Aquatic Biotechnology & Genomics Research and Development Strategy

Aquatic Biotechnology & Genomics Research and Development Strategy

Aquatic Biotechnology & Genomics Research and Development Strategy (PDF, 2.12 MB)

Table of Contents

  1. Introduction
  2. Priority Research Themes
  3. Vision for 2015
  4. Issues, Trends, Drivers and Opportunities
  5. The Aquatic Biotechnology and Genomics R&D Strategy
  6. Conclusion - Charting a Path Forward

Introduction

Biotechnology is a powerful "enabling technology" with applications in many sectors and holding much promise for the future. It is a term that covers a broad spectrum of scientific applications. The Canadian Environmental Protection Act defines biotechnology as "the application of science and engineering in the direct and indirect use of living organisms or parts or products of living organisms in their natural or modified forms."

Aquatic biotechnology involves the application of science and engineering for the direct or indirect use of aquatic organisms or parts or products of living aquatic organisms in their natural or modified forms. It includes genomics, a discipline that aims to decipher and understand the entire genetic information content of plants, animal/fish organisms, and micro organism. It is fundamental to all biological and biotech research.

Components of aquatic biotechnology include aquaculture biotechnology (e.g., fish health and broodstock optimization); aquatic bioprocessing (e.g., obtaining valuable compounds from marine organisms); and aquatic bioremediation (e.g., use of microorganisms to degrade toxic chemicals in the aquatic environment).

Fisheries and Oceans Canada (DFO) is linking innovative biotechnology and genomics science with higher level policy making and on-the-ground fishery and aquatic ecosystem management decisions.

The development and application of biotechnology and genomics tools to enhance sustainable resource management and environmental conservation and protection is increasing in Canada and around the world. Advances and application developments in biotechnology and genomics present the possibility for lower-cost biotechnology applications with advantages, such as greater sensitivity, accuracy, faster results and increased efficiency, over more traditional technologies. DFO is part of this biotechnology and genomics wave with innovative science across the country supporting our mandate.

As biotechnology and genomics tools and information are increasingly incorporated into DFO research and development activities, an integrative approach to identifying opportunities for sharing expertise, coordinating efforts and increasing efficiencies within DFO's biotechnology and genomics R&D activities was taken.

DFO's Aquatic Biotechnology Program has been in place since the late 1980s, with the majority of our developments occurring within the last 10 years. With targeted start-up funding, DFO has strategically developed expertise and capabilities in biotechnology and genomics. DFO researchers and key partners have developed new biotechnology techniques that support policy and management decisions to enhance the ecological sustainability of the wild fishery, aquaculture and oceans ecosystems. Our success has been a result of being able to quickly apply our research through effective partnerships, deploying products and tools to enable clients in other government agencies, and the private and public sectors to adopt and benefit from the application of new technologies, while keeping the research aligned with departmental priorities.

DFO's Mandate and Aquatic Biotechnology

Key departmental priorities, as outlined in the 2005-2010 Strategic Plan: Our Waters, Our Future, can be supported by biotechnology and genomics research, development and innovations. The Department's strategic plan clearly states that sustainable development is a priority. An underlying premise of sustainable development is that a strong sustainable economy is a product of a healthy natural environment and healthy society. Habitat destruction, loss of biodiversity, and land and sea-based pollution all have a negative impact on our culture, society and economy. Properly managed, our natural resources and aquatic environment will be sustained for future generations, and provide the basis for growth and co-existence of current and emerging aquatic resource users.

Biotechnology and genomic tools and products contribute to the three inter-related DFO priority outcomes:

  1. Healthy and Productive Aquatic Ecosystems - Refers to the sustainable development and integrated management of resources in or around Canada's aquatic environment through oceans and fish habitat management, and the critical science activities that support these two programs.
  2. Sustainable Fisheries and Aquaculture - Refers to an integrated fisheries and aquaculture program that is credible, science-based, affordable and effective, and contributes to sustained wealth for Canadians.
  3. Safe and Accessible Waterways- is about providing access to Canadian waterways, and ensuring the overall safety and integrity of Canada's marine infrastructure for the benefit of all Canadians.

DFO Science Renewal

In 2004, DFO embarked on a review of all science activities in order to identify and match all science activities to the three key departmental and government priorities, review commitments and capacity in order to balance advice needs with ability to deliver the advice, and to finalize and implement a long-term plan to ensure relevance and sustainability of the Science Program.

DFO's Science Sector must also be responsive to internal drivers, such as the increase in demand for science advice, products, and services. These requests are increasingly complex, requiring integrative approaches and ecosystem considerations. Additionally, the scientific information, products, services and advice needs to be flexible and responsive to rapidly emerging departmental and federal priorities. However, there is an acknowledgement that the scientific capacity and resources required to meet these ever increasing demands are not available.

