Aquatic Biotechnology & Genomics Research and Development ... · biotechnology include aquaculture biotechnology ... 2 Aquatic Biotechnology & Genomics Research and Development Strategy

Aquatic Biotechnology & Genomics Research and Development Strategy

Aquatic Biotechnology & Genomics Research and Development Strategy

Aquatic BitechnologyProgram

Table of Contents

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

Priority Research Themes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6

Vision for 2015 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8

Issues, Trends, Drivers and Opportunities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10

4.1 Canadian Trends and Initiatives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10

4.2 The International Context . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11

The Aquatic Biotechnology and Genomics R&D Strategy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

Theme 1. Biotechnology and Aquatic Resource Management . . . . . . . . . . . . . . . . . . . . . . . . .15

Theme 2. Biotechnology and Aquatic Animal Health . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20

Theme 3. Biotechnology and Aquatic Ecosystem Integrity . . . . . . . . . . . . . . . . . . . . . . . . . . . .24

Theme 4. Novel Aquatic Animal Regulatory Science . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27

Conclusion – Charting a Path Forward . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33

Shaping the Future

IntroductionIntroduction

1Shaping the Future

Biotechnology is a powerful "enablingtechnology" with applications inmany sectors and holding muchpromise for the future. It is aterm that covers a broadspectrum of scientificapplications. The CanadianEnvironmental ProtectionAct defines biotechnology as"the application of scienceand engineering in the directand indirect use of livingorganisms or parts orproducts of living organismsin their natural or modifiedforms."

Aquatic biotechnologyinvolves the application ofscience and engineering for thedirect or indirect use of aquaticorganisms or parts or productsof living aquatic organisms intheir natural or modified forms. It includes genomics, a disciplinethat aims to decipher and understandthe entire genetic information content ofplants, animal/fish organisms, and microorganism. It is fundamental to allbiological and biotech research.

Components of aquaticbiotechnology include aquaculturebiotechnology (e.g., fish health andbroodstock optimization); aquaticbioprocessing (e.g., obtainingvaluable compounds from marineorganisms); and aquaticbioremediation (e.g., use ofmicroorganisms to degrade toxicchemicals in the aquaticenvironment).

F isheries and Oceans Canada (DFO) is linking innovativebiotechnology and genomics science with higher level policymaking and on-the-ground fishery and aquatic ecosystem

management decisions.

The development and application of biotechnology and genomics toolsto enhance sustainable resource management and environmentalconservation and protection is increasing in Canada and around theworld. Advances and application developments in biotechnology andgenomics present the possibility for lower-cost biotechnologyapplications with advantages, such as greater sensitivity, accuracy,faster results and increased efficiency, over more traditionaltechnologies. DFO is part of this biotechnology and genomics wavewith innovative science across the country supporting our mandate.

As biotechnology and genomics tools and information are increasinglyincorporated into DFO research and development activities, anintegrative approach to identifying opportunities for sharing expertise,coordinating efforts and increasing efficiencies within DFO’sbiotechnology and genomics R&D activities was taken.

DFO’s Aquatic Biotechnology Program has been in place since the late1980s, with the majority of our developments occurring within the last10 years. With targeted start-up funding, DFO has strategicallydeveloped expertise and capabilities in biotechnology and genomics.DFO researchers and key partners have developed new biotechnologytechniques that support policy and management decisions to enhancethe ecological sustainability of the wild fishery, aquaculture and oceansecosystems. Our success has been a result of being able to quicklyapply our research through effective partnerships, deploying productsand tools to enable clients in other government agencies, and theprivate and public sectors to adopt and benefit from the application ofnew technologies, while keeping the research aligned withdepartmental priorities.

DFO’s Mandate and Aquatic BiotechnologyKey departmental priorities, as outlined in the 2005-2010 StrategicPlan: Our Waters, Our Future, can be supported by biotechnology andgenomics research, development and innovations. The Department’sstrategic plan clearly states that sustainable development is a priority.An underlying premise of sustainable development is that a strongsustainable economy is a product of a healthy natural environment andhealthy society. Habitat destruction, loss of biodiversity, and land andsea-based pollution all have a negative impact on our culture, societyand economy. Properly managed, our natural resources and aquaticenvironment will be sustained for future generations, and provide thebasis for growth and co-existence of current and emerging aquaticresource users.

Biotechnology and genomic tools and productscontribute to the three inter-related DFO priorityoutcomes:

1. Healthy and Productive Aquatic Ecosystems –Refers to the sustainable development andintegrated management of resources in or aroundCanada’s aquatic environment through oceans andfish habitat management, and the critical scienceactivities that support these two programs.

2. Sustainable Fisheries and Aquaculture – Refers to an integrated fisheries and aquacultureprogram that is credible, science-based, affordableand effective, and contributes to sustained wealthfor Canadians.

3. Safe and Accessible Waterways –is about providing access to Canadian waterways,and ensuring the overall safety and integrity ofCanada’s marine infrastructure for the benefit of allCanadians.

2 Aquatic Biotechnology & Genomics Research and Development Strategy

DFO Strategic Outcomes

Sustainable Fisheries andAquaculture

(SFA)

Healthy and ProductiveAquatic Ecosystem

(HAPAE)

Healthy and ProductiveAquatic Ecosystem

(HAPAE)

Healthy and ProductiveState of Aquatic EcosystemsImpacts of Human Activities

Safety, Security and Sovereignty

Status of the FisheryResources

Species at Risk

Aquatic Invasive Species

Aquaculture Production

Aquaculture-EnvironmentInteractions

Impacts of developmentactivities

State of ecosystems andintegrated management

Roles of Oceans in GlobalClimate

Genomics andBiotechnology

Aquatic Animal Health

Products & services for navigation

Mapping the Ocean Floor(UNCLOS)

Impacts of Climate Variability & Change

DFO Science RenewalIn 2004, DFO embarked on a review of all scienceactivities in order to identify and match all scienceactivities to the three key departmental andgovernment priorities, review commitments andcapacity in order to balance advice needs with abilityto deliver the advice, and to finalize and implement along-term plan to ensure relevance and sustainability ofthe Science Program.

DFO’s Science Sector must also be responsive tointernal drivers, such as the increase in demand forscience advice, products, and services. Theserequests are increasingly complex, requiring integrativeapproaches and ecosystem considerations.Additionally, the scientific information, products,services and advice needs to be flexible andresponsive to rapidly emerging departmental andfederal priorities. However, there is anacknowledgement that the scientific capacity andresources required to meet these ever increasingdemands are not available.

In response to these drivers, Science Renewal aims toproduce a vibrant aquatic science program based onexcellence that supports and informs DFO andGovernment needs and best serves Canadians. Theframework to deliver on this objective is to ensure thatDFO science is relevant, and responsive to priorities;effective, through a modern and effective sciencefunctions; affordable; and valued.

To support DFO priorities, 13 clusters of scienceactivities have been identified, including Biotechnologyand Genomics (see figure, above). These clustershave been identified as key program areas that supportnational Science Sector priorities through research,monitoring, providing science advice, products andservices, data management, and sciencemanagement. Many of the core clusters have beenidentified as Centres of Expertise, a new managementand coordination approach to streamline scienceservice delivery and national coordination, therebyincreasing efficiency and effectiveness.

Standard biotechnology tools are now used throughoutthe Department with the more specializeddevelopmental work concentrated in biotechnologycentres across the country, resulting in thedevelopment of core capacity and expertise. DFO iscontinually increasing its capacity in terms of highly

skilled personnel, and specialized equipment andfacilities in order to develop and deploy leading-edgebiotechnology and genomics tools. In part, thesuccess that DFO has had in integrating and deployingbiotechnology and genomics tools and information isdue to the development of strong and vibrantpartnerships with researchers in other governmentdepartments, academia and industry, as appropriate.This has enabled DFO researchers and DFO Scienceto capitalize on third party resources to deliver betterand stronger programs, to meet its mandate and keypriority objectives more efficiently, to foster and supportworld-class scientific and technological innovation, totrain new scientific personnel, and to develop andmaintain a national and international reputation forscientific excellence in aquatic biotechnology andgenomics research.

Partnering with CanadiansDFO scientists take on research in support of issuesthat matter to our stakeholders. We work closely withthe aquatic resource managers, users andconservation groups and identify priorities based onthe needs of these communities. Biotechnologyresearch also provides information that supportCanada’s national and international commitments inaquatic animal health, stock management andassessment of risks associated with biotechnology-derived products.

The multi-faceted nature of fisheries, aquaculture, andmanagement of aquatic ecosystems, and theinterdisciplinary nature of biotechnology requires, andbenefits from, strong partnerships and effectivestakeholder relations. DFO works with a diverse rangeof stakeholder groups and individuals including: localcommunities; fishery biologists; enforcement personnel;international scientists; international research andregulatory organizations; international governments;aboriginal groups with fishing and resource rights;commercial aquaculture and wild fishery organizations;companies; and, provincial and territorial counterpartswith shared resource management responsibilities. DFOhas partnerships with governments and researchinstitutes in the United States, Norway, France, theUnited Kingdom, Sweden, Japan, Korea, and Germany.

