lines, possibly due to population subdivision caused by hatchery initiation, the integrated line had significantly lower levels in some subsequent generations (relatedness: F2 -F4 ; inbreeding F2 ). Generally, inbreeding was similar between the lines despite large differences in effective numbers of breeders. Inbreeding did not affect fecundity, reproductive effort, return timing, fork length, weight, condition factor, and daily growth coefficient. However, it delayed spawn timing by 1.75 days per one standard deviation increase in F (~0.16). The results indicate that integrated management may reduce inbreeding but also suggest that it is relatively low in a small, segregated hatchery population that maximized number of breeders. Our findings demonstrate the utility of genomics to monitor inbreeding under alternative management strategies in captive breeding programs.

Physiological disturbances in juvenile sockeye salmon (Oncorhynchus nerka) exposed to the water-soluble fraction of diluted bitumen.

Current and proposed transcontinental pipelines for the transport of diluted bitumen (dilbit) from the Canadian oil sands traverse the coastal watersheds of British Columbia, habitat essential to Pacific salmonids. To determine the potential risks posed to these keystone species, juvenile sockeye (Oncorhynchus nerka; 1+ parr) were acutely (24-96 h) or subchronically (21-42 d) exposed to 4 concentrations of the water-soluble fraction (WSF) of unweathered Cold Lake Blend dilbit (initial total PAC concentrations: 0, 13.7, 34.7 and 124.5 µg/L) in a flow-through system. Dilbit effects on iono-osmoregulation, the physiological stress response, and the immune system were assessed by both biochemical and functional assays. Hydrocarbon bioavailability was evidenced by a significant induction of liver ethoxyresorufin-O-deethylase (EROD) activity in exposed fish. Acute and subchronic exposure significantly reduced gill Na+-K+-ATPase activity and resulted in lower plasma osmolality, Cl-, and Na+ concentrations. Acute exposure to dilbit resulted in a classic physiological stress response, however at 21 d of exposure, plasma cortisol remained elevated while other measured parameters had returned to baseline values. A compromised immune system was demonstrated by a 29.5 % higher mortality in fish challenged with Vibrio (Listonella) anguillarum following dilbit exposure compared to unexposed controls. Exposure of juvenile salmonids to the WSF of dilbit (at TPAC concentrations at the ppb level) resulted in sublethal effects that included a classic physiological stress response, and alterations in iono-osmoregulatory homeostasis and immunological performance.