In response to these drivers, Science Renewal aims to produce a vibrant aquatic science program based on excellence that supports and informs DFO and Government needs and best serves Canadians. The framework to deliver on this objective is to ensure that DFO science is relevant, and responsive to priorities; effective, through a modern and effective science functions; affordable; and valued.

To support DFO priorities, 13 clusters of science activities have been identified, including Biotechnology and Genomics (see figure, above). These clusters have been identified as key program areas that support national Science Sector priorities through research, monitoring, providing science advice, products and services, data management, and science management. Many of the core clusters have been identified as Centres of Expertise, a new management and coordination approach to streamline science service delivery and national coordination, thereby increasing efficiency and effectiveness.

Standard biotechnology tools are now used throughout the Department with the more specialized developmental work concentrated in biotechnology centres across the country, resulting in the development of core capacity and expertise. DFO is continually increasing its capacity in terms of highly skilled personnel, and specialized equipment and facilities in order to develop and deploy leading-edge biotechnology and genomics tools. In part, the success that DFO has had in integrating and deploying biotechnology and genomics tools and information is due to the development of strong and vibrant partnerships with researchers in other government departments, academia and industry, as appropriate. This has enabled DFO researchers and DFO Science to capitalize on third party resources to deliver better and stronger programs, to meet its mandate and key priority objectives more efficiently, to foster and support world-class scientific and technological innovation, to train new scientific personnel, and to develop and maintain a national and international reputation for scientific excellence in aquatic biotechnology and genomics research.

Partnering with Canadians

DFO scientists take on research in support of issues that matter to our stakeholders. We work closely with the aquatic resource managers, users and conservation groups and identify priorities based on the needs of these communities. Biotechnology research also provides information that support Canada's national and international commitments in aquatic animal health, stock management and assessment of risks associated with biotechnology-derived products.

The multi-faceted nature of fisheries, aquaculture, and management of aquatic ecosystems, and the interdisciplinary nature of biotechnology requires, and benefits from, strong partnerships and effective stakeholder relations. DFO works with a diverse range of stakeholder groups and individuals including: local communities; fishery biologists; enforcement personnel; international scientists; international research and regulatory organizations; international governments; aboriginal groups with fishing and resource rights; commercial aquaculture and wild fishery organizations; companies; and, provincial and territorial counterparts with shared resource management responsibilities. DFO has partnerships with governments and research institutes in the United States, Norway, France, the United Kingdom, Sweden, Japan, Korea, and Germany.

Moving Forward - Aquatic Biotechnology and Genomics Research and Development Strategy: Shaping the Future

Despite progress made possible through start-up funding, the incremental costs associated with ongoing research and its application are challenging the Department to regularly seek additional funds to meet the increasing capacity needs and maximize the application of these tools for sustainable development. As enabling technologies that are inherently multidisciplinary, biotechnology and genomics may have applications and information to support the aims of many of the other science clusters, including Aquatic Animal Health, Aquatic Invasive Species, Species at Risk, Aquaculture Production, etc.

To build on success to date, and chart a clear path forward, DFO has developed the following Aquatic Biotechnology and Genomics R&D Strategy to support DFO's departmental and national obligations over the next number of years. This Strategy is the product of input from DFO's scientists, the National Biotechnology Coordinators, biotechnology regulators, and managers.

This strategy was intended to capture the wide range of science initiatives either underway or proposed within DFO. The biotechnology and genomics R&D opportunities and priorities have been mapped out over a variety of timeframes, allowing for the actions and outcomes to build on one another, thus permitting the integration of experiences, and outputs from previous activities.

By increasing the awareness and understanding of the multiple benefits derived from the application of biotechnology tools, senior government officials will be better able to make informed policy decisions and invest in areas where science gaps remain. Risk assessments and critical decisions need to be made at all levels, reinforcing the need for an integrated approach.

The Strategy also outlines the inherent multidisciplinary aspect of biotechnology and genomics, and provides examples of applications of these enabling technologies to many of DFO's mandated science advice and activities. The opportunities for biotechnology and genomics research and development to provide new and precise tools and information to help meet the Department's mandate will continue to be explored as the science and technology matures. Science Renewal involves linking the science program to Departmental and federal strategic outcomes and priorities within a new Departmental reporting structure. Biotechnology and genomics tools and applications can add value, efficiencies and improve effectiveness in meeting core mandated science advice and information needs.

Priority Research Themes

Four priority research themes form the Strategy's key elements and include goals, objectives and actions designed to shape DFO's biotechnology agenda for the next four years. It is expected that this Strategy will continuously evolve in dynamic response to 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 2015

The following Strategy proposes a vision of where we want to be in 2015 and a roadmap to get there.

To have in place by 2015:

A successful, innovative, dynamic biotechnology and genomics program to enhance the sustainability of our aquatic resources and the ecological health of our aquatic ecosystems, that is characterized by strong partnerships and stakeholder involvement; innovative research programs; the application of effective biotechnology and genomics tools and products; and funding to maintain required expertise.

