Canadian Aquaculture R&D Review 2015

Finfish: Salmon

INNOVATION THROUGH COLLABORATION: RECOVERING AN ENDANGERED POPULATION OF ATLANTIC SALMON THROUGH PARTNERSHIP WITH ATLANTIC CANADA’S AQUACULTURE INDUSTRY

The development of a ‘conservation sea cage’ rearing strategy for wild salmon has the potential to return adults to their native rivers in numbers rivalling historic highs, provided sufficient smolts can be collected. This model could then boost not only salmon demographics, but aquatic ecosystem processes which are currently limited by a lack of diadromous fish populations. This project is an important demonstration of collaborative species recovery involving government, non-government, industry, academic and First Nation partners.

Building on the success of a pilot project in 2009–2012, an innovative yet practical rearing strategy has been implemented to boost endangered inner Bay of Fundy (iBoF) Atlantic salmon populations in two native rivers. Inner Bay of Fundy salmon smolts are collected from the wild by Parks Canada and Fort Folly First Nation and are transported to specially designed ‘conservation sea cages’ maintained by Cooke Aquaculture, with support from the Atlantic Canada Fish Farmers Association. Prior to stocking, wild smolts undergo rigorous health testing in a closed containment, salt water rearing facility at Huntsman Marine Science Centre. Three important benefits of conservation sea cage rearing are expected: (1) post-smolts will mature in a semi-natural environment in the Bay of Fundy; (2) significant numbers of adults can be produced for release back to native rivers to spawn; and (3) by reproducing in the wild, these adults will produce progeny that are free of captive exposure and associated domestication effects. Annual iterations of this program are hoped to contribute to wild population fitness through increasing generations of wild-produced smolts.

Mar. 2014–Mar. 2019

Funded By: Government of Canada, National Conservation Plan funding Co-Funded By: All collaborators providing in-kind contributions.

Project Lead: Corey Clarke (Parks Canada)

Project Team: Betty House (ACFFA); Tom Taylor (Cooke Aquaculture); Chris Bridger (Huntsman Marine Science Centre); Michael Beattie (NB – Agriculture and Aquaculture); Tim Robinson (Fort Folly First Nations); John Whitelaw (DFO)

Collaborators: Atlantic Canada Fish Farmers Association; Cooke Aquaculture; Fisheries and Oceans Canada (DFO); Fort Folly First Nation; Huntsman Marine Science Centre; New Brunswick Department of Agriculture and Aquaculture

Contact: Corey.Clarke@pc.gc.ca

Stocking the conservation sea cages with wild inner Bay of Fundy Atlantic Salmon smolts. Photo: Parks Canada

ATLANTIC SALMON SELECTION AND BROODSTOCK DEVELOPMENT PROGRAM FOR USE IN COMMERCIAL SALTWATER AQUACULTURE PRODUCTION ON THE EAST COAST OF CANADA

The overall goal of the Atlantic Salmon Performance Selection and Broodstock Development Program is to assess genetic variability of commercially relevant traits and improve commercial productivity.

Atlantic Salmon individuals and families with superior attributes for commercially important traits are selected to establish a pedigreed line. Up to 86 families are created each year using a partial factorial mating design to create half-sibling links between families. The partial factorial design also helps to maximize genetic variation. Half-sibling genetic links are necessary to assess the amount of variability in measured traits and the effects of genetics versus environment. Individual salmon from known families are PIT tagged to create a communally reared breeding nucleus as well as to conduct short-term challenges. Individuals from the same families are also reared in commercial sea cages to complete harvest assessments. To date, 300 families have been created and PIT tagged from four year classes. Genetic variation and heritability are assessed for all traits of interest prior to individual and family selection to create the next generational year class using a Total Merit Index. For instance, total body weight (growth) was assessed for 41,918 individuals from two year classes, 132 families, 67 sires and 77 dams which resulted in an estimated heritability of 0.27 at 2.5 years. This is within the range of published heritabilities for Atlantic Salmon from different geographic locations.

Oct. 2010–Sep. 2015

Funded By: Atlantic Canada Opportunities Agency – Atlantic Innovation Fund (ACOA – AIF) Co-Funded By: New Brunswick Innovation Foundation; Northern Harvest Sea Farms; Huntsman Marine Science Centre

Project Lead: Amber Garber (Huntsman Marine Science Centre)

Project Team: Susan Hodkinson, Chris Bridger (Huntsman Marine Science Centre); Jane Tosh (U Guelph); Aaron Craig, Robin Muzzerall (Northern Harvest Sea Farms)

Contact: agarber@huntsmanmarine.ca

www.huntsmanmarine.ca

EFFECTS OF FEEDING HIGH PLANT PROTEIN DIET ON GROWTH AND NUTRIENTS UTILIZATION OF GROWTH-HORMONE TRANSGENIC DIPLOID AND TRIPLOID ATLANTIC SALMON (SALMO SALAR L.)

Previous studies have shown that transgenic (TG) Atlantic Salmon (Salmo salar L.) grew significantly faster and consumed less feed than non-transgenics (NTG). Moreover, the limited supply of fishmeal (FM) and fish oil from wild fisheries highlights concerns for the sustainable and responsible development of aquaculture production. The goal of this project was to assess the ability of juvenile diploid (2N) and triploid (3N) TG, and NTG Atlantic Salmon to use high plant protein (PP) diets. Triplicate groups of 2N/NTG, 3N/NTG, 2N/TG and 3N/TG salmon (30 g) were reared in freshwater and fed two isoproteic, isolipidic, and isoenergetic diets containing either high PP (68% PP) or high FM (36% PP) until achieving 400% growth. At the end of the experiment, TG salmon exhibited increased growth rates regardless of ploidy and diet compared with the NTG salmon. Food conversion ratio was reduced in TG (20-25% less) due to improved protein gain and retention efficiencies compared to the NTG. Protein, lipid, and energy digestibility was high for all the groups when compared to the reported values. Likewise, TG and NTG final body composition was similar to the values reported for the same size. More emphasis is currently placed on the optimization of cost effective feeds for triploid transgenic Atlantic Salmon.

The results of the present study indicate that 2N TG and 3N/TG Atlantic Salmon have the ability to maintain accelerated growth even when fed a high plant protein diet (68%), which may have important benefits for the optimization of production of transgenic Atlantic Salmon.