3Shaping the Future

Moving Forward – AquaticBiotechnology and GenomicsResearch and Development Strategy:Shaping the FutureDespite progress made possible through start-upfunding, the incremental costs associated with ongoingresearch and its application are challenging theDepartment to regularly seek additional funds to meetthe increasing capacity needs and maximize theapplication of these tools for sustainable development.As enabling technologies that are inherentlymultidisciplinary, biotechnology and genomics mayhave applications and information to support the aimsof many of the other science clusters, includingAquatic Animal Health, Aquatic Invasive Species,Species at Risk, Aquaculture Production, etc.

To build on success to date, and chart a clear pathforward, DFO has developed the following AquaticBiotechnology and Genomics R&D Strategy to supportDFO’s departmental and national obligations over thenext number of years. This Strategy is the product ofinput from DFO’s scientists, the National BiotechnologyCoordinators, biotechnology regulators, and managers.

This strategy was intended to capture the wide rangeof science initiatives either underway or proposedwithin DFO. The biotechnology and genomics R&Dopportunities and priorities have been mapped outover a variety of timeframes, allowing for the actionsand outcomes to build on one another, thus permittingthe integration of experiences, and outputs fromprevious activities.

By increasing the awareness and understanding of themultiple benefits derived from the application ofbiotechnology tools, senior government officials will bebetter able to make informed policy decisions andinvest in areas where science gaps remain. Riskassessments and critical decisions need to be made atall levels, reinforcing the need for an integratedapproach.

The Strategy also outlines the inherent multidisciplinaryaspect of biotechnology and genomics, and providesexamples of applications of these enablingtechnologies to many of DFO’s mandated scienceadvice and activities. The opportunities forbiotechnology and genomics research anddevelopment to provide new and precise tools andinformation to help meet the Department’s mandate willcontinue to be explored as the science and technologymatures. Science Renewal involves linking the scienceprogram to Departmental and federal strategicoutcomes and priorities within a new Departmentalreporting structure. Biotechnology and genomics toolsand applications can add value, efficiencies andimprove effectiveness in meeting core mandatedscience advice and information needs.


Priority Research ThemesPriority Research Themes

F our priority research themes form the Strategy’skey elements and include goals, objectives andactions designed to shape DFO’s biotechnology

agenda for the next four years. It is expected that thisStrategy will continuously evolve in dynamic responseto departmental priorities.

1. Biotechnology and Aquatic Resource Profiling

2. Biotechnology and Aquatic Animal Health

3. Biotechnology and Aquatic Ecosystem Health

4. Regulatory Science for Aquatic Animals with Novel Traits


Vision for 2015Vision for 2015

T he following Strategy proposes a vision of where we want to be in 2015 and a roadmapto get there.

To have in place by 2015:

A successful, innovative, dynamic biotechnologyand genomics program to enhance thesustainability of our aquatic resources and theecological health of our aquatic ecosystems, thatis characterized by strong partnerships andstakeholder involvement; innovative researchprograms; the application of effectivebiotechnology and genomics tools and products;and funding to maintain required expertise.

The successful implementation of this Strategy willdepend on leadership, commitment, creativity andexpertise of DFO’s management, scientists, externalstakeholders, resource managers and decision-makersacross the country.


Issues, Trends, Driversand Opportunities

Issues, Trends, Driversand Opportunities

D evelopments at the national and internationalscale shape DFO’s priorities. For instance, weknow that competing resource demands;

human population growth; climate and environmentalchange; scientific and technological advances;international responsibilities and obligations; shiftingeconomic paradigms; traditional funding of highvalue/high visibility species; and, societal demands area just a few of the drivers shaping DFO’s agenda. We are faced with the challenge of understanding thecomplex interrelationship between these and othervariables, in order to target our science, and informpolicy choices, ultimately ensuring the long-termviability of the aquatic resources, and health of aquaticecosystems for which we are responsible.

Public expectations for government action on theseissues are high. The department is facing pressurefrom industry and communities, to increase investmentin science and apply efficient and effective tools tobetter comprehend and manage aquatic resources.The public also sees a role for government to help incapitalizing on the potential of biotechnology toincrease jobs and economic growth in Canada. This is especially true for coastal and rural Canadians.

DFO is responding by, as part of a department-widescience renewal, expanding its Aquatic Biotechnologyand Genomics R&D Program. It has been proven thatthe speed, sensitivity and accuracy of usingbiotechnology and genomics tools provides manyadvantages in addition to more traditional methods of,for example, species identification, contaminated siteremediation, and disease diagnosis.

Key TrendsCanada stands to gain from aquatic biotechnology andgenomics innovation as these tools directly andindirectly support aquatic resource management andecosystem integrity. To put this into context:

In 2004, Fish and seafood was the largest singleexport food commodity, by value, in Canada. Weare the fifth largest seafood exporter in the world.

The quantity of fish and seafood productsexported increased in 2005 with more than703,000 tonnes of Canadian fish and seafoodproducts exported worldwide, valued at $4.3 billion – up 2.6 per cent compared to 2004.

The United States remains Canada’s largestexport destination, with 62 percent of its seafoodproducts, valued at $2.7 billion sold to the U.S.market. Japan ranked second with Canadianimports valued at more than $471 million. Chinaand Hong Kong followed at $383 million.

In 2004, aquaculture products were worth nearly$527 million in Canada. The value of aquacultureexports exceeded $425 million in 2004. For somevaluable species of salmon, aquacultureproduction far exceeds wild harvest.3

Resource availability is a concern, and thepassage of the Species at Risk Act has focusedattention on threatened and endangered species.The impact of bycatch of threatened orendangered species, habitat and the economiesof coastal communities are all of DFO concern.

4.1 Canadian Biotechnology Trendsand Activities

The National Context

The rapid pace of biotechnology discoveries continuesto accelerate with some viewing its potential analogousto the impact of information and communicationtechnologies. According to Canadian Trends inBiotechnology, Second Edition 2005:

In fiscal year 2003-04, Canada’s federal scienceand technology (S&T) expenditures onbiotechnology totalled $746 million, whichrepresented 8% of all federal S&T expenditures.Close to 95% of the federal S&T spending onbiotechnology was dedicated to R&D activities.

Most federally funded biotechnology S&T activitieswere conducted outside the federal government.

The number of product/processes that reachedthe market almost doubled between 1999 and2003.

As of 2003, firms had at least 17,000 productsand processes under development and on themarket.

Biotechnology is spread across the country:Ontario, Quebec and B.C. account for well overhalf of all revenues generated by biotechnologycompanies.


3 Vista October 2005.p.3

From 1997 to 2003, biotechnology revenues more thanquadrupled, from $813 million to $3.8 billion. Over thatentire period, more than half of biotechnology revenueswere received by companies in the human healthsector. As noted earlier, this figure could change if thenational and federal focus were to be expanded toinclude a greater emphasis on natural resources andthe environment, in recognition of the correlationbetween a healthy population, environment andeconomic growth.

The Canadian Biotechnology Strategy: A Federal Initiative

The federal government plays a major role as aninnovator, commercializer and regulator of biotechnologyproducts with provinces and territories valuable partners.DFO has been a partner at the federal level in theimplementation of the Canadian Biotechnology Strategy(CBS) since its inception in 1998.

The CBS provides a framework to guide nationalbiotechnology activities. The CBS is led by IndustryCanada in partnership with a number of federaldepartments, agencies, and research institutes such asEnvironment Canada (EC), Canadian Food Inspection

Agency (CFIA), Natural Resources Canada (NRCan),Health Canada (HC), National Research Council (NRC),Agriculture and Agrifood Canada (AAFC), DFO andothers.

The CBS vision is: “to enhance the quality of life ofCanadians in terms of health, safety, the environmentand social and economic development by positioningCanada as a responsible world leader in biotechnology”.The CBS is comprised of three pillars: Innovation,Regulation and Public Outreach. This strategy outlinesDFO’s role in all three of these pillars, and highlights bothDFO’s future role and direction in supporting thesepillars, and some current accomplishments.