The successful implementation of this Strategy will depend on leadership, commitment, creativity and expertise of DFO's management, scientists, external stakeholders, resource managers and decision-makers across the country.

Issues, Trends, Drivers and Opportunities

Developments at the national and international scale shape DFO's priorities. For instance, we know that competing resource demands; human population growth; climate and environmental change; scientific and technological advances; international responsibilities and obligations; shifting economic paradigms; traditional funding of high value/high visibility species; and, societal demands are a just a few of the drivers shaping DFO's agenda. We are faced with the challenge of understanding the complex interrelationship between these and other variables, in order to target our science, and inform policy choices, ultimately ensuring the long-term viability of the aquatic resources, and health of aquatic ecosystems for which we are responsible.

Public expectations for government action on these issues are high. The department is facing pressure from industry and communities, to increase investment in science and apply efficient and effective tools to better comprehend and manage aquatic resources. The public also sees a role for government to help in capitalizing on the potential of biotechnology to increase jobs and economic growth in Canada. This is especially true for coastal and rural Canadians.

DFO is responding by, as part of a department-wide science renewal, expanding its Aquatic Biotechnology and Genomics R&D Program. It has been proven that the speed, sensitivity and accuracy of using biotechnology and genomics tools provides many advantages in addition to more traditional methods of, for example, species identification, contaminated site remediation, and disease diagnosis.

Key Trends

Canada stands to gain from aquatic biotechnology and genomics innovation as these tools directly and indirectly support aquatic resource management and ecosystem integrity. To put this into context:

The National Context

The rapid pace of biotechnology discoveries continues to accelerate with some viewing its potential analogous to the impact of information and communication technologies. According to Canadian Trends in Biotechnology, Second Edition 2005:

From 1997 to 2003, biotechnology revenues more than quadrupled, from $813 million to $3.8 billion. Over that entire period, more than half of biotechnology revenues were received by companies in the human health sector. As noted earlier, this figure could change if the national and federal focus were to be expanded to include a greater emphasis on natural resources and the environment, in recognition of the correlation between a healthy population, environment and economic growth.

The Canadian Biotechnology Strategy: A Federal Initiative

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

The CBS provides a framework to guide national biotechnology activities. The CBS is led by Industry Canada in partnership with a number of federal departments, agencies, and research institutes such as Environment Canada (EC), Canadian Food Inspection Agency (CFIA), Natural Resources Canada (NRCan), Health Canada (HC), National Research Council (NRC), Agriculture and Agrifood Canada (AAFC), DFO and others.

The CBS vision is: "to enhance the quality of life of Canadians in terms of health, safety, the environment and social and economic development by positioning Canada as a responsible world leader in biotechnology". The CBS is comprised of three pillars: Innovation, Regulation and Public Outreach. This strategy outlines DFO's role in all three of these pillars, and highlights both DFO's future role and direction in supporting these pillars, and some current accomplishments.

4.2 The International Context

One of the priorities of the federal government is to place Canada as a world leader in biotechnology. According to Organization for Economic Cooperation and Development (OECD) data for the year 2000, the number of dedicated biotechnology firms per million inhabitants is highest in Sweden, Switzerland and Canada. We also rank second in the proportion of total publicly funded R&D investments that is devoted to biotechnology. Denmark, Canada and New Zealand invest more than 10% of their total publicly funded R&D budgets in biotechnology. 5

Internationally, in 2003 nearly 89% of all biotechnology R&D expenditures were in the human health sector, with 6% of biotechnology R&D in the agriculture and food processing sectors. Biotechnology investment in the natural 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-based economic development in Canada, and economic growth, along with the direct and indirect impact of the quality of the natural environment on human health and environment are two reasons why a shift in R&D investments is necessary. Canada can become a global leader in the development, application and transfer of innovative aquatic biotechnology techniques and products. Doing so will not only benefit the international community with the uptake of products that will ultimately foster a more sustainable global fishery, but also Canadian industry and coastal communities, and consumers.

International Fisheries and Oceans Management

Global production from capture fisheries and aquaculture supplied about 101 million tonnes of food fish in 2002.6

International fisheries and oceans management issues are complex. Uncertainty arises from many factors including cumulative impacts, climate change, an increase in the number of people using ocean resources, the variety of ocean activities, as well as international markets and socio-economic pressure.

For many years, a major challenge for the management of the international fishery has been the quest to establish appropriate fishing quotas in light of the high level of uncertainty and complexity.