May 2012–May 2013

Funded By: Atlantic Canada Opportunities Agency-Atlantic Innovation Fund (ACOA – AIF)

Project Lead: Rachid Ganga (CATC)

Project Team: Debbie Plouffe (CATC); Dawn Runighan (AquaBounty Technologies); John Buchanan (CAT)

Collaborators: Santosh Lall, Sean Tibbetts, Cheryl Wall (NRC)

Contact: rganga@aquatechcenter.com

THE EFFECT OF OPERCULAR DEFORMITY ON FISH WELFARE AND AEROBIC CAPACITY

Culling fish represents an economic loss, so anything that can be done to minimize the number of fish culled will help to sustain the industry. This research will also determine whether opercular deformities affect fish welfare.

As part of routine stock management, salmon farmers selectively cull fish with visible deformities in spite of there being, often, no clear evidence that these fish fail to thrive under controlled aquaculture conditions. For instance, fish with short opercula (i.e., gill covers), which are easily spotted because of their visible gills, often appear to be in good condition otherwise, based both on their size and weight-to-length ratio. Culling such fish may represent a needless economic loss. Fish with short opercula lack the opercular flaps necessary for maintaining unidirectional water flow across their gills, and therefore have diminished oxygen extraction efficiency and, by extension, reduced aerobic capacity. Although this would be a concern for wild fish with respect to activities such as migration, prey capture and predator avoidance, it is unclear whether it matters to farmed salmon. The objectives of this project are therefore: (1) to follow tagged juvenile Atlantic salmon with varying degrees of opercular shortening through time to see how this affects their survival and growth; (2) to assess the aerobic capacity of these same fish using standard physiological tests; and (3) to determine how genetics (family effects) influence these measured variables.

Jul. 2014–Dec. 2014

Funded By: Natural Sciences and Engineering Research Council (NSERC) Partnerships Program – Engage Grant

Project Lead: Tillmann Benfey (UNB)

Project Team: Tillmann Benfey, Krista Latimer (UNB); Amber Garber, Chris Bridger, Anne McCarthy (HMSC); Aaron Craig (NHSF)

Collaborators: Huntsman Marine Science Centre; Northern Harvest Sea Farms Inc.

Contact: Benfey@unb.ca

Juvenile salmon with complete operculum (left) and short operculum with exposed gill filaments (right). Photo: Tillmann Benfey (UNB)

ANALYSIS OF THE INCIDENCE OF ATLANTIC SALMON DEFORMITIES IN PRODUCTION – ENVIRONMENTAL OR GENETICS?

Discerning the effects of environmental and genetic factors on the occurrence and prevalence of deformities in Atlantic Salmon production will inform commercial producers of relevant factors under their production control and the importance of appropriate individual and family selection within broodstock programs. Reducing deformities in production stocks will improve fish welfare and decrease downgrades at harvest.

Various deformities/abnormalities are often evident in Atlantic Salmon commercial production. The occurrence and prevalence of many of these deformities are often believed to be the result of environmental conditions but the influence of genetics is not well understood. This project standardizes early rearing environmental effects between family specific combi tanks and recirculation systems – density, feeding, temperature, saturated oxygen, mg per liter of oxygen, pH, CO2, alkalinity, total ammonia, nitrite/nitrate, and total gas pressure. A random group of progeny is assessed for type and prevalence of various deformities within each family when individuals are a 5 g minimum size. Skeletal deformities assessed include: short opercula, abnormal jaw or head, and spinal curvature. Irregularities associated with eye issues, missing fins, short fins, and eroded fins are also recorded. All recorded information (including normality) is noted and included in the analysis to determine whether occurrence prevalence can be attributed to environmental effects such as tank density or other factors. Nearly 94,000 Atlantic Salmon from 300 families over four year classes have been assessed to date to determine the effects of various environmental and genetic factors on variability and heritability in the prevalence of a specific deformity or combinations of deformities.

Oct. 2010–Sep. 2015

Funded By: Atlantic Canada Opportunities Agency – Atlantic Innovation Fund (ACOA – AIF) Co-Funded By: New Brunswick Innovation Foundation; Northern Harvest Sea Farms; Huntsman Marine Science Centre

Project Lead: Amber Garber (Huntsman Marine Science Centre)

Project Team: Susan Hodkinson, Chris Bridger (Huntsman Marine Science Centre); Jane Tosh (U Guelph); Aaron Craig, Robin Muzzerall (Northern Harvest Sea Farms)

Contact: agarber@huntsmanmarine.ca

www.huntsmanmarine.ca

DETERMINATION OF THE POTENTIAL SPATIAL OVERLAP AND INTERACTION BETWEEN COMMERCIAL FISHERIES (AMERICAN LOBSTER, SNOW CRAB) AND FINFISH AQUACULTURE ACTIVITIES IN CONNAIGRE BAY, NEWFOUNDLAND

The outcomes of this project will provide valuable information that will inform future site development initiatives and contribute to the sustainability of the fishing and aquaculture industries on the south coast of Newfoundland and Labrador.

There is rarely an opportunity to collect and compare ecological data before, during, and after a salmon farming site has been approved and under production. This four year project will allow for the collection of environmental and biological data at two newly approved salmon aquaculture sites in Connaigre Bay, Newfoundland and Labrador – a bay that has not yet held salmon production sites. Pertinent data will be collected prior to the sites being established and during the full production cycle, as well as during the fallow period. In the siting area, there is particular concern for alterations to crab and lobster habitat and resulting changes in habitat utilization. As a result, this research will also examine potential changes in the benthic environment that could potentially impact lobster and snow crab populations. The ultimate goal of the research project will be to identify any measurable impacts caused by the introduction of fish farming on the commercial species currently harvested in Connaigre Bay.

Apr. 2012–Jun. 2017

Funded By: DFO – Aquaculture Collaborative Research and Development Program (DFO – ACRDP) Co-Funded By: Fish, Food and Allied Workers (FFAW); Cold Ocean Salmon Inc.