4.2 The International ContextOne of the priorities of the federal government is toplace Canada as a world leader in biotechnology.According to Organization for Economic Cooperationand Development (OECD) data for the year 2000, thenumber of dedicated biotechnology firms per millioninhabitants is highest in Sweden, Switzerland andCanada. We also rank second in the proportion oftotal publicly funded R&D investments that is devoted

11Shaping the Future

Biotechnology Companies By Sector – 2004

*Other: Aquaculture, Bioinformatics*Source: Statistics Canada

Natural Resources 4%

Environment 8%

Other 6%Human Health53%

Agriculture28%

to biotechnology. Denmark, Canada and New Zealandinvest more than 10% of their total publicly fundedR&D budgets in biotechnology. 5

Internationally, in 2003 nearly 89% of all biotechnologyR&D expenditures were in the human health sector, with6% of biotechnology R&D in the agriculture and foodprocessing sectors. Biotechnology investment in thenatural resource and environment sector is minimal,despite the untapped potential for benefits to Canadians.DFO can be instrumental in changing this trend.

The strong link between natural resource-basedeconomic development in Canada, and economicgrowth, along with the direct and indirect impact of thequality of the natural environment on human health andenvironment are two reasons why a shift in R&Dinvestments is necessary. Canada can become aglobal leader in the development, application andtransfer of innovative aquatic biotechnology techniquesand products. Doing so will not only benefit theinternational community with the uptake of productsthat will ultimately foster a more sustainable globalfishery, but also Canadian industry and coastalcommunities, and consumers.

International Fisheries and Oceans Management

Global production from capture fisheries andaquaculture supplied about 101 million tonnes of foodfish in 2002. 6

International fisheries and oceans management issuesare complex. Uncertainty arises from many factorsincluding cumulative impacts, climate change, anincrease in the number of people using oceanresources, the variety of ocean activities, as well asinternational markets and socio-economic pressure.

For many years, a major challenge for the managementof the international fishery has been the quest toestablish appropriate fishing quotas in light of the highlevel of uncertainty and complexity.

With the development of genetic tools to ”geneticallyfingerprint” fish as individuals and populations, newinformation can be generated that enables theattribution of fish stocks that straddle internationalboundaries to country of origin. This additionalinformation can be used by the Department, and theinternational community, to develop and proposequotas that are more reflective of migratory patterns

and the need to maintain the health of fish stocks.Through the development of sensitive, accurate andrapid tests that provide valuable information to fisheriesand oceans managers, Canada is contributing to theinternational knowledge and tool base for addressing thechallenge of managing international fisheries, therebysupporting and contributing to our responsibilities underthe United Nations Convention on the Law of the Sea(UNCLOS), International Council for the Exploration of theSea (ICES), the Pacific Salmon Commission, NorthPacific Anadromous Fisheries Commission, and, theNorth Atlantic Fisheries Organization.

Aquaculture in the World

Worldwide, aquaculture is the fastest-growing sector inagri-food, with fish accounting for more than 40% ofrevenues. The United Nations’ Food and AgricultureOrganization (FAO) reports total aquaculture productionwas 39 million tonnes in 2002, and predicts totalaquaculture fish production will exceed 130 milliontonnes per year by 2030.

Under the Department’s 2005-2010 Strategic Plan,DFO will “seek opportunities to create the conditionsfor the development of an environmentally sustainable,internationally competitive aquaculture industry inCanada.” Biotechnology and genomics innovations willcontinue to contribute to the industry’s growth andsuccess through development and application of tools,including those for regulatory and production support.

In support of sustainable aquaculture, DFO’sbiotechnology and genomics research is investigatingand evaluating methods to mitigate the interactionsbetween wild and domesticated strains. Through thedevelopment of accurate and efficient methods thatallow for aquaculture strains to be distinguished fromwild populations, assessment of the impact ofinteractions can be made, as well as allowing for thetracing of aquaculture products. In addition, theapplication of sensitive and specific techniques fordetecting aquatic animal pathogens will provideinformation on disease transmission. The tools andresults from these studies can then be used to informaquaculture management decisions.


5 Canadian Trends in Biotechnology 2nd ed. Government of Canada. 20056 FAO. World Review of Fisheries and Aquaculture. The State of World

Fisheries and Aquaculture.

Biotechnology and genomics tools have applications tosupport the development of robust aquaculturebroodstock, both for species that have been usedextensively in aquaculture and for new aquaculturespecies. For example, DFO scientists, in collaborationwith academic partners are developing two elite codbroodstocks, one in New Brunswick and one inNewfoundland and Labrador, both based on localstocks of cod, using traditional and biotechnology andgenomics tools and information. The geneticinformation anticipated to be generated from thisproject will be used to direct the selective breeding toprevent inbreeding and to select for fast growingand/or disease resistant families for use in aquaculture.

Aquatic Ecosystem Health

There is now growing international acceptance forecosystem-based integrated management practices toprotect our aquatic resources. Ecosystem health

information can be informed by the development anduse of standardized indicators, which can then beused as part of the risk management decision process.The application of outcomes from biotechnology andgenomics research provide the means to monitoraquatic ecosystem health using biomarkers – multiplebiomolecular signatures that when examined togetherpresent a unique pattern of molecular change in anorganism and identify an exposure or response to aspecific environmental stressor. Furthermore,advances in biotechnology will provide novel meansmonitor and address the remediation of existingcontaminated sites (e.g., bioremediation strategies).


The Aquatic Biotechnology and Genomics R&D Strategy

The Aquatic Biotechnology and Genomics R&D Strategy

D he following Strategy elaborates on the fourthemes and includes goals, objectives andactions designed to shape DFO’s

biotechnology and genomics. It is expected that thestrategy will continuously evolve in response todepartmental priorities, but that the broad themes andobjectives capture key opportunities and activities thatbiotechnology and genomics applications andinformation can address, as it relates to DFO’smandate, strategic objectives and Science Sector’sRenewal.

As biotechnology and genomics are enablingtechnologies and therefore multidisciplinary in nature,there are opportunities for the results from each of theresearch themes’ activities and objectives to beincorporated and built on in other research themes. By mapping out the strategic direction andopportunities for biotechnology and genomics R&D, itis anticipated that new collaborations and partnershipscan be identified, additional opportunities to transferknowledge, expertise and applications will be realized,and efficiencies identified and implemented.

Theme #1: Biotechnology andAquatic Resource ProfilingThis research theme encompasses all activities relatedto understanding the genetic make-up of our aquaticresources. Biotechnology and genomics in this areainclude studying the genome of aquatic species,studying the population structure of these species andstudying the genetics behind interactions betweenaquatic species and their environment (other speciesand environmental conditions).

Aquatic resource profiling directly supports sustainablefisheries, sustainable aquaculture, protection ofbiodiversity and recovery of species at risk. The goal isto optimize the productivity of the aquatic environment(from wild capture and aquaculture) while maintainingenvironmental health and biodiversity.

By charting each species, population by population,scientists can better assess which populations cansupport fisheries and how to prevent the loss ofgenetic diversity in designing breeding programs.

Endangered populations can also be identified andprotected to ensure the genetic variability of eachsurvives and thrives. Collated data on bothendangered populations is housed in genomic librarieswhere the information is used to establish a clearunderstanding of population dynamics.

On the enforcement side, the development of forensicDNA capability in DFO has expanded the scope ofenforcement actions while reducing expendituresassociated with prosecutions for illegal harvest or saleof fish and shellfish.

Goal: By 2015, to have developed biotechnologytools for genetic profiling of aquaticspecies and facilitated their widespreadapplication in Canada and abroad,contributing to the sustainable use ofaquatic resources.

Objectives:

1. Identify genetic markers to improve species, strainand stock identification for fisheries managementand to allow for the protection and enhancement ofbiodiversity and aquatic fish habitat, includingspecies at risk.

2. Improve biotechnology knowledge base forenhanced sustainability of aquaculture production:increase strain development and enhancebiotechnology tools for identification and control ofaquaculture species.

3. Enhance and apply research on populationgenetics and genomics to identify and monitorresponse of aquatic organisms due toenvironmental factors.


Objective #1. Identify genetic markers to improvespecies identification for fisheries managementand to allow for the protection and enhancementof biodiversity and aquatic fish habitat.

Action #1: Develop genetic markers forcommercially important fisheriesspecies to integrate into sustainablefisheries management practices.

There is an increased demand for the “real-time”management of fisheries through stockidentification techniques using genetic informationderived from non-lethal sampling. This informationand the speed at which it can be collected helpsfishery managers decide if and when the fisheryshould open. This enables managers to avoid theharvest of populations of conservation concern,including endangered stocks.

The US/Canada Coded Wire Tagging (CWT)program is expensive, slow and effectively tagsonly a fraction of the fish (hatchery only) caught infisheries or recovered from the spawning grounds.Genetic markers, however, allow identification ofdifferent populations or groups whenever theybecome a conservation or management priority,replacing the need to tag the group years inadvance of fishery analysis. This is of particularinterest when the fisheries occur along migrationroutes used by mixed stock groupings.

For estimating population abundance,conventional mark and recapture techniquescannot be used for some species (e.g. rockfish dieif brought to the surface for tagging). However,using genetic markers individuals can begenetically “marked” by creating a genetic profilefrom a non-destructive tissue sample (e.g.,samples taken using a barbless hook) and thenre-identified during the recapture process, eitherthrough resampling with barbless hooks or duringa commercial or recreational fishery.