With the development of genetic tools to "genetically fingerprint" fish as individuals and populations, new information can be generated that enables the attribution of fish stocks that straddle international boundaries to country of origin. This additional information can be used by the Department, and the international community, to develop and propose quotas that are more reflective of migratory patterns and the need to maintain the health of fish stocks. Through the development of sensitive, accurate and rapid tests that provide valuable information to fisheries and oceans managers, Canada is contributing to the international knowledge and tool base for addressing the challenge of managing international fisheries, thereby supporting and contributing to our responsibilities under the United Nations Convention on the Law of the Sea (UNCLOS), International Council for the Exploration of the Sea (ICES), the Pacific Salmon Commission, North Pacific Anadromous Fisheries Commission, and, the North Atlantic Fisheries Organization.

Aquaculture in the World

Worldwide, aquaculture is the fastest-growing sector in agri-food, with fish accounting for more than 40% of revenues. The United Nations' Food and Agriculture Organization (FAO) reports total aquaculture production was 39 million tonnes in 2002, and predicts total aquaculture fish production will exceed 130 million tonnes per year by 2030.

Under the Department's 2005-2010 Strategic Plan, DFO will "seek opportunities to create the conditions for the development of an environmentally sustainable, internationally competitive aquaculture industry in Canada." Biotechnology and genomics innovations will continue to contribute to the industry's growth and success through development and application of tools, including those for regulatory and production support.

In support of sustainable aquaculture, DFO's biotechnology and genomics research is investigating and evaluating methods to mitigate the interactions between wild and domesticated strains. Through the development of accurate and efficient methods that allow for aquaculture strains to be distinguished from wild populations, assessment of the impact of interactions can be made, as well as allowing for the tracing of aquaculture products. In addition, the application of sensitive and specific techniques for detecting aquatic animal pathogens will provide information on disease transmission. The tools and results from these studies can then be used to inform aquaculture management decisions.

Biotechnology and genomics tools have applications to support the development of robust aquaculture broodstock, both for species that have been used extensively in aquaculture and for new aquaculture species. For example, DFO scientists, in collaboration with academic partners are developing two elite cod broodstocks, one in New Brunswick and one in Newfoundland and Labrador, both based on local stocks of cod, using traditional and biotechnology and genomics tools and information. The genetic information anticipated to be generated from this project will be used to direct the selective breeding to prevent inbreeding and to select for fast growing and/or disease resistant families for use in aquaculture.

Aquatic Ecosystem Health

There is now growing international acceptance for ecosystem-based integrated management practices to protect our aquatic resources. Ecosystem health information can be informed by the development and use of standardized indicators, which can then be used as part of the risk management decision process. The application of outcomes from biotechnology and genomics research provide the means to monitor aquatic ecosystem health using biomarkers - multiple biomolecular signatures that when examined together present a unique pattern of molecular change in an organism and identify an exposure or response to a specific environmental stressor. Furthermore, advances in biotechnology will provide novel means monitor and address the remediation of existing contaminated sites (e.g., bioremediation strategies).

The Aquatic Biotechnology and Genomics R&D Strategy

The following Strategy elaborates on the four themes and includes goals, objectives and actions designed to shape DFO's biotechnology and genomics. It is expected that the strategy will continuously evolve in response to departmental priorities, but that the broad themes and objectives capture key opportunities and activities that biotechnology and genomics applications and information can address, as it relates to DFO's mandate, strategic objectives and Science Sector's Renewal.

As biotechnology and genomics are enabling technologies and therefore multidisciplinary in nature, there are opportunities for the results from each of the research themes' activities and objectives to be incorporated and built on in other research themes. By mapping out the strategic direction and opportunities for biotechnology and genomics R&D, it is anticipated that new collaborations and partnerships can be identified, additional opportunities to transfer knowledge, expertise and applications will be realized, and efficiencies identified and implemented.

Theme #1: Biotechnology and Aquatic Resource Profiling

This research theme encompasses all activities related to understanding the genetic make-up of our aquatic resources. Biotechnology and genomics in this area include studying the genome of aquatic species, studying the population structure of these species and studying the genetics behind interactions between aquatic species and their environment (other species and environmental conditions).

Aquatic resource profiling directly supports sustainable fisheries, sustainable aquaculture, protection of biodiversity and recovery of species at risk. The goal is to optimize the productivity of the aquatic environment (from wild capture and aquaculture) while maintaining environmental health and biodiversity.

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

Endangered populations can also be identified and protected to ensure the genetic variability of each survives and thrives. Collated data on both endangered populations is housed in genomic libraries where the information is used to establish a clear understanding of population dynamics.

On the enforcement side, the development of forensic DNA capability in DFO has expanded the scope of enforcement actions while reducing expenditures associated with prosecutions for illegal harvest or sale of fish and shellfish.

Goal:

By 2015, to have developed biotechnology tools for genetic profiling of aquatic species and facilitated their widespread application in Canada and abroad, contributing to the sustainable use of aquatic resources.