Project Lead: Dounia Hamoutene, Pierre Goulet (DFO)

Collaborators: Cold Ocean Salmon Inc.; Fish, Food and Allied Workers (FFAW)

Contact: Dounia.Hamoutene@dfo-mpo.gc.ca, Pierre.Goulet@dfo-mpo.gc.ca

www.dfo-mpo.gc.ca/aquaculture/acrdp-pcrda/index-eng.htm

REDUCTION OF AMMONIA AND SOLIDS FROM CHINOOK SALMON CULTURE FACILITIES

Metabolic processes in farmed fish, as with all animals, produce wastes. Some of these are nitrogenous, principally ammonia, and they are released into the environment. Increases in nitrogen can occur with a decrease in the efficiency with which feed is utilized by the fish for growth and maintenance. The release of nitrogenous wastes into the environment can have implications for both the ecosystem and for the fish farming facility from which it is being released. Excess nitrogen release represents a potential economic loss in that it is an indication that feed is not being fully utilized by the cultured fish. The excess release can also result in regulatory consequences for culture facilities. Regulators and industry alike are looking for best practices to help reduce the greater levels of these compounds that can be found near farm sites.

This project will explore how feed regimes designed to stimulate compensatory growth may be used to reduce nitrogen excretion into the environment during Chinook Salmon production. Adequately exploiting compensatory growth using alternating periods of feed deprivation and re-feeding has the potential to reduce the excretion of nitrogenous wastes from the fish in culture facilities into the environment while increasing better feed utilization by the cultured fish. This research will help improve the ecological sustainability of Chinook Salmon reared in seawater and may be applicable to the culture of all salmon species.

Apr. 2012–Sept. 2015

Funded By: DFO – Aquaculture Collaborative Research and Development Program (DFO – ACRDP) Co-Funded By: Agrimarine Industries Inc.

Project Lead: Ian Forster (DFO)

Collaborators: Agrimarine Industries Inc.

Contact: Ian.Forster@dfo-mpo.gc.ca

www.dfo-mpo.gc.ca/aquaculture/acrdp-pcrda/index-eng.htm

DEVELOPMENT OF HIGH PERFORMANCE CHINOOK SALMON STOCKS FOR COMMERCIAL AQUACULTURE: GENETIC HYBRIDIZATION TO MAXIMIZE CULTURE EFFICIENCY AND MINIMIZE ENVIRONMENTAL IMPACT

The optimized commercial hybrid stocks, calibrated for variation in rearing conditions, will be marketed domestically and internationally, supporting the economic and environmental development of Canada’s large and growing aquaculture. The research will also address important questions in the conservation of salmonids.

Salmon farming is one of Canada’s growing industries and is extremely valuable. However, salmon farming must balance production economics with environmental impacts. Farmed Chinook Salmon are a valuable niche market with substantial growth potential, coupled with lower perceived environmental concerns (being a native species); however, their performance has not been systematically assessed. We are developing a performance-enhanced hybrid Chinook salmon stock with higher survival and growth and reduced feed costs. The new stock will use less wild-sourced lipid and protein for feed and minimize drug and chemical use for disease control, thereby minimizing the environmental footprint. The project will generate data on Chinook Salmon production stocks that will serve to improve salmon farming efficiency, which will help make Canada a global leader in Pacific salmon farming. Performance is being measured in offspring from crosses between inbred farmed and wild stocks. These offspring are expected to exhibit hybrid vigour, analogous to hybrid corn lines. We are examining molecular, physiological, and behavioural aspects of growth, survival, and flesh quality.

Oct. 2013–Oct. 2016

Funded By: Natural Sciences and Engineering Council of Canada (NSERC)

Project Lead: Daniel Heath (U Windsor)

Project Team: Trevor Pitcher, Christina Semeniuk, Oliver Love, Dennis Higgs (U Windsor); Bryan Neff (Western U); Brian Dixon (U Waterloo)

Collaborators: Yellow Island Aquaculture Ltd.

Contact: dheath@uwindsor.ca

Yellow Island Aquaculture Ltd. net pens near Quadra Island, British Columbia. Photo: Trevor Pitcher (U Windsor)

DETECTING HYBRIDIZATION AMONG WILD AND FARMED ESCAPED ATLANTIC SALMON IN SOUTHERN NEWFOUNDLAND: FIELD COLLECTIONS

The monetary value of aquaculture production has now surpassed the total value of wild fisheries. Balancing the rapid industry expansion with environmental sustainability remains a challenge, with impacts for both wild populations and industry production. Aquaculture escapees represent a continued threat to the genetic integrity of wild populations, and have been shown to interbreed with wild fish, eroding local adaptation. In southern Newfoundland, wild Atlantic Salmon populations remain at record lows and are considered threatened by COSEWIC. Potential impacts associated with the developing aquaculture industry cannot be ruled out as contributing factor. The aim of the present study is to collect young of the year Atlantic Salmon following a large (>20,000 individuals) escape event in 2013 in southern Newfoundland. This escape event was equal to or greater than the estimate of wild salmon abundance in the region. Given the magnitude of this release event, and reports of mature escapees in freshwater, these samples are expected to contain a mixture of wild and hybrid individuals. Future genomic screening of these samples will be used to quantify the rates of successful hybridization and evaluate the potential genetic impact of aquaculture escapees on wild populations in Newfoundland and Labrador.

Aug. 2014–Sep. 2014

Funded By: DFO – Program for Aquaculture Regulatory Research (DFO – PARR)

Project Lead: Ian Bradbury (DFO)

Project Team: Lorraine Hamilton, Geoff Perry, Martha Roberston (DFO)

Contact: Ian.Bradbury@dfo-mpo.gc.ca

THERMAL AND pH TOLERANCE OF FARMED, WILD, AND FIRST GENERATION FARMED-WILD HYBRID SALMON

The results of this research will help to provide information on the potential impact of farmed escapees on wild stocks.

In Newfoundland and Labrador (NL), all farmed Atlantic Salmon (Salmo salar) originate from the Saint John River strain (New Brunswick). It is believed that wild stocks have developed adaptations to the local environment therefore the vulnerability of these local, genetically distinct stocks to farmed escapees through interbreeding is a concern. Farmed salmon escapees may share breeding grounds with wild counterparts, potentially interbreed and produce hybrids which might be poorly suited to survive in the wild. This in turn could impact the overall fitness and survival of the local wild salmon stocks. Studies on interactions between wild and farmed salmon have shown that this issue is area-specific and therefore these interactions need to be further explored within Newfoundland and Labrador.