Similarly, estimation of several cetacean populationabundance is very difficult using conventionaltechniques as they occur over a wide geographicalrange, have clumped distribution and spend muchtime under water. Skin samples taken from variouswhale species including narwhal, beluga andbowhead are taken by aboriginal hunters via non-lethal sample harpoons. As well as being used forstock identification, these samples could be used toestimate the population number by mark andrecapture estimation.


Did You Know That…

DFO is using genomic tools such asmitochondrial DNA (mtDNA) and nuclearDNA (nDNA) to identify stocks of belugawhales. The tools are used to estimate theproportion of beluga belonging to differentstocks in an aboriginal mixed-stock fisheriesand establish maximum harvest limits thatreflect the sustainable harvest of each stock.Management actions are taken to enforce areaclosures when the DNA indicates that the

area is frequented by a stock at a lowerabundance level.


Due to its commercial viability and ease of tracking,salmon have become one of the most studied aquaticspecies in Canada and globally. Large, geneticbaseline datasets for Pacific salmon, developed byDFO scientists, are used for the most intensive geneticmanagement of fisheries on a real-time basis in theworld. Over 10,000 chinook, sockeye and cohosalmon samples are analyzed each year to managefishery openings, enabling Canada to maximize catchunder the US/Canada Pacific Salmon Treaty (PST)allocations while maintaining strict harvest limits onstocks of conservation concern. For example, real-timegenetic management of the 2003 and 2004 northcoast troll fishery on chinook salmon enabled the PSTquota to be achieved for the first time since 1994without overharvesting west coast Vancouver Islandpopulations of conservation concern, resulting inincreased annual revenue to the fisheries of over $3 million dollars.

Action #2: Develop genetic markers for speciesof interest to Habitat Managementincluding vulnerable species such asthose listed by the Committee on theStatus of Endangered Wildlife inCanada (COSEWIC) for protectionunder the Species at Risk Act (SARA)or under the Convention on theInternational Trade of EndangeredSpecies (CITES).

DFO has developed tools that help theDepartment fulfill its responsibilities under theSpecies at Risk Act (SARA). Genetic methods areapplied to identify population units deserving ofdesignation (as vulnerable, threatened orendangered) according to COSEWIC.

These methods are also used in developing acaptive breeding program for Atlantic salmon;determining the establishment of Marine ProtectedAreas for marine organisms; and to investigate theeffects of population bottlenecks and extensivetransplantation on genetic diversity in salmon.

Action #3: Enhance the use of forensic speciesidentification for enforcement offisheries and for the implementationof traceability requirements in otherregulations.

This action will build on the work done underActions #1 and #2.

The same genetic information that will supportimproved management decisions can also beused to increase the certainty and strength of theevidence base for prosecutions for the illegalharvest and sale of aquatic organisms.

DFO also needs to enhance its ability to meet itsCITES obligation to issue “non-detriment” permitsfor export of cultured product while ensuring thatillegally harvested wild product is not launderedthrough the culture operations. This is required toensure certainty for exporters of our products.

Action #4: Expand the scope of genetics andgenomics databases for speciesunder DFO management and thoseaquatic species managed throughinternational agreements.

Information derived from DFO’s genetics andgenomics databases is used to manage domesticand international fisheries to enable harvest ofabundant populations (species) while protecting“listed” populations and species of concern (e.g.,species listed as endangered or threatened underthe Species at Risk Act).



Using genetic profiling tools, DFO scientists havebeen able to distinguish the ‘inner’ yelloweyerockfish population resident in the Strait of Georgiaand Queen Charlotte Sound from an outer coastalpopulation that extends from Oregon to Alaska.The genetic isolation and reduced abundance of theinner yelloweye rockfish population have beendocumented in a status report on the species forCOSEWIC.

Objective #2. Improve biotechnology knowledgebase for enhanced sustainable aquacultureproduction: increase strain development andenhance biotechnology tools for identificationand control of aquaculture fish.

Action #1: Develop genetic markers todistinguish aquaculture strains fromwild populations in order to assesstheir interactions.

Genetic markers can be used for the accurateidentification of escaped domesticated fish in thewild environment and to monitor their ecologicaland reproductive interactions with wildpopulations.

Being able to identify aquaculture fish also enablesthe branding and tracing of aquaculture products,which is increasingly important as consumersdemand more information and assurance on thesource of seafood products.

Action #2: Incorporate genetic markers intopedigree identification of aquaticspecies and estimate the geneticmerit in selective breeding programs.

The identification of individuals to a family within abreeding program can be accomplished withgenetic markers. This eliminates the need forrearing individual families in separate tanks andthen applying tags for identification. Theelimination of individual tanks saves hatcherycosts and improves the estimation of “geneticmerit” in breeding programs.

Selective breeding may be revolutionized in nearfuture by incorporating molecular markers into theidentification of fish with superior performancetraits, such as growth and survival, while they arestill juveniles.

Atlantic salmon aquaculture industries on bothcoasts rely on North American and Europeandomesticated strains, respectively, withimportation of new genetic material severelylimited because of disease and ecologicalconcerns. Productivity of both groups of fish willrequire constant improvement by selectivebreeding in order for the industries to remaincompetitive in the world market.



Molecular markers are being used to determinethe population structure of redfish (Sebastes sp.)in the Northwest Atlantic. This information isparticularly important given the transbordernature of these stocks. The use of microsatellitemarkers has highlighted the important role ofhybridization that occurs between redfish speciesS. fasciatus, S. mentella, and S. marinus in theGulf of St. Lawrence and Laurentian Channel.Population genetic structure and geneticdiversity of these marine species are being

determined, and the analysis of archived otolithsis providing key information on the distribution of

these species as well as their recruitment history.


Molecular markers are being used to study molluscspecies such as giant scallop, soft shell clam, andblue mussels, in order to provide information to theaquaculture industry on the origin of collected spat,to help optimize production and to evaluatepotential impacts of aquaculture practices on wildpopulations.

Action #3: Develop methods of reproductivecontrol.

Various methods of reproductive control have andare continuing to be developed to avoid inter-breeding between aquaculture and wild fishpopulations that may have a negative impact onthe wild fish. The effects of the reproductivecontrol methods on the growth and survival ofaquaculture strains will determine the feasibility oftheir implementation in aquaculture.Biotechnology and genomics tools can be used inthe development and evaluation of reproductivecontrol methods.

Reproductive containment of cultured shellfishstrains will become more important as moreinvertebrate species are cultured. Shellfish culturetends to be co-located with wild populations inthe aquatic environment, increasing theopportunity and likelihood of reproductiveinteractions between cultured and wildpopulations.

Research is also ongoing to evaluate theeffectiveness of sterilization of male and femalesalmonids to prevent the breeding of escapedfarmed salmon with wild salmon stocks.

Objective #3. Enhance and apply research onpopulation genetics and genomics to identify andmonitor responses of aquatic organisms toenvironmental factors.

Action #1: Develop laboratory andbioinformatics capability for theapplication of cDNA microarrays andother genomics tools to detectphysiological responses of aquaticorganisms to environmental factors.

Genomic and molecular biology technologies suchas qPCR, Bacterial Artificial Chromosome (BAC)and Expressed Sequence Tag (EST) libraryscreening and sequencing, and microarrayanalysis are being developed in-house andthrough partnership with large national andinternational collaborative efforts.

DFO has begun to use these tools to determinethe basis for altered behaviour and development(e.g., altered migration, reproduction and growth)and reduced survival due to environmentaldisruption. This information is becomingincreasingly important for regulatory andmanagement decisions in order to ensuresustainable use of aquatic resources. Forexample, applying DNA marker technology hasallowed detection of endocrine disruption effectson salmon gonadal development caused bymunicipal and industrial effluents.

Specialized genomics techniques include thosethat determine gene expression (i.e., when genesare ‘turned on’). Examples include quantitativePCR (qPCR), RNA isolation, microarray analysis,large-scale genome sequencing, genome-wideidentification of important genes (QTLs),proteomics, metabolomics (the characterization ofthe metabolites in an organism), meta-genomicsand analysis of genomes via bacterial artificialchromosome technology.



The development of Y-chromosome DNAmarkers associated with male sexual development

have simplified the methods for production andmaintenance of monosex salmon strains which haveimportant benefits for production and conservation in

aquaculture. For chinook salmon, monosextechnology has been critical for the survival of theentire industry for more than 20 years; more

recently, with Y-marker technology greatlysimplifying the development of

all-female monosex strains.

Theme #2: Biotechnology andAquatic Animal Health DFO contributes to the viability of our internationalseafood trade through the development andapplication of biotechnology tools to manage andprotect aquatic animal health thereby enabling theDepartment to meet it’s dual role in aquatic animalhealth: (1) to protect our aquatic ecosystems and (2) to meet the ever changing international standards,through the new National Aquatic Animal HealthProgram (NAAHP).