Objectives:

  1. Identify genetic markers to improve species, strain and stock identification for fisheries management and to allow for the protection and enhancement of biodiversity and aquatic fish habitat, including species at risk.
  2. Improve biotechnology knowledge base for enhanced sustainability of aquaculture production: increase strain development and enhance biotechnology tools for identification and control of aquaculture species.
  3. Enhance and apply research on population genetics and genomics to identify and monitor response of aquatic organisms due to environmental factors.

Objective #1

Identify genetic markers to improve species identification for fisheries management and to allow for the protection and enhancement of biodiversity and aquatic fish habitat.

Action #1:

Develop genetic markers for commercially important fisheries species to integrate into sustainable fisheries management practices.

Did You Know That…

DFO is using genomic tools such as mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) to identify stocks of beluga whales. The tools are used to estimate the proportion of beluga belonging to different stocks in an aboriginal mixed-stock fisheries and establish maximum harvest limits that reflect the sustainable harvest of each stock. Management actions are taken to enforce area closures when the DNA indicates that the area is frequented by a stock at a lower abundance level.

Did You Know That…

Due to its commercial viability and ease of tracking, salmon have become one of the most studied aquatic species in Canada and globally. Large, genetic baseline datasets for Pacific salmon, developed by DFO scientists, are used for the most intensive genetic management of fisheries on a real-time basis in the world. Over 10,000 chinook, sockeye and coho salmon samples are analyzed each year to manage fishery openings, enabling Canada to maximize catch under the US/Canada Pacific Salmon Treaty (PST) allocations while maintaining strict harvest limits on stocks of conservation concern. For example, real-time genetic management of the 2003 and 2004 north coast troll fishery on chinook salmon enabled the PST quota to be achieved for the first time since 1994 without overharvesting west coast Vancouver Island populations of conservation concern, resulting in increased annual revenue to the fisheries of over $3 million dollars.

Action #2:

Develop genetic markers for species of interest to Habitat Management including vulnerable species such as those listed by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) for protection under the Species at Risk Act (SARA) or under the Convention on the International Trade of Endangered Species (CITES).

Did You Know That…

Using genetic profiling tools, DFO scientists have been able to distinguish the ‘inner' yelloweye rockfish population resident in the Strait of Georgia and Queen Charlotte Sound from an outer coastal population that extends from Oregon to Alaska. The genetic isolation and reduced abundance of the inner yelloweye rockfish population have been documented in a status report on the species for COSEWIC.

Action #3:

Enhance the use of forensic species identification for enforcement of fisheries and for the implementation of traceability requirements in other regulations.

Action #4:

Expand the scope of genetics and genomics databases for species under DFO management and those aquatic species managed through international agreements.

Did You Know That…

Molecular markers are being used to determine the population structure of redfish (Sebastes sp.) in the Northwest Atlantic. This information is particularly important given the transborder nature of these stocks. The use of microsatellite markers has highlighted the important role of hybridization that occurs between redfish species S. fasciatus, S. mentella, and S. marinus in the Gulf of St. Lawrence and Laurentian Channel. Population genetic structure and genetic diversity of these marine species are being determined, and the analysis of archived otoliths is providing key information on the distribution of these species as well as their recruitment history.

Objective #2:

Improve biotechnology knowledge base for enhanced sustainable aquaculture production: increase strain development and enhance biotechnology tools for identification and control of aquaculture fish.

Action #1:

Develop genetic markers to distinguish aquaculture strains from wild populations in order to assess their interactions.

Did You Know That...

Molecular markers are being used to study mollusc species such as giant scallop, soft shell clam, and blue mussels, in order to provide information to the aquaculture industry on the origin of collected spat, to help optimize production and to evaluate potential impacts of aquaculture practices on wild populations.

Action #2:

Incorporate genetic markers into pedigree identification of aquatic species and estimate the genetic merit in selective breeding programs.

Did You Know That…

The development of Y-chromosome DNA markers associated with male sexual development have simplified the methods for production and maintenance of monosex salmon strains which have important benefits for production and conservation in aquaculture. For chinook salmon, monosex technology has been critical for the survival of the entire industry for more than 20 years; more recently, with Y-marker technology greatly simplifying the development of all-female monosex strains.

Action #3:

Develop methods of reproductive control.

Objective #3

Enhance and apply research on population genetics and genomics to identify and monitor responses of aquatic organisms to environmental factors.

Action #1:

Develop laboratory and bioinformatics capability for the application of cDNA microarrays and other genomics tools to detect physiological responses of aquatic organisms to environmental factors.

Theme #2: Biotechnology and Aquatic Animal Health

DFO contributes to the viability of our international seafood trade through the development and application of biotechnology tools to manage and protect aquatic animal health thereby enabling the Department to meet it's dual role in aquatic animal health: (1) to protect our aquatic ecosystems and (2) to meet the ever changing international standards, through the new National Aquatic Animal Health Program (NAAHP).