This project will examine the effect of genetic origin on the environmental tolerance and fitness of wild, farmed, and first generation hybrid (F1 farmed-wild crosses) juvenile salmon when exposed to low pH and low seawater temperatures. This will clarify the ability of these fish (in particular the F1 hybrids) to survive under local environmental conditions (i.e., reduced pH level of river waters and low spring seawater temperatures) occurring in Newfoundland and Labrador.

Apr. 2014–Mar. 2015

Funded By: DFO – Aquaculture Collaborative Research and Development Program (DFO – ACRDP) Co-Funded By: Cold Ocean Salmon; Northern Harvest Sea Farms NL Ltd.

Project Lead: Dounia Hamoutene (DFO)

Project Team: Lynn Lush, Kimberely Burt (DFO); Julia Bungay (Cold Ocean Salmon); Jennifer Caines (Northern Harvest Sea Farms NL Ltd.)

Collaborators: Cold Ocean Salmon; Northern Harvest Sea Farms NL Ltd.

Contact: Dounia.Hamoutene@dfo-mpo.gc.ca

www.dfo-mpo.gc.ca/aquaculture/acrdp-pcrda/index-eng.htm

INVESTIGATION OF FARM-ORIGIN ESCAPED ATLANTIC SALMON IN NEWFOUNDLAND

Information collected in this project will aid in management of escapes from Atlantic Salmon aquaculture and inform methods for removal of escapes and minimizing impacts on wild Atlantic Salmon and other species.

Atlantic Salmon aquaculture production has grown steadily in Newfoundland and Labrador in the past decade from aproximately 3000 tonnes in 2001 to 22,196 tonnes in 2013. Concerns about genetic and ecological effects of escaped fish on wild populations of Atlantic Salmon and other species exist but little local empirical information is available. DFO is managing experimental fisheries for farm- origin escaped fish, collecting biological characteristics samples, and actively responding to reports of observations of suspected escaped farm-origin salmon in inland and coastal waters of the South Coast. Information on distribution, feeding, survival, life history stage, reproductive status, and cataloguing of gross morphological characteristics is being collected to aid in the development of an identification guide to accurately discriminate farmed and wild origin salmon and to guide escape incident response and recovery efforts to minimize potential environmental effects.

Oct. 2013–Ongoing

Funded By: Fisheries and Oceans Canada (DFO)

Project Lead: Chris Hendry (DFO)

Project Team: Geoff Perry, Ellen Careen, Carole Grant, Ian Bradbury (DFO)

Contact: Chris.Hendry@dfo-mpo.gc.ca

Escaped farmed Atlantic Salmon captured in Garnish River, Newfoundland, in May, 2013. It is being sampled for biological characteristics and subsequent scale and genetic analysis. Photo: Chris Hendry (DFO)

DEVELOPMENT OF A LOW DENSITY SNP ARRAY FOR PARENTAGE ASSIGNMENT IN ATLANTIC SALMON

The Centre for Aquaculture Technologies Canada (CATC) was established in 2012, with a focus on the use of advanced technologies to improve aquaculture productivity. Recognizing the need for rapid and cost-effective parentage assignment in fish, CATC endeavored to develop a low-density panel of 96 single nucleotide polymorphisms (SNPs) to assign parentage in Atlantic Salmon. The benefits of using the CATC low density SNP genotyping platform include adaptability for high-througput analysis, flexibility, and user specificity at a relatively low cost per sample.

SNP loci previously identified for Atlantic Salmon and two SNPs intended to detect the presence of the male-specific gene conserved amongst salmonids were selected for the array. Results of the validation work including more than 2500 full half sibilings from 57 families showed that a minimum of 69 SNPs could be used to determine parentage and genetic sex with 99% accuracy. The additional space on the array can be used for user-specific markers.

The use of a low density SNP array allows cost-effective, automated, genotyping of Atlantic Salmon for support of selective breeding programs, tracability, and management of wild populations. Most importantly, the relatively low cost encourages end users to apply the results of decades of salmon genomics research.

CATC is now offering this SNP genotyping service to other Atlantic Salmon producers and breeders. Now that the SNP panel has been tested and validated, the same technology can be applied to stock assessment, traceability, and monitoring of wild populations.

Oct. 2013–Feb. 2014

Funded By: PEI Aquaculture and Fisheries Research Initiative Inc. Co-Funded By: Natural Sciences and Engineering Research Council (NSERC) Industrial Post-Doctoral Award

Project Lead: Debbie Plouffe (CATC)

Project Team: Marcia Chiasson (CATC); America Fujimoto, Jason Stannard, John Buchanan (Center for Aquaculture Technologies)

Contact: dplouffe@aquatechcenter.com

aquatechcenter.com

Eyed eggs. Photo: Valerie Barbosa

Center for Aquaculture Tecnologies Canada (CATC) staff. Photo: Berni Wood Photography

DEVELOPMENT OF QUANTITATIVE HISTOLOGICAL METHODS FOR UNDERSTANDING THE BONE METABOLISM OF FISH AND PREVENTING THE OCCURRENCE OF VERTEBRAL ANOMALIES IN FARMED SALMONIDS

The goal of our work is to contribute to the formulation of new low-phosphorus feeds and to provide preliminary tools to facilitate the selection of superior-performing, less polluting trout strains.

The occurrence of vertebral anomalies linked to nutritional deficiencies in intensive salmonid culture has negative impacts, both on production yield and on fish health and well-being. The early signs of chronic phosphorus deficiency in the Rainbow Trout include the development of small, widely spaced or biconcave vertebrae. Development of new quantitative histological methods (see figure) for analyzing the morphology, mineralization, and structure of various vertebral tissues may assist in differentiating certain bone mechanisms based on the nature of the anomaly observed. In individuals developing spaced vertebrae, production of nonmineralized (osteoid) matrix apparently continues during a deficiency episode, allowing the vertebrae to become mineralized after the situation returns to normal. In individuals with biconcave vertebrae, which tend to evolve into more severe anomalies (compressed vertebrae), bone mineralization appears instead to continue to the detriment of other bone remodelling mechanisms. Based on these outcomes, some individuals may have a better strategy for coping with phosphorus-deficiency episodes. If these various phenotypes could be correlated with specific genotypes, our results could lead to the identification of selection criteria for fish strains that are less inclined to develop skeletal anomalies.