To control disease and its spread in aquatic animals,DFO scientists work with epidemiologists andveterinarians, deploying lab tests in commercialaquaculture settings and surveying wild stocks fordiseases of concern. Quarantine and disease controlmeasures are applied to aquaculture in order topreserve stocks and export trade. Diagnosticdevelopment, validation and application for reportablediseases is now administered through the new NationalAquatic Animal Health Program (NAAHP), whichinvolves the Canadian Food Inspection Agency (CFIA)and DFO.

These measures generate the knowledge to makerecommendations in the management and control ofsignificant aquatic animal diseases in Canada includingeconomically important diseases like Infectious SalmonAnaemia (ISA) and Infectious Hematopoietic Necrosis(IHN) and the pathogen Haplosporidium nelsoni (MSXdisease of oysters).

The health of aquatic animals is critical as Canadaexports approximately $4.3 billion worth of seafoodproducts each year. To protect this trade Canadamust meet international standards set by organizationssuch as the World Organization for Animal Health(Office International des Epizooties, or OIE), which setsstandards for controlling diseases of international tradeimportance.

Our research helps set international standards fordiagnostic tests – including the development andvalidation of new molecular assays. The application ofmolecular tools also demonstrates that organismsonce believed to be pathogens of international concernare in fact innocuous (benign) host-specific parasites.DFO research into the development of DNA vaccinesand how fish respond to these treatments provides

additional health management tools to the Canadianaquaculture industry. Enhancing health throughvaccination and other husbandry activities minimizesany risk that cultured aquatic animals will serve as asource of infection for susceptible wild species.

The major advantage of molecular tools is theirspecificity and sensitivity as applied to understandingdiseases, disease progressions, host /carriers, andopportunities for mitigation and prevention.

Goal: By 2015, to have developed and appliedleading edge biotechnology-basedtechniques to detect, monitor and minimizethe impact of pathogens on aquaticanimals and apply this information toassess and improve the health of aquaticanimals.

Objectives:

1. Develop, validate and employ molecular techniquesto detect and identify endemic and exoticpathogens.

2. Incorporate molecular techniques in studies onepidemiology and transmission of aquaticpathogens for disease management.

3. Apply biotechnology-based techniques for thetreatment and prevention of aquatic animaldiseases.

4. Integrate biotechnology and other technologies inassessing the impact of disease in aquatic animalsthrough risk analysis.

Objective #1. Develop, validate and employmolecular techniques to detect and identifyendemic and exotic pathogens.

Action #1: Develop, validate and apply reliablegene-based tests for parasites andpathogens.

The detection of aquatic animal pathogensremains a priority for DFO and the seafood sectoras a whole. Molecular techniques providesensitive and pathogen- specific tools to meetthese obligations.


Currently, validated molecular tests are notavailable for most pathogens of concern, andbiotechnology is therefore under-utilised in aquaticanimal health. There is a need to develop, validateand apply this technology to investigate aquaticanimal diseases.

The development and application of moleculartechniques in Canada is necessary for theimplementation of a national surveillance program.Surveillance is internationally required todemonstrate freedom from diseases of economicand ecological concern.

Licences required for product export may beissued only if health certification is based onsensitive and specific diagnostic techniques.Certification confirms that the product is free ofdisease agents that may be harmful to theprotection and conservation of fish, and therefore,facilitates trade and the activities of theaquaculture industry.

Action #2: Identify and characterize emergingpathogens of economic andecological concern.

As aquaculture techniques are developed forcommercially valuable native species, previouslyunknown diseases are likely to be encountered.Identifying the disease agents and understandingtheir biology and pathogenesis will be facilitatedby the application of biotechnology.

The application of molecular techniques willsignificantly decrease the time required to identifyemerging pathogens, to evaluate their dispersal inthe environment and to determine the diseasestatus of different geographical zones. Thisinformation will contribute to the prevention and/orcontrol of emerging pathogens economic andecological concern.

Action #3: Establish standard quality assuranceand quality control methods and takesteps to facilitate their general use.

Successful application of molecular diagnostictechniques depends on the reliability of the results.Strict applications of prescribed procedures in aquality assurance and quality control (QA/QC)laboratory setting will ensure this reliability.

Validation of novel molecular techniques willassure that the assays can be reliably reproducedin all certified QA/QC laboratories.

The strength of our seafood exports will beenhanced if Canada maintains the level ofexpertise that is required to meet the everchanging international standards that reflect theemergence of new technologies of disease controland surveillance.



DFO scientists identified a “universal non-metazoan” polymerase chain reaction assay thatselectively amplifies a segment of the non-metazoanSmall Subunit rDNA gene. This assay was validatedas a powerful tool for obtaining molecular informationon pathogens that have not been isolated frommetazoan host tissue. Thus, solving the dilemma ofidentifying the DNA of protistan pathogens thatcannot be obtained free of host DNA, which is usuallyamplified by the application of conventional universalprimers.

Objective #2. Incorporate molecular techniques instudies on epidemiology and transmission ofaquatic pathogens for disease management.

Action #1: Use high resolution genetic typingtechniques to characterizeeconomically significant pathogens.

To enhance our understanding of pathogenesis,the development and application of moleculartools to detect pathogens in situ, and thuscharacterize pathogen dissemination within andbetween hosts is needed.

Understanding the genetic types or strains of aparticular aquatic pathogen that exists throughoutgeographic zones over extended periods of timeis essential in determining epidemiologicalinferences.

The characterization of specific strains of diseaseagents supports the implementation of appropriateresponses (e.g., virulent vs. avirulent strains ofsome viruses require different control measures).

The establishment of epidemiologically-robustmolecular-based pathogen surveys of wild andcultured stocks of aquatic animals will serve toidentify trends in the health of these populationsand to identify new potentially harmful pathogens.The detection of sub-clinically infected animalsallows for the application of preventative controlmeasures to limit disease outbreaks.

Genetic typing, combined with phylogeneticanalyses, provides information on pathogenevolution, which can be used to develop sensitivemolecular assays that can be applied tounderstanding pathogen dispersal and mode oftransmission. The ability to track pathogens thatundergo differentiation and transmission throughunexpected routes, such as host reproductiveproducts or intermediate host(s), will allow for theapplication of measures to prevent diseasetransmission.

Action #2: Develop and implement an accessibleaquatic pathogen genetic straindatabase.

A database documenting the genetic variabilityamong strains of a particular disease agent willfacilitate fish health management decisions on themovement of infected fish stocks as well asprovide epidemiological information detailingtransmission events and disease sources.

Information on the expression of genes within ahost exposed to selected pathogens, generatedthrough the use of microarrays, add to ourunderstanding of the genetic and physiologicalimpact of the pathogen on the host. Through thecollection and comparison of this type of data,additional information on the similarities anddifferences in host-pathogen responses and theimpact on gene regulation can be generated.



DFO scientists use polymerase chainreaction-based (PCR) test to differentiate

between MSX and SSO infections in oysters duringthe outbreak in Nova Scotia. The differentiation

allowed the control measures to be concentrated on areasaffected by the more pathogenic MSX infections and limitedthe economic impacts of culture operation closures. As aresult of the Canadian diagnostic experience, the Office

international des epizooties (OIE) has declared thePCR confirmation as the international standard for

the diagnosis of MSX and SSO infections inoysters. Canada, through its extensive

research, has gained internationalrecognition as a world leader

in molecular diagnostictechniques.

Objective #3. Apply biotechnology-basedtechniques for the treatment and prevention ofaquatic animal diseases.

Action #1: Develop biotechnology-basedtherapies for aquaculture andhatchery aquatic animals.

Infectious diseases are a major constraint to thedevelopment and success of aquaculture inCanada and negatively impact stockenhancement programs. The development ofprophylaxes against economically significantpathogens will greatly benefit the survival ofaquatic animals in culture facilities. Biotechnologyand genomics tools can be applied to thedevelopment of new therapies against aquaticpathogens to not only benefit aquaculture, butalso reduce the spread of pathogens to wildstocks. In addition, using molecular techniques todevelop and evaluate fish responses to newtherapies against aquatic pathogens of concernwill speed up the development phase of theseprophylaxis treatments.

DNA vaccines are proven to be effective againstsome virus pathogens of finfish and overcomemany of the problems encountered withconventional vaccines such as safety, cost andstorage. Considerable basic genomics research isstill required to identify the appropriate geneticelements of most known parasitic, bacterial andviral pathogens.

Conventional vaccination of cultured finfishinvolves intraperitoneal injection or immersiondelivery, whereas current technology requires theintramuscular delivery of DNA vaccines. Researchis necessary to explore alternative deliverymethods for DNA vaccines and ideally, to integratethe delivery of conventional and DNA vaccines.