To control disease and its spread in aquatic animals, DFO scientists work with epidemiologists and veterinarians, deploying lab tests in commercial aquaculture settings and surveying wild stocks for diseases of concern. Quarantine and disease control measures are applied to aquaculture in order to preserve stocks and export trade. Diagnostic development, validation and application for reportable diseases is now administered through the new National Aquatic Animal Health Program (NAAHP), which involves the Canadian Food Inspection Agency (CFIA) and DFO.

These measures generate the knowledge to make recommendations in the management and control of significant aquatic animal diseases in Canada including economically important diseases like Infectious Salmon Anaemia (ISA) and Infectious Hematopoietic Necrosis (IHN) and the pathogen Haplosporidium nelsoni (MSX disease of oysters).

The health of aquatic animals is critical as Canada exports approximately $4.3 billion worth of seafood products each year. To protect this trade Canada must meet international standards set by organizations such as the World Organization for Animal Health (Office International des Epizooties, or OIE), which sets standards for controlling diseases of international trade importance.

Our research helps set international standards for diagnostic tests - including the development and validation of new molecular assays. The application of molecular tools also demonstrates that organisms once believed to be pathogens of international concern are in fact innocuous (benign) host-specific parasites. DFO research into the development of DNA vaccines and how fish respond to these treatments provides additional health management tools to the Canadian aquaculture industry. Enhancing health through vaccination and other husbandry activities minimizes any risk that cultured aquatic animals will serve as a source of infection for susceptible wild species.

The major advantage of molecular tools is their specificity and sensitivity as applied to understanding diseases, disease progressions, host /carriers, and opportunities for mitigation and prevention.

Goal:

By 2015, to have developed and applied leading edge biotechnology-based techniques to detect, monitor and minimize the impact of pathogens on aquatic animals and apply this information to assess and improve the health of aquatic animals.

Objectives:

  1. Develop, validate and employ molecular techniques to detect and identify endemic and exotic pathogens.
  2. Incorporate molecular techniques in studies on epidemiology and transmission of aquatic pathogens for disease management.
  3. Apply biotechnology-based techniques for the treatment and prevention of aquatic animal diseases.
  4. Integrate biotechnology and other technologies in assessing the impact of disease in aquatic animals through risk analysis.

Objective #1

Develop, validate and employ molecular techniques to detect and identify endemic and exotic pathogens.

Action #1:

Develop, validate and apply reliable gene-based tests for parasites and pathogens.

Action #2:

Identify and characterize emerging pathogens of economic and ecological concern.

Did you know that…

DFO scientists identified a "universal non-metazoan" polymerase chain reaction assay that selectively amplifies a segment of the non-metazoan Small Subunit rDNA gene. This assay was validated as a powerful tool for obtaining molecular information on pathogens that have not been isolated from metazoan host tissue. Thus, solving the dilemma of identifying the DNA of protistan pathogens that cannot be obtained free of host DNA, which is usually amplified by the application of conventional universal primers.

Action #3:

Establish standard quality assurance and quality control methods and take steps to facilitate their general use.

Did you know that…

DFO scientists use polymerase chain reaction-based (PCR) test to differentiate between MSX and SSO infections in oysters during the outbreak in Nova Scotia. The differentiation allowed the control measures to be concentrated on areas affected by the more pathogenic MSX infections and limited the economic impacts of culture operation closures. As a result of the Canadian diagnostic experience, the Office international des epizooties (OIE) has declared the PCR confirmation as the international standard for the diagnosis of MSX and SSO infections in oysters. Canada, through its extensive research, has gained international recognition as a world leader in molecular diagnostic techniques.

Objective #2

Incorporate molecular techniques in studies on epidemiology and transmission of aquatic pathogens for disease management.

Action #1:

Use high resolution genetic typing techniques to characterize economically significant pathogens.

Action #2:

Develop and implement an accessible aquatic pathogen genetic strain database.

Objective #3

Apply biotechnology-based techniques for the treatment and prevention of aquatic animal diseases.

Action #1:

Develop biotechnology-based therapies for aquaculture and hatchery aquatic animals.

Action #2:

Use biotechnology to understand the host immune response to natural infections and follow vaccination against specific pathogens.

Objective #4

Integrate biotechnology and other technologies in assessing the impact of disease in aquatic animals by risk analysis.

Action #1:

Work closely with CFIA to develop a formal risk-analysis process for established and emerging pathogens and diseases of aquatic animals.

Theme #3: Biotechnology and Aquatic Ecosystem Health

DFO's mandate is to conserve, protect and enhance aquatic ecosystem health. Healthy and productive aquatic ecosystems are not only home to an enormous number of species, but also the basis for a thriving resource industry. Effective conservation and protection of this valuable resource remains a challenge with so much to learn about the living organisms in aquatic environments, their life-cycles and broader ecosystem structure and functions.