Sep. 2010–Aug. 2014

Funded By: Ministère du Développement économique, de l’Innovation et de l’Exportation – Programme de soutien à des initiatives internationales de recherche et d’innovation (PSIIRI) Co-Funded By: DFO – Aquaculture Collaborative Research and Development Program (DFO – ACRDP); Société de recherche et de développement en aquaculture continentale Inc. (SORDAC); Ressources Aquatiques Québec (RAQ) – Programme de bourse FONCER; Université Laval – Programme de bourse du Bureau International

Project Lead: Grant Vandenberg (U Laval)

Project Team: Marie-Hélène Deschamps, Jérémy Le Luyer, Noémie Poirier Stewart, Émilie Proulx (U Laval)

Collaborators: Nadia Aubin-Horth, Claude Robert, Arnaud Droit (U Laval); Dominique Bureau (U Guelph); Ann Huysseune, Eckhard Witten (Universiteit Gent); Jean-Yves Sire (U Paris 6); Chantal Cahu, Dominique Mazurais (IFREMER); Kenneth Overturf, Ron Hardy (U Idaho); Tom Hansen, Anna Wargelius, P.E. Fjelldal (Havforskningsinstituttet)

Contact: Grant.Vandenberg@fsaa.ulaval.ca

Schematic depiction of image analysis techniques developed in the laboratory for measuring the mineralization of basalia and the trabecular bone based on Sirius red-stained longitudinal sections (200x) of trout vertebrae. Photo: Marie-Hélène Deschamps (U Laval)

REPRODUCTION TRIALS BETWEEN WILD AND FARMED SALMON

The Atlantic Salmon currently farmed on the south coast of Newfoundland and Labrador originate from the Saint John River, New Brunswick, strain fish. The introduction of this non-native strain of the species had raised the question of the potential impact that escapes of these cultured fish might have on wild stocks. This study aimed to determine the potential mating success between mature farmed fish and wild fish from local Newfoundland river stocks by performing artificial crosses between the two groups.

Wild gametes (eggs and sperm) were found to be of higher quality (larger egg mass and diameter; higher overall energy availability) when compared to those from farmed fish. Hybrid crosses (wild-farmed) displayed higher fertilization rates than wild-wild or farmed-farmed crosses, with the highest fertilizations rates observed when the eggs originated from wild females. However, survival of these hybrid crosses was lower when compared to wild-wild crosses. Additionally, river water (e.g., pH) was not found to be a physical barrier to the eggs and sperm of farmed fish.

While the crosses performed were completely artificial, this research contributes to an increased understanding of the potential effects of interactions between escaped farmed salmon and their wild counterparts. Future studies on the survival and fitness of first and second generation hybrids in river conditions must be completed to ensure an accurate understanding of the outcome of these potential interactions.

Apr. 2010–Mar. 2013

Funded By: DFO – Aquaculture Collaborative Research and Development Program (DFO – ACRDP) Co-Funded By: Gray Aqua Group Ltd.

Project Lead: Dounia Hamoutene (DFO)

Collaborators: Gray Aqua Group Ltd.

Contact: Dounia.Hamoutene@dfo-mpo.gc.ca

www.dfo-mpo.gc.ca/aquaculture/acrdp-pcrda/index-eng.htm

MIGRATION TIMING AND DISTRIBUTION OF JUVENILE SALMON IN DISCOVERY ISLANDS AND JOHNSTONE STRAIT

This research will help explain how juvenile salmon utilize the Strait of Georgia, including the Discovery Islands area, with a focus on Fraser River Sockeye Salmon and to a lesser extent, Chinook Salmon. It will also provide the information required to fully assess the risks of disease transfer from salmon farms to the wild, understand the potential consequences of such transfers, and inform farm management policies.

Purse seines and DFO trawl surveys have greatly increased the understanding of the migration and health of juvenile salmon within the Strait of Georgia, BC, especially for Sockeye Salmon. Surveys conducted in 2010–2012 revealed that Fraser River Sockeye Salmon do not enter the Discovery Islands area (a fish farming area) until the end of May, and that they are widely distributed throughout this area for at least part of June. To further assess risks associated with interactions between farmed and wild fish, information in the following key areas is needed: (1) knowledge of migratory pathways of salmon and the duration of their residency in the vicinity of fish farms; (2) knowledge of the prevalence of pathogens and diseases within wild and farmed populations; and (3) knowledge of environmental and host conditions during the periods wild salmon reside in the vicinity of fish farms. Additionally, more information is required to further understand when and for how long juvenile salmon are present in the vicinity of fish farms, as well as to describe migration timing of juvenile Fraser River Sockeye Salmon out of the Strait of Georgia. To gain this required information, sampling will be performed using a three-year trawl survey in the Strait of Georgia and a three-year purse seine combined with hydroacoustic surveys in Johnstone Strait.

Apr. 2014–Mar. 2016

Funded By: DFO – Aquaculture Collaborative Research and Development Program (DFO – ACRDP) Co-Funded By: Marine Harvest Canada Inc.; Grieg Seafood BC Ltd.; Cermaq Canada

Project Lead: Stewart Johnson (DFO)

Project Team: Marc Trudel, Chrys Neville (DFO); Diane Morrison (Marine Harvest Canada Inc.); Barry Milligan (Grieg Seafood BC Ltd.); Peter McKenzie (Cermaq Canada)

Collaborators: Marine Harvest Canada Inc.; Grieg Seafood BC Ltd.; Cermaq Canada

Contact: Stewart.Johnson@dfo-mpo.gc.ca

www.dfo-mpo.gc.ca/aquaculture/acrdp-pcrda/index-eng.htm

INDIVIDUAL AND FAMILY RESISTANCE TO BACTERIAL KIDNEY DISEASE IN SAINT JOHN RIVER STRAIN ATLANTIC SALMON

Atlantic Salmon resistance to Bacterial Kidney Disease (BKD; causative pathogen Renibacterium salmoninarum) will improve fish health, welfare, growth, and survival. Selection for resistance will also reduce the need for antibiotic treatments in stocks that are BKD positive.