DNA vaccines and other new therapies such asheat shock protein-based recombinant vaccineswill be explored as new therapies for hatcheryreared animals.

Action #2: Use biotechnology to understand thehost immune response to naturalinfections and follow vaccinationagainst specific pathogens.

The presence of infection is a necessary, but notunique prerequisite for disease. The ability of anaquatic animal to defend itself against the effectsof infection will determine the outcome ofinfection. Basic research is required to betterunderstand how aquatic animals respond toinfection and to vaccination. Biotechnology canprovide molecular markers of exposure and fishresponse to infection. Knowledge of the defensemechanisms of aquatic animals will enable thedevelopment of “host response” moleculardiagnostic techniques. The combined ability todiagnose infection and host response to infectionwill permit a more thorough assessment of thehealth of wild and cultured species.

Significant progress has been made elucidatingmany of the genes relevant to the salmonidimmune system and these gene sequencesprovide new tools for studying the teleost immunesystem response to pathogens and vaccines.

By collaborating nationally and internationallythrough the Genome Canada projects on aquaticorganisms such as the Genomics Research onAtlantic Salmon Project (GRASP) or theConsortium for Genomics Research on allSalmonid Projects, and by using technologiessuch as qRT-PCR and microarray analysis, DFOlaboratories will investigate expression changes ofimportant cytokine and immune response genesduring natural infections or following immunestimulation due to vaccination. New markers mayalso be identified and differential responses topathogen variants are expected.


Objective #4. Integrate biotechnology and othertechnologies in assessing the impact of diseasein aquatic animals by risk analysis.

Action #1: Work closely with CFIA to develop aformal risk-analysis process forestablished and emerging pathogensand diseases of aquatic animals.

Biotechnology will provide pathogen and hostresponse data of sufficient resolution that togetherwith conventional tools, will substantiate thefoundation of risk analysis. The risk analysisapproach may be useful in establishing prioritypathogen/host/disease combinations for policydevelopment or research.

Theme #3: Biotechnology andAquatic Ecosystem HealthDFO’s mandate is to conserve, protect and enhanceaquatic ecosystem health. Healthy and productiveaquatic ecosystems are not only home to an enormousnumber of species, but also the basis for a thrivingresource industry. Effective conservation andprotection of this valuable resource remains achallenge with so much to learn about the livingorganisms in aquatic environments, their life-cycles andbroader ecosystem structure and functions.

While we are a long way from fully understandingecosystem dynamics, recent advances in biotechnologyenable us to assess and in certain cases, mitigate theimpact of anthropogenic and environmental stressors.For example, changes in community structure andfunction can be monitored using new techniques inmeta-genomics and novel bioremediation techniquessuch as biostimulation, and bioaugmentation can beused to treat contaminated sites.

DFO has a history of monitoring contaminated sites inaquatic environments. With increased concern overthe negative impact of contaminants on the ecosystemincluding fish habitat and human health, theDepartment takes a proactive approach to siteremediation. In this regard, habitat restoration is now arecognized component of the Oceans Action Plan.

Healthy ecosystems are the basis for biodiversity,healthy communities and development. Environmentalhealth assessments are an essential component ofintegrated management initiatives including protection,conservation, mitigation and/or restoration.Biotechnology and genomics tools can generateinformation about populations, individuals, physiologicaland metabolic responses to alterations, all of whichcan provide discrete information that can be integratedinto models and approaches for evaluating ecosystemintegrity.

Goal: By 2015, to develop and applybiotechnology and genomics tools toenable assessment, mitigation andrestoration of aquatic ecosystems.

Objectives:

1. Develop and apply genomic indicators to detectand monitor environmental stress in aquaticecosystems.

2. Develop genomic tools to understand biologicalprocesses for mediating natural recovery incontaminated sites, and for development of bio-remediation technologies for mitigation.

3. Develop sensitive tools based on genetic methodsto detect and monitor invasive species and assesspotential impacts.

4. Improve measures of ecosystem health usingmeta-genomics and other biotechnology andgenomics tools.

Objective #1. Develop and apply genomicindicators to detect and monitor environmentalstress in aquatic ecosystems.

Action #1: Evaluate biological stress indicators,using biotechnology and genomicstools, for key species and ecosystemcomponents within various aquaticecosystems

Ecosystem components may respond different tothe same environmental stress, resulting in theneed to develop and implement tools that candetect environmental stress within differentorganisms representing different ecosystemcomponents, including microbial populations andsensitive species.


Changes in fitness and genetic alterations in fishcan been used as indicators for environmentalstress. For example, genetic markers have beenidentified that are tightly genetically linked to thesex determination locus in salmon, therebyallowing for unambiguous determination of geneticsex independent of the developmental state of thegonad. These genetic markers provide a valuabletool for sensitizing assays identifying endocrinedisruption effects, like gonadal sex reversal, whichhave been linked to exposure to effluents in theenvironment. Evaluation and further developmentof sensitive tools like these allow researchers toquickly and sensitively monitor the effects ofchanges in the environment and provides valuableinformation for evaluating ecosystem integrity, andmaking recommendations for changes in human-based activities.

Action #2: Develop and apply biotechnology andgenomics tools to to detectenvironmental alterations.

The application of genomics to identify changes inthe genetic structure of living organisms and theway in which they function provides a unique toolfor the delineation of impacted zones and as ameans to monitor contaminant degradationpotential and/or habitat recovery.

Gene expression profiling distinguishes alteredphysiological pathways in fish in response toenvironmental changes, and may provide an “earlywarning” system for detecting pollution, stress,habitat degradation, etc., in the aquaticenvironment.

Genomics capability allows for the investigationinto the effects of alterations in the environment onthe physiological, metabolic, protein and geneexpression within aquatic organisms. From thisinformation, potential end point indicators can beidentified through the evaluation of reference sitesor laboratory studies that focus on the impact ofhabitat degradation, pollution, climate change, etcon the organism.

Objective #2. Develop genomic tools tounderstand biological processes mediating naturalrecovery in contaminated sites, and further developbio-remediation technologies for mitigation.

Action #1: Develop genomic tools tocharacterize biological processesthatremediate contaminated sites.

Develop genomic assays to identify, isolate andcharacterize microorganisms responsible for thebiodegradation and biotransformation ofcontaminants.

Action #2: Develop biostimulation andbioaugmentation methods to promote thebiodegradation and/or biotransformation ofcontaminants.

Laboratory development and evaluation ofpotential bioremediation strategies for use incontaminated aquatic environments.

Develop application methods for bioremediationstrategies and protocols for monitoring treatmentefficacy.

Assess bioremediation strategies in field trials andpublish guidance documents for technologytransfer to internal (resource managers) andexternal (industry) clients.



The National Centre for Offshore Oil and Gas EnvironmentalResearch is developing new sensitive, cost-effective and rapidassays, based on recent advances in biotechnology formonitoring habitat recovery. A coupled application of analysisin meta-genomics and physical oceanography has improved ourunderstanding of natural recovery and the feasibility of pro-active remediation procedures in contaminated harbours(e.g., Sydney Harbour). Bioremediation strategies developedby DFO have provided direct benefit to government emergencyresponse agencies (e.g., Canadian Coast Guard) and privatesector industries that offer advice and products for oil spillcleanup on a national and international scale.

Objective #3. Develop sensitive tools usinggenetic methods to detect and monitor invasivespecies and assess potential impacts.

Action #1: Develop tools for early detection ofinvasive aquatic species.

Invasive species cost the Canadian economybillions of dollars annually and wreak havoc onaquatic ecosystems. There is internationalrecognition that invasive species are a globalenvironmental, economic and political issuewarranting urgent attention.

Action #2: Develop tools to assess and mitigatepathogens and parasites associatedwith exotic species.

Ballast water may contain exotic species, andassociated pathogens and parasites, which may bedifficult and time-consuming to identify usingconventional techniques. Through biotechnologyand genomics tools and information scientists canquickly and accurately assess which pathogens,parasites and exotic species are found in a sample.

Objective #4. Improve measures of ecosystemhealth using meta-genomics and otherbiotechnology and genomics tools

Action #1: Examine microorganism gene poolswithin aquatic ecosystems to monitordegradation or recovery(metagenomics).

Microorganisms are essential for the basicmetabolic processes controlling ecosystemfunction such as primary production, nutrientcycling, the biodegradation and biotransformationof contaminants. Advances in biotechnology andgenomics will help us better understand theircommunity structure and function.

Studies on the application of meta-genomics (i.e.,quantification of changes in genomic structure andexpression in natural microbial populations as ameans to identify changes in environmentalconditions and/or ecosystem health), have beenconducted in partnership with the BiotechnologyResearch Institute (BRI) of the National ResearchCouncil located in Montreal, Quebec.