While we are a long way from fully understanding ecosystem dynamics, recent advances in biotechnology enable us to assess and in certain cases, mitigate the impact of anthropogenic and environmental stressors. For example, changes in community structure and function can be monitored using new techniques in meta-genomics and novel bioremediation techniques such as biostimulation, and bioaugmentation can be used to treat contaminated sites.

DFO has a history of monitoring contaminated sites in aquatic environments. With increased concern over the negative impact of contaminants on the ecosystem including fish habitat and human health, the Department takes a proactive approach to site remediation. In this regard, habitat restoration is now a recognized component of the Oceans Action Plan.

Healthy ecosystems are the basis for biodiversity, healthy communities and development. Environmental health assessments are an essential component of integrated management initiatives including protection, conservation, mitigation and/or restoration. Biotechnology and genomics tools can generate information about populations, individuals, physiological and metabolic responses to alterations, all of which can provide discrete information that can be integrated into models and approaches for evaluating ecosystem integrity.

Goal:

By 2015, to develop and apply biotechnology and genomics tools to enable assessment, mitigation and restoration of aquatic ecosystems.

Objectives:

  1. Develop and apply genomic indicators to detect and monitor environmental stress in aquatic ecosystems.
  2. Develop genomic tools to understand biological processes for mediating natural recovery in contaminated sites, and for development of bio-remediation technologies for mitigation.
  3. Develop sensitive tools based on genetic methods to detect and monitor invasive species and assess potential impacts.
  4. Improve measures of ecosystem health using meta-genomics and other biotechnology and genomics tools.

Objective #1:

Develop and apply genomic indicators to detect and monitor environmental stress in aquatic ecosystems.

Action #1:

Evaluate biological stress indicators, using biotechnology and genomics tools, for key species and ecosystem components within various aquatic ecosystems

Action #2:

Develop and apply biotechnology and genomics tools to to detect environmental alterations.

Objective #2

Develop genomic tools to understand biological processes mediating natural recovery in contaminated sites, and further develop bio-remediation technologies for mitigation.

Action #1:

Develop genomic tools to characterize biological processes that remediate contaminated sites.

Action #2:

Develop biostimulation and bioaugmentation methods to promote the biodegradation and/or biotransformation of contaminants.

Did You Know That…

The National Centre for Offshore Oil, Gas and Energy Research is developing new sensitive, cost-effective and rapid assays, based on recent advances in biotechnology for monitoring habitat recovery. A coupled application of analysis in meta-genomics and physical oceanography has improved our understanding of natural recovery and the feasibility of pro-active remediation procedures in contaminated harbours (e.g., Sydney Harbour). Bioremediation strategies developed by DFO have provided direct benefit to government emergency response agencies (e.g., Canadian Coast Guard) and private sector industries that offer advice and products for oil spill cleanup on a national and international scale.

Objective #3

Develop sensitive tools using genetic methods to detect and monitor invasive species and assess potential impacts.

Action #1:

Develop tools for early detection of invasive aquatic species.

Action #2:

Develop tools to assess and mitigate pathogens and parasites associated with exotic species.

Objective #4

Improve measures of ecosystem health using meta-genomics and other biotechnology and genomics tools

Action #1:

Examine microorganism gene pools within aquatic ecosystems to monitor degradation or recovery (metagenomics).

Action #2:

Generate ecosystem integrity information, using biotechnology and genomics tools that can be integrated into aquatic ecosystem science management approaches.

Action #3:

Develop and apply the expertise to enable the evaluation of the biological significance and compatibility of genomics, proteomics and metabolic profiling data, and the integration of this data into ecosystem integrity models.

Theme #4: Regulatory Science for Aquatic Animals with Novel Traits

DFO is responsible for the regulation of aquatic organisms with novel traits under the New Substances Notification Regulations (Organisms). In support of this regulatory responsibility, DFO undertakes a research program which involves the development and assessment of aquatic animals with novel traits, including transgenic fish. The majority of this research takes place in the Centre for Aquaculture and Environmental Research (CAER) in British Columbia, with other projects at the Pacific Biological Station in Nanaimo, British Columbia, and Bedford Institute of Oceanography in Halifax, Nova Scotia.

Included in the scope of organisms addressed under this theme are aquatic animals that express a trait (or traits) that is new to the organism, is no longer expressed in the organism, or is expressed outside the normal range of expression for that trait in that organism. In order to obtain factual information on performance characteristics, fitness parameters and food safety characteristics of aquatic animals with novel traits, DFO has developed non-commercial salmon strains with novel traits using conventional approaches such as selective breeding and modern biotechnology. This information is important in order to assess potential impacts that escaped fish with novel traits might have on wild populations. The transgenic strains are also used by other federal regulatory departments and agencies (e.g. Health Canada and the Canadian Food Inspection Agency) in support of biotechnology regulatory responsibilities.