BKD is a consistent and reoccurring pathogenic problem that arises throughout the Atlantic Salmon aquaculture industry on a yearly basis. No method presently exists to successfully remove the pathogen completely despite use of various strategies to cope with BKD. In our study, individual Atlantic Salmon were intraperitoneally injected with BKD from Bay of Fundy Field Isolate FFA-198 (Research and Productivity Council, Fredericton). In the first challenge, 1037 Atlantic Salmon representing 48 families were injected. The study was terminated when mortality subsided at 40 days post injection (59.4% cumulative mortality). The estimated heritability from this year class for days to succumb adjusted for total body weight was 0.28. Indirect Fluorescent Antibody Technique (IFAT) was completed on each of the 421 Atlantic Salmon remaining at study termination. Of these, 148 had IFAT scores of 0 indicating that the injected BKD might have effectively cleared (additional confirmatory testing is planned). From the following year class, 1304 salmon from 83 different families have also been challenged. This challenge lasted for 117 days with <50% mortality; however, survival variations between families are evident. Further data analysis will occur for this year class.

Oct. 2010–Sep. 2015

Funded By: Atlantic Canada Opportunities Agency – Atlantic Innovation Fund (ACOA – AIF)

Project Lead: Amber Garber (HMSC)

Contact: agarber@huntsmanmarine.ca

www.huntsmanmarine.ca

ECOLOGICAL EFFECTS OF BLUE LED LIGHTS USED AT MARINE FINFISH AQUACULTURE SITES IN BRITISH COLUMBIA

The use of artificial lighting within finfish aquaculture operations is a common technique used to delay sexual maturation and produce larger fish. Currently, finfish growers in British Columbia are interested in exploring the use of blue light emitting diode (LED) lights. These blue LED lights are more efficient, use less energy, and last longer than the traditionally used white metal halide lights, making them an attractive, economical choice. However, artificial lighting may affect both the diversity and abundance of the native organisms surrounding an aquaculture site, and this study evaluated these potential effects. The use of blue LED lights at an experimental site at night was found to attract fish and zooplankton, when compared to unlit controls. No statistical difference was observed for phytoplankton abundance (in the absence of blooms) or the settlement of benthic invertebrates between blue LED lights and controls. A commercial finfish site was also equipped with blue LED lights to determine their effects on fish maturation, growth, and sea lice counts in comparison to a site equipped with traditional white halide lights. There was no statistical difference in sea lice counts between farm sites equipped with blue LED lights or white halide lights, but direct comparisons were difficult. The results of this project have led to an increased understanding of the effects of blue LED lights on the native biota, but continued research is necessary in order to determine the effects and implications of blue LED lights directly at an aquaculture site. This information will allow both industry and Fisheries and Oceans Canada (DFO) to continue to support the sustainable development of finfish operations in British Columbia, and better manage the intricate relationship between aquaculture and the environment.

Apr. 2011–Dec. 2013

Funded By: DFO – Aquaculture Collaborative Research and Development Program (DFO – ACRDP) Co-Funded By: Grieg Seafood

Project Lead: Hannah Stewart (DFO)

Collaborators: Grieg Seafood

Contact: Hannah.Stewart@dfo-mpo.gc.ca

www.dfo-mpo.gc.ca/aquaculture/acrdp-pcrda/index-eng.htm

Artificial night lighting at an aquaculture site. Photo: DFO

Aquaculture site in British Columbia. Photo: Hannah Stewart (DFO)

Blue LED units attached to chain with weights to keep vertical. Photo: Hannah Stewart (DFO)

DEVELOPING STANDARD OPERATING PROCEDURES TO QUANTIFY SPERM DENSITY AND DILUTE OR EXTEND MILT FROM MALE SAINT JOHN RIVER STOCK ATLANTIC SALMON TO ENHANCE MANAGEMENT OF A BROODSTOCK PROGRAM

Unfertilized, poorly fertilized, or sub-optimally fertlized eggs result in lost revenue to the aquaculture industry. In addition, reducing the number of males present in a breeding population is a cost savings and also allows for more widespread use of higher ranked males (e.g., males having the highest estimated breeding values in a broodstock program).

Milt cryopreservation represents an essential technology to enhance commercial broodstock programs and live gene bank efforts. Products are available to dilute milt having high density so that a consistent milt-to-egg ratio is used and also to extend the life span of sperm cells well beyond the natural expectation. These products are regularly used elsewhere with Atlantic Salmon; however, methodical exploration on Saint John River stock Atlantic Salmon has not been completed. Our efforts chronicled use of an Atlantic Salmon calibrated photometer supplied by Cryogenetics to quantify sperm density from representative males from the Atlantic Salmon broodstock program at the Huntsman Marine Science Centre (HMSC). Results to date suggest a generally better fertilization rate using diluted milt compared with fresh milt. Diluted milt also fertilized a greater number of stripped eggs compared to standard industry practices using undiluted milt. Extending milt for up to 16 days is possible using the AquaBoost Extender and results showed similar fertilization rates between fresh diluted and extended milt. Extending milt presents time saving opportunities for a broodstock program as stripping milt is no longer necessary each day that eggs are collected. Genetic linkages will also be more manageable in a broodstock program requiring less frequent access to specific males.