Metagenomics could be applied to study theimpact of seawater netpens on the benthicmicrobial community. A progression of microbialpopulations within these communities has beenobserved, and metagenomics could be applied totrack this progression and the rate and effect ofchanges in these microbial communities inresponse to the presence of aquaculture activities.

Metagenomics could also be applied to identifythe microbial communities that are currently foundfrozen in northern arctic sea-ice. This could helpresearchers understand whether these bacteriaare still viable, whether there are pathogenspresent in these communities, and thus contributeto the knowledge and understanding of thehistoric microbial community within the arctic.

Action #2: Generate ecosystem integrityinformation, using biotechnology and genomicstools that can be integrated into aquaticecosystem science management approaches.

Biotechnology and genomics tools can provideinformation that helps to identify changes inbiodiversity, and in some cases, can reveallinkages between ecosystem health and the healthand biodiversity of species.

Linkages between biodiversity changes andecosystem integrity can be very complex, andalthough the information generated throughbiotechnology and genomics tools can greatlyenhance our understanding, ecosystem scienceand ecosystem management approaches willcontinue to require additional biological andecosystem science information as well asrefinement. Ultimately, the aim is to be able todetect and interpret linkages, which can contributeto informing management decisions, settingecosystem objectives, and supporting actions torestore or enhance ecosystem health.


Action #3: Develop and apply the expertise toenable the evaluation of thebiological significance andcompatibility of genomics,proteomics and metabolic profilingdata, and the integration of this datainto ecosystem integrity models.

As genomics, proteomics and metabolic profilingtools and techniques become more sophisticatedand are increasingly integrated into research, thequantity of data that is produced rapidly increases.A critical function that will have to be addressedwill be both the standardization, evaluation andhandling of data from specific, relatedexperiments, as well as addressing questions onhow to evaluate and integrate information frommultiple sources and experiments.

Biotechnology and genomics tools can provideinformation on changes in environments (e.g.,population structure), and responses toenvironmental changes (e.g., gene expressionchanges), but do not immediately indicate that animpact has occurred. In order to asses impacts,the genomics information will need to beintegrated into existing in-house DFO knowledgeand understanding of ecosystems and aquaticorganism biology, and placed in context of thenormal variance seen for ecosystems andorganisms.

Through the further development, understandingand application of biotechnology tools, morerefined estimates and interpretations of ecosystemimpacts, habitat recovery and overall ecosystemintegrity can be incorporated into scientific advicegiven to support DFO’s activities to conserve,protect and enhance aquatic ecosystems.

Theme #4: Regulatory Science forAquatic Animals with Novel Traits DFO is responsible for the regulation of aquaticorganisms with novel traits under the New SubstancesNotification Regulations (Organisms). In support of thisregulatory responsibility, DFO undertakes a researchprogram which involves the development andassessment of aquatic animals with novel traits,including transgenic fish. The majority of this research

takes place in the Centre for Aquaculture andEnvironmental Research (CAER) in British Columbia,with other projects at the Pacific Biological Station inNanaimo, British Columbia, and Bedford Institute ofOceanography in Halifax, Nova Scotia.

Included in the scope of organisms addressed underthis theme are aquatic animals that express a trait (ortraits) that is new to the organism, is no longerexpressed in the organism, or is expressed outside thenormal range of expression for that trait in thatorganism. In order to obtain factual information onperformance characteristics, fitness parameters andfood safety characteristics of aquatic animals withnovel traits, DFO has developed non-commercialsalmon strains with novel traits using conventionalapproaches such as selective breeding and modernbiotechnology. This information is important in order toassess potential impacts that escaped fish with noveltraits might have on wild populations. The transgenicstrains are also used by other federal regulatorydepartments and agencies (e.g. Health Canada andthe Canadian Food Inspection Agency) in support ofbiotechnology regulatory responsibilities.

Our program has identified regulatory science issuesthat must be addressed in the design of DFO’sregulations including the interactions with wild fish;data requirement hurdles such as sample sizeuncertainty; lab scale uncertainty; the scope of“novelty”; the effectiveness of containmentapproaches; and what information is needed in orderto complete a risk assessment.

Goal: By 2015, to undertake research to providesufficient understanding to be able toassess the use of aquatic novel livingorganisms and to allow effectiveregulation.

Objectives:

1. Enable risk assessment science through theidentification, development and evaluation ofappropriate novel aquatic animal models.

2. Conduct studies in support of risk assessmentmethodology and the design and implementationof regulations.


3. Develop and evaluate the efficacy of preventativeand mitigative measures to prevent interactionbetween wild and novel aquatic animal strains(containment strategies).

4. Assess potential ecosystem impacts of transgenicaquatic animals.

Objective #1: Enable risk assessment sciencethrough the identification, development andevaluation of appropriate novel aquatic animalmodels.

Action #1: Identify domesticated and invasiveaquatic animal species and strainswith potential threats to Canadianecosystems.

Aquatic animal strains that differ phenotypically orgenetically from those found in a specificecosystem being considered have the potential tohave short or long term effects on conspecificsand other members of the ecosystem. Examplesinclude strains of Canadian aquaculture speciesthat have been selectively bred to possesscharacteristics not found in nature; fish whichhave been enhanced in mass scale in hatcheries;foreign introduced species; and invasive"stowaway" species.

Action #2: Develop and maintain containedtransgenic strains of aquatic animalsto inform regulatory development.

It is difficult to evaluate novel aquatic animalsthrough modelling and theoretical assessmentsdue to the complex unpredictability of phenotypesarising from many genetic modifications. Thus,assessments are best performed on actualtransgenic organisms. In Canada transgenicaquatic animals are being developed forcommercial use, but such animals are notavailable for risk assessment research by thefederal government.

The synthesis of similar public domain strains foruse by DFO, other government departments, andother national and international researchers iscritical to allow development of empirical riskassessment information in support of emergingregulations. Information derived from thiscollaborative and public domain approach greatlyenhances the knowledge base for DFO scientistsand regulators on transgenic organisms, keepsDFO in contact with the latest developments in thefield and creates access to a network ofcollaborative expertise.

Action #3: Evaluate environmental parametersrequired for growth, survival andoverwintering of common R&Daquatic animals, particularly thosethat are not native to Canada

Aquatic animals are increasingly being used asmodels for research and development purposes,due to the rapid growth and short life-span forcommon R&D aquatic organisms like zebrafishand medaka. The generation of knowledge of theranges and tolerances to environmentalparameters required for growth, survival andoverwintering in Canada will provide regulatorswith scientific information that can be incorporatedinto the design and implementation of regulatoryapproaches for the oversight of R&D activitiesinvolving novel aquatic animals.

Objective #2: To conduct studies in support ofrisk assessment methodology development andthe design and implementation of regulations fornovel aquatic organisms.

Action #1: Evaluate specific phenotypes ofvarious strains of novel anddomesticated aquatic animals inorder to better determine keyparameters that influenceenvironmental risk.


Physiology provides the link between genotypeand phenotype and behaviour, and thus canprovide a critical insight into processes that areaffected by transgenesis and domestication.Experiments are needed to measure key survivalfitness characteristics (such as risk takingbehaviour, growth and energy metabolism,reproductive performance) and reproductivefitness characteristics (spawning success, fertility,fecundity, gamete quality) of transgenic anddomesticated salmon. The results of these studieswill provide knowledge to help in the assessmentof possible risks to wild salmon should thetransgenic salmon escape to naturalenvironments, and to identify key parameters toinvestigate in newly developed aquatic animals.

Assessments of behaviour, physiology andgenetics of wild, domesticated and transgenicstrains provide baseline data and knowledge thatare used to develop the optimum approachesneeded for risk assessments.

Similar phenotypes can arise through the applicationof selective breeding or modern biotechnology,including recombinant DNA techniques. Detailedcomparisons of domesticated and transgenic strainsare required to determine the nature of genotypicchanges resulting from traditional selective breedingtechniques or recombinant DNA techniques,respectively. Empirical studies ofgenotype/phenotype relationships can help provideclarity for the definition of a regulatory trigger.

Action #2: Evaluate ecosystem impacts andfitness of transgenic aquatic animalsusing model systems, prior to theirrelease.

The main objectives of risk assessments oftransgenic fish are: 1) to evaluate the phenotypeof the animal compared to nontransgenic animalsto estimate the potential impacts the former maycause on ecosystems; and 2) evaluate the relativefitness of transgenic organisms to determine ifthey can effectively compete in nature and persistthrough subsequent generations. To undertakethese assessments, knowledge of factors affectingthe ability of the novel organisms to survive tomaturation and their ability to reproduce arecritical to assess the overall lifetime fitness.

Many factors continue to be evaluated to assesssurvival and reproductive performance,invasiveness, and potential ecosystem effects(e.g., resource utilization or habitat degradation),using simple laboratory apparatus (e.g., swimtunnels, disease challenge facilities, behaviourchambers, nutrition tanks, etc.)