Our program has identified regulatory science issues that must be addressed in the design of DFO's regulations including the interactions with wild fish; data requirement hurdles such as sample size uncertainty; lab scale uncertainty; the scope of "novelty"; the effectiveness of containment approaches; and what information is needed in order to complete a risk assessment.

Goal:

By 2015, to undertake research to provide sufficient understanding to be able to assess the use of aquatic novel living organisms and to allow effective regulation.

Objectives:

  1. Enable risk assessment science through the identification, development and evaluation of appropriate novel aquatic animal models.
  2. Conduct studies in support of risk assessment methodology and the design and implementation of regulations.
  3. Develop and evaluate the efficacy of preventative and mitigative measures to prevent interaction between wild and novel aquatic animal strains (containment strategies).
  4. Assess potential ecosystem impacts of transgenic aquatic animals.

Objective #1:

Enable risk assessment science through the identification, development and evaluation of appropriate novel aquatic animal models.

Action #1:

Identify domesticated and invasive aquatic animal species and strains with potential threats to Canadian ecosystems.

Action #2:

Develop and maintain contained transgenic strains of aquatic animals to inform regulatory development.

Action #3:

Evaluate environmental parameters required for growth, survival and overwintering of common R&D aquatic animals, particularly those that are not native to Canada

Objective #2:

To conduct studies in support of risk assessment methodology development and the design and implementation of regulations for novel aquatic organisms.

Action #1:

Evaluate specific phenotypes of various strains of novel and domesticated aquatic animals in order to better determine key parameters that influence environmental risk.

Action #2:

Evaluate ecosystem impacts and fitness of transgenic aquatic animals using model systems, prior to their release.

Objective #3:

Develop and evaluate the efficacy of preventative and mitigative measures to prevent interaction between wild and novel strains (containment strategies).

Action #1:

Develop and evaluate biological containment methods.

Action #2:

Evaluate physical containment methods for tetraploid shellfish broodstock.

Action #3:

Evaluate mitigative strategies for limiting and/or preventing interactions between wild and novel aquatic animals.

Objecitive #4:

Assess potential ecosystem impacts of transgenic aquatic animals

Action #1:

Generate knowledge to enable the evaluation of potential ecosystem impacts resulting from intentional mass introductions of novel aquatic animals into various environments

Action #2:

Evaluate potential ecosystem impacts resulting from unintentional releases of novel aquatic animals into various environments

Action #3:

Evaluate ecosystem factors that may influence competitive ability of novel aquatic animals.

Action #4:

Generate knowledge to better understand the nature of ecosystems that may be most affected by novel aquatic animals

Conclusions - Charting a Path Forward

The realization of the goals and objectives outlined in this strategy will require significant support. Investment will be required to support the research and development activities, the increased capacity and expertise to carry out the R&D activities, and a proactive approach to succession planning for senior scientists. Senior management support will remain a critical component to help foster a coordinated approach that integrates regional and national needs. Further investments are also anticipated in order

  1. to meet the incremental costs that are associated with ongoing research and equipment requirements to enable the development of innovative biotechnology applications for internal use and for technology transfer to appropriate end-users,
  2. to generate research information in support of DFO's mandate and regulatory responsibilities, and
  3. to allow for effective partnering and collaborations with external scientists.

In order to move from this strategy for aquatic biotechnology and genomics to an action plan for research and development activities, a number of steps must be undertaken including increased engagement of researchers, scientists and scientific advisors within DFO in order to further explore opportunities for incorporating biotechnology and genomics tools and applications to support goals such as sustainable fisheries and aquaculture, aquatic ecosystem health, protecting and managing aquatic natural resources and biodiversity. Although standard biotechnology tools are now used throughout the Department, with the more specialized developmental work concentrated in biotechnology centres across the country, the stabilization of existing expertise and development of additional and new expertise, through enhanced partnerships and collaborations within DFO, will be necessary in order to achieve these goals. Enhanced partnerships will also help to identify opportunities for the incorporation of biotechnology and genomics in delivering core mandate Science Sector services. This will help to keep the Strategy current and responsive to departmental pressures, Science Sector goals and approaches, and the goals and objectives of the Canadian Biotechnology Strategy.

It is important to build on the success that has been realized to date. One of the key successes has been in integrating and deploying biotechnology and genomics tools and information through the development of strong and vibrant partnerships with researchers in other government departments, academia and industry, as appropriate. This has enabled DFO researchers and DFO Science to capitalize on third party resources to deliver better and stronger programs, meet its mandate and key priority objectives more efficiently, foster and support world-class scientific and technological innovation, train new scientific personnel, and develop and maintain a national and international reputation for scientific excellence in aquatic biotechnology and genomics research. As we move forward to realizing the goals and objectives in this Strategy, there will continue to be a concerted effort to identify and maximize external partnerships and collaborations in order to best place and utilize DFO resources and expertise.

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