Oct. 2014–Mar. 2015

Funded By: NRC – Industrial Research Assistance Program (NRC – IRAP)

Project Lead: Amber Garber (HMSC)

Project Team: Susan Hodkinson, Chris Bridger (HMSC); Maureen Ritter (Canada Cryogenetics Services); Jorn Ulheim (Cryogenetics)

Contact: agarber@huntsmanmarine.ca

www.huntsmanmarine.ca

GENETIC AND GENOMIC IMPACTS OF ESCAPED FARMED SALMON IN ATLANTIC CANADA: EVALUATING THE USE OF ARCHIVED ATLANTIC SALMON SCALES AS A SOURCE OF PRE-IMPACT DNA

Aquaculture escapes represent a demonstrable threat to the persistence and stability of wild salmon populations, with impacts occurring through both genetic and ecological interactions. Direct genetic interactions result from interbreeding of farm escapes with wild fish, causing population-level changes including erosion of local adaptation and loss of fitness. However, the presence and magnitude of these genetic impacts are difficult to quantify in practice, largely due to a lack of pre-impact genetic baseline. Historically, monitoring activities for Atlantic Salmon have collected scales for aging purposes, and these archived scales could represent a powerful source of pre-impact DNA. The main objective of this project is to explore the use of various extraction methodologies to maximize DNA yield and estimate genotyping success rate from archived Atlantic Salmon scales. Extracted DNA will be quantified and used for preliminary microsatellite genotyping to demonstrate the utility of this approach. The ultimate goal is future comparison of pre- and post-aquaculture DNA samples from Atlantic Salmon in Atlantic Canada to quantify the presence and magnitude of genetic impacts due to escaped farmed salmon; thereby directly informing mitigation strategies through a quantification of impacts in space and time.

Sep. 2014–Mar. 2015

Funded By: DFO – Program for Aquaculture Regulatory Research (DFO – PARR)

Project Lead: Ian Bradbury (DFO)

Project Team: Lorraine Hamilton, Patrick O’Reilly, Geoff Perry (DFO)

Contact: Ian.Bradbury@dfo-mpo.gc.ca

SPATIAL AND TEMPORAL DISTRIBUTION AND SURVIVAL OF FARMED ATLANTIC SALMON AFTER EXPERIMENTAL RELEASE FROM SEA CAGE LOCATIONS

The expansion of the aquaculture industry in Newfoundland and the decline in wild salmon stocks have raised questions as to the possible impacts escaped cultured salmon may have on local wild populations. Despite increased industry awareness and the implementation of a code of containment, escapements still occur. Recently, escapements occurred in 2013 resulting in farmed fish recaptured in Garnish River and Little River (South Coast of Newfoundland), as well as in coastal waters. Research is needed to better understand the potential risk of escapees on wild salmon populations as spawning of aquaculture origin Atlantic Salmon has been demonstrated in international studies as well as in Canadian rivers in British Columbia and New Brunswick. The objective of this project is to determine the residency time, locations, migratory routes, and survival of escaped farmed Atlantic Salmon by monitoring the movements of groups of smolts, post-smolts, and adults in a simulated escape at different times of the year. Identification of the migratory routes followed by escapees, as well as residency patterns and how they vary with time of escapement (seasonal effects), will aid in designing more efficient recapture strategies.

The knowledge generated by this initiative will lead to improved and informed federal and provincial ecosystem-based environmental regulation allowing for the development of strategies to eventually lessen the impacts of escaped farmed Atlantic Salmon on the environment and wild salmon populations.

Aug. 2014–Mar. 2017

Funded By: DFO – Program for Aquaculture Regulatory Research (DFO – PARR)

Project Lead: Dounia Hamoutene (DFO)

Project Team: Brian Dempson, Keith Clarke, Curtis Pennell, Kimberley Burt, Lynn Lush, Geoff Perry (DFO)

Contact: Dounia.Hamoutene@dfo-mpo.gc.ca

SALMON AND CHIPS: COMMERCIAL APPLICATION OF GENOMICS TO MAXIMIZE GENETIC IMPROVEMENT OF FARMED ATLANTIC SALMON ON THE EAST COAST OF CANADA

Aquaculture companies are increasingly incorporating genomics technologies into their breeding programs in order to develop desirable stock traits for improved growth and disease resistance. To retain its ability to compete internationally, Cooke Aquaculture/Kelly Cove Salmon (KCS) will partner with Elizabeth Boulding and her academic group from the University of Guelph to incorporate genomics marker technology into Kelly Cove Salmon’s current breeding program. This will allow the company to improve the effectiveness of its breeding program and increase the resistance of its salmon to diseases and parasites.

The company aims to implement an advanced genomics micro-array technology that compares single nucleotide polymorphisms (SNPs) known as SNP-chips. When blended with conventional animal breeding techniques, this can yield significant increases in the survival rates of eggs and juvenile stages, as well as improved saltwater performance. The implementation of this genomics technology is expected to increase the quality and sales of Kelly Cove’s salmon, and improve profitability by reducing expenditures on vaccines and medication.

Apr. 2014–Mar. 2017

Funded By: Genome Canada, Genome Atlantic Co-Funded By: NRC – IRAP

Project Lead: Keng Pee Ang (KCS); Elizabeth Boulding (U Guelph)

Project Team: Jake Elliott, Frank Powell (KCS); Larry Schaeffer (U Guelph)

Contact: Keng.Pee.Ang@cookeaqua.com

genomeatlantic.ca/projects

Cooke Aquaculture Inc.’s Keng Pee Ang at one of their New Brunswick sites. Photo: KCS

RAPID GENOMIC SCREENING FOR ATLANTIC SALMON AQUACULTURE ESCAPEES AND HYBRIDS USING A HIGH THROUGHPUT NANOFLUIDIC DYNAMIC ARRAY

In Newfoundland, the cultivation of Atlantic Salmon has increased exponentially since the late 1960s. Coincident with this increased growth has been an increased incidence of farmed escapes and hence the likelihood of genetic interactions between wild and farmed Atlantic Salmon. Assessing the potential impacts of these escapes on wild salmon populations is complicated by the complexity of domesticated strains, including the potential use of European strains used to improve production. As part of this project, we are developing a panel of single nucleotide polymorphism (SNP) genetic markers. These will be used to quantify the genetic impacts of escaped farmed Atlantic Salmon on wild populations, as well as the frequency and geographic extent of interbreeding between domesticated and wild salmon.

Using existing genomics data, and new data generated from genome-wide scans, we are identifying a panel of markers that can be used to screen samples on a high throughput genotyping platform (i.e., Fluidigm nanofluidic dynamic array). This genomic screening tool will rapidly, accurately, and cost effectively quantify the presence of escapes, recent hybrids, and the extent of introgression into wild populations. This work is a first step towards identifying impacts of wild/farmed salmon interactions in Atlantic Canada and the development of appropriate mitigation measures.