Comparisons of behaviour (predation avoidance,competitive growth, spawning success) areunderway for nontransgenic and transgenic fisheither raised in tanks or semi-naturalenvironments. However, there is much uncertaintyin the conduct of empirical research of transgenicaquatic animals because the way an organisminteracts with its environment profoundly affectssurvival and reproductive fitness. While suchinformation provides the foundation for planningmore detailed investigations, more complexexperimental habitats are urgently required toundertake such studies under conditions thatsimulate natural conditions more realistically.

Information from the semi-natural environmentsdeveloped to date indicates that much morecomplicated interactions among fish of differentgenotypes occur, and that pleiotropic phenotypictraits are extremely complicated to evaluate due togenotype by environment interactions, becausedifferent data is generated depending on theexperimental conditions employed. Theseobservations suggest that risk assessments basedon data generated in simple laboratory apparatusmay have very little practical use for assessmentsof risk to the natural environment.

Pleiotrophic effects in fish are known to besignificant. Therefore, the process by which anovel aquatic animal has been developed mayinfluence other traits and phenotypic expression,particularly when the method uses modernbiotechnology. In order to design and implementappropriate and effective regulations, informationon the effect of the method (or process) used todevelop the novel aquatic animal is needed.


Objective #3: Develop and evaluate the efficacyof preventative and mitigative measures toprevent interaction between wild and novelstrains (containment strategies).

Action #1: Develop and evaluate biologicalcontainment methods.

Biological containment options for finfish andshellfish have been identified and developed asmethods to limit the impact of these novel aquaticanimals on aquatic ecosystems, by preventinginterbreeding with wild strains. The evaluation ofthe efficacy of biological containment is required todetermine its appropriateness as a containmentmethod.

Triploidy (pressure shock induced within all-femalestrains) is currently the most achievable method ofinducing sterility in finfish and shellfish on a largescale. DFO now has a large series of experimentsunderway to test the efficacy of this approach forcontainment of finfish.

Previous DFO research has shown that triploidymay not provide sufficient containment for somesituations (e.g. use of transgenic strains). Thus,biological containment strategies including thoseinvolving transgenic techniques, that provide ahigher level of containment are desirable, but havenot yet been fully developed. These techniquesrequire further development and efficacyassessment which may in turn require thedevelopment of model strains.

Action #2: Evaluate physical containmentmethods for tetraploid shellfishbroodstock.

Physical containment strategies are required forpreventing environmental release and interactionswith wild populations of fertile tetraploid shellfishbroodstock that are used to produce triploidshellfish. Potential challenges for physicalcontainment exist due to the lifecycle andlifestages of shellfish. Therefore, scientists needto evaluate the efficacy of various physicalcontainment methods in order to inform thedevelopment of appropriate standards andapproaches for effectively containing these fertileaquatic animals.

Action #3: Evaluate mitigative strategies forlimiting and/or preventinginteractions between wild and novelaquatic animals.

The development and evaluation of mitigativestrategies is important as an backup approach topreventing interactions between wild and novelaquatic animals. One such approach is todevelop conditional expression systems that cancontrol survival and reproduction of escapedindividuals in nature.

Objecitive #4: Assess potential ecosystemimpacts of transgenic aquatic animals

Action #1: Generate knowledge to enable theevaluation of potential ecosystemimpacts resulting from intentionalmass introductions of novel aquaticanimals into various environments

Potential ecosystem impacts from massintroductions (e.g., triploid shellfish) will depend,among other factors, on the type of introducednovel aquatic animal, it’s novel trait, the ecosystemit is introduced into, including the presence ofconspecifics or competitors, the lifecycle of theintroduced organism, adjacent ecosystems, andthe current environmental conditions. Thesefactors and their interactions will require anecosystem approach, integrating informationgenerated from various studies.

Determination of potential ecosystem impacts isnecessary for evaluation of likely short and longterm impacts resulting from mass introductions ofnovel aquatic organisms both on the ecosysteminto which it is intended to be introduced, andadjacent ecosystems.


Action #2: Evaluate potential ecosystem impactsresulting from unintentional releasesof novel aquatic animals into variousenvironments

The potential ecosystem impacts that may resultfrom an unintentional release of novel aquaticanimals, particularly novel fertile aquatic animals,will need to be evaluated and the informationgenerated from these studies incorporated intoregulatory considerations. Potential impacts of anunintentional release of novel aquatic animals willlikely be influenced by the scale of theunintentional release. The development andevaluation of models that take into account thescale of unintentional release in addition to factorsthat would be used to estimate potentialecosystem impacts of an intentional introduction,can inform estimates of potential ecosystemimpacts from unintentional releases.

Action #3: Evaluate ecosystem factors that mayinfluence competitive ability of novelaquatic animals.

Ecosystem factors, such as the size andcomplexity of a habitat, the type and availability offood resources, population density and thepotential for migration within the ecosystem, arethought to influence the competitive ability ofaquatic animals. By evaluating the significanceand complexity of such ecosystem factors,scientists will be able to identify which factors arelikely to effect predictions of behaviour and survivalof novel aquatic animals in an ecosystem, whichare important for risk assessment models.

Action #4: Generate knowledge to betterunderstand the nature of ecosystemsthat may be most affected by novelaquatic animals

The generation of baseline data (e.g., speciesdiversity, food resources, and habitat availability)on the different ecosystems that may beimpacted, particularly from the introduction ofanadromous novel aquatic animals (e.g., salmon),is required to further develop the knowledge baseupon which assessments can be made.


Conclusions – Charting a Path Forward

Conclusions – Charting a Path Forward

T he realization of the goals and objectivesoutlined in this strategy will require significantsupport. Investment will be required to support

the research and development activities, the increasedcapacity and expertise to carry out the R&D activities,and a proactive approach to succession planning forsenior scientists. Senior management support willremain a critical component to help foster a coordinatedapproach that integrates regional and national needs.Further investments are also anticipated in order 1) tomeet the incremental costs that are associated withongoing research and equipment requirements to enablethe development of innovative biotechnologyapplications for internal use and for technology transferto appropriate end-users, 2) to generate researchinformation in support of DFO’s mandate and regulatoryresponsibilities, and 3) to allow for effective partneringand collaborations with external scientists.

In order to move from this strategy for aquaticbiotechnology and genomics to an action plan forresearch and development activities, a number of stepsmust be undertaken including increased engagementof researchers, scientists and scientific advisors withinDFO in order to further explore opportunities forincorporating biotechnology and genomics tools andapplications to support goals such as sustainablefisheries and aquaculture, aquatic ecosystem health,protecting and managing aquatic natural resources andbiodiversity. Although standard biotechnology tools arenow used throughout the Department, with the morespecialized developmental work concentrated inbiotechnology centres across the country, thestabilization of existing expertise and development ofadditional and new expertise, through enhancedpartnerships and collaborations within DFO, will benecessary in order to achieve these goals. Enhancedpartnerships will also help to identify opportunities forthe incorporation of biotechnology and genomics indelivering core mandate Science Sector services. Thiswill help to keep the Strategy current and responsive todepartmental pressures, Science Sector goals andapproaches, and the goals and objectives of theCanadian Biotechnology Strategy.

It is important to build on the success that has beenrealized to date. One of the key successes has beenin integrating and deploying biotechnology andgenomics tools and information through thedevelopment of strong and vibrant partnerships withresearchers in other government departments,academia and industry, as appropriate. This hasenabled DFO researchers and DFO Science tocapitalize on third party resources to deliver better andstronger programs, meet its mandate and key priorityobjectives more efficiently, foster and support world-class scientific and technological innovation, train newscientific personnel, and develop and maintain anational and international reputation for scientificexcellence in aquatic biotechnology and genomicsresearch. As we move forward to realizing the goalsand objectives in this Strategy, there will continue to bea concerted effort to identify and maximize externalpartnerships and collaborations in order to best placeand utilize DFO resources and expertise.

Through fostering an active, internationally respectedand innovative R&D program for aquatic biotechnologyand genomics, DFO can help to shape thedevelopment of expertise in aquatic biotechnologywithin Canada, can better influence the researchagenda and support for academic research in aquaticbiotechnology and genomics, as well as be aninternational leader in the field. This Strategyarticulates a collective vision of where biotechnologyand genomics research and development can best beincorporated in a value-added, innovative, efficient andeffective manner, into DFO Science activities andservices to help position the Department in delivery ofits mandate and achieving the three strategic priorityobjectives of safe and accessible waterways,sustainable fisheries and aquaculture, and healthy andproductive aquatic ecosystems.



Documents

Aquatic Biotechnology & Genomics Research and Development ... · biotechnology include aquaculture biotechnology ... 2 Aquatic Biotechnology & Genomics Research and Development Strategy