Sep. 2014–Mar. 2015

Funded By: DFO – Program For Aquaculture Regulatory Research (DFO – PARR)

Project Lead: Ian Bradbury (DFO)

Project Team: Lorraine Hamilton, Geoff Perry, Patrick O’Reilly, Dounia Hamoutene, Martha Robertson (DFO)

Collaborators: Elizabeth Barlow (NL); Jon Carr (Atlantic Salmon Federation); Ross Hinks (Miawpukek First Nation)

Contact: Ian.Bradbury@dfo-mpo.gc.ca

Atlantic Salmon cages in southern Newfoundland. Photo: Chris Hendry (DFO)

Sampling for possible offspring of escaped farmed Atlantic Salmon. Photo: Chris Hendry (DFO)

SUSTAINABILITY OF FISH FARMING: AN ECOSYSTEM APPROACH

Farming of fish and shellfish in the ocean is equal in importance to harvest fisheries as a means of seafood production. Concerns about disease and waste management, as well as interactions with commercial fisheries, has led to controversy among the industry, government regulators, and coastal communities. There are, however, many feasible environmental improvements for the culture of salmon in net pens.

Cooke Aquaculture, the largest locally owned aquaculture company in North America, has partnered with Dalhousie University, Canada’s Ocean University, in a research program on aquaculture sustainability. Professor Jon Grant has been awarded the NSERC-Cooke Industrial Research Chair in Sustainable Aquaculture with research that includes simulation modelling. This approach is being employed using computer models and mapping of aquaculture ecosystems to predict the transport of diseases and waste particles by ocean currents. A field program of oceanographic instruments and sampling at coastal sites, including Cooke’s farms, is being used to check the reliability of the predictions. Various planning scenarios are explored with this method, which can be used to arrange farm sites to minimize the spread of disease or accumulation of waste. At the local farm scale, these models will be used to test net designs to improve net security and healthy growing conditions for fish.

Dalhousie’s capacity for aquaculture training of students will increase significantly as a result of this program, leading to a trained workforce for the aquaculture industry, and a new chapter in the practice of environmentally conscious fish farming.

Jan. 2014–Jan. 2019

Funded By: NSERC Co-Funded By: Cooke Aquaculture Inc.

Project Lead: Jon Grant (Dalhousie U)

Contact: Jon.Grant@dal.ca

myweb.dal.ca/jgrant

Sediment profile image device and image of coastal sediments used in assessing benthic health. Photo: Michelle Simone

Modelling scheme for simulation of sea lice dynamics in aquaculture.

BETTER FEED FOR BETTER FISH: BIOMARKER PLATFORM FOR COMMERCIAL AQUACULTURE FEED DEVELOPMENT

The health of farmed salmon in Canada can be threatened by infectious diseases. The quality of feed can affect salmon health and impact their ability to withstand infection, but currently there is no way to measure how effective it is apart from growth rates – if fish grow bigger, faster, then presumably the feed is effective.

This project seeks to develop tools to better assess salmon health by examining their genes. Scientists at Memorial University of Newfoundland (MUN) and EWOS Innovation will jointly develop a platform to quantify the expression of multiple genes related to health and performance, using a single biological sample. The team will use genomics technologies to assess the effects of various diets on fish health at the molecular level. The highly-detailed information will help EWOS Innovation fine-tune feed formulas that include non-marine products, such as land-based plants, to maximize fish performance and to develop clinical feeds that will combat the diseases that are currently reducing salmon numbers. Within the life of this project, EWOS Innovation, one of the world’s largest producers of aquafeeds, will be able to commercialize new, high-quality feeds that help to promote healthy fish.

The research will strengthen salmon aquaculture in Canada, in particular by reducing disease among farmed salmon. In addition, some project results will be shared as intellectual property, supporting growth in the sector. Finally, a focus on the use of Canadian raw materials in developing the feeds will also strengthen the feed supply industry.

Oct. 2014–Sep. 2017

Funded By: Genome Canada; Genome Atlantic Co-Funded By: EWOS Innovation

Project Lead: Richard Taylor (EWOS Innovation); Matthew Rise (MUN)

Project Team: Simon Wadsworth, Adel El-Mowafi, Jason Mann (EWOS); Christopher Parrish (MUN)

Contact: Richard.Taylor@ewos.com; mrise@mun.ca

www.genomeatlantic.ca/projects

CYCLICAL FEEDING STRATEGY TO REDUCE ENVIRONMENTAL IMPACT OF MARINE SALMON FARMING

Compensatory growth, the rapid growth observed upon re-feeding after a period of food deprivation, has been associated with greater feed utilization (protein retention) for fish. Inducing compensatory growth of fish under culture conditions could require less feed for a given biomass gain, resulting in reduced loss of nitrogen and other by-products of feeding to the environment.

A trial was conducted with juvenile Chinook Salmon in seawater to ascertain the value of using a cyclical feeding (periodic withholding of feed) strategy to improve efficiency and reduce environmental impact of salmon farming. A commercial salmon feed was fed to Chinook under a variety of feeding cycles, including: daily feeding (control); 5 days feeding to satiation, 2 days no feeding; 7 days feeding, 7 days no feeding; 14 days feeding, 14 days half ration; and daily feeding at half ration.

Fish fed daily exhibited the best growth, but the weight gain of fish fed on a cycle of 5 days feeding 2 days no feed experienced was 89.2% of full fed fish, while feed consumption was only 81.9%. The improved feed efficiency could relate to a reduced level of nitrogen lost to the marine environment in the form of ammonia from salmon culture.

Improving the utilization of feed by salmon, at least at the juvenile stage, has the potential to reduce the environmental impact and improve the efficiency (cost per unit production) of salmon aquaculture. Extending the effect of improved efficiency with cyclical feeding to larger fish remains a challenge to be met with further research.

Apr. 2013–Mar. 2015

Funded By: DFO – Aquaculutre Collaborative Research and Development Program (DFO – ACRDP)

Project Lead: Ian Forster (DFO)

Project Team: Lawrence Albright, Robert Walker (Agrimarine); Biswas Biswajit, Mahmoud Rowshandeli (DFO)

Collaborators: Agrimarine

Contact: Ian.Forster@dfo-mpo.gc.ca

Biswajit Biswas feeding tanks of juvenile Chinook Salmon. Photo: Ian Forster (DFO)