Genomics research

Learn about genomics research, strategy, initiatives and projects.

About genomics research

Genomics is the science that studies:

DNA sequences
the functions of the tens of thousands of genes found in living organisms
the complexity of their multiple interactions

At Fisheries and Oceans Canada (DFO), genomics research is building the scientific knowledge base and expertise necessary to support fisheries and oceans management.

Genomics research produces:

technical papers and book chapters
scientific information and peer reviewed publications
knowledge that's used to inform the development of scientific advice through:
- the Canadian Science Advisory Secretariat
- other advisory processes

Together, these activities seek to ensure that DFO decision makers have access to:

genomics knowledge
advice for the management of fisheries and oceans

Research and development strategy

Through DFO's Aquatic Biotechnology and Genomics Research and Development Strategy, genomics research is advancing Canada's responsibilities for:

species at risk
aquatic ecosystems
fishery management
monitoring fish habitat
sustainable fisheries and aquaculture

Under the strategy, key themes for genomics research include aquatic:

animal health
resource profiling
ecosystem health

This focus on aquatic ecosystems and organisms is strategically aligned with Canada's responsibilities for:

environmental sustainability
scientific support for regulatory and policy decisions
using modern technology within federal science-based departments to manage the diverse range of human activities in Canadian waters

Research and development initiative

DFO's genomics research is supported by Canada's Genomics Research and Development Initiative. Through the initiative, DFO is currently receiving $2.3 million in funding over 3 years for research projects that contribute to delivery of our mandate.

We're also receiving funding for interdepartmental collaborative research on quarantine and invasive species. This is a new federal shared priority project under the fifth phase of the initiative.

Benefits of genomics

Genomics research makes important contributions to fisheries and oceans management. Genomics tools can identify similar species and assign fish to their population or stock of origin. This helps us address questions that can't be answered using traditional science tools alone, such as:

what species a fish is
which population or stock the fish belongs in

Applying these tools while managing mixed-stock fisheries increases effectiveness of conserving threatened salmonids by:

reducing the bi-catch of threatened stocks
allowing the sustainable harvesting of more abundant stocks

Accurate identification is important to:

conserve and protect:
- species at risk
- aquatic biodiversity
- vulnerable fish stocks
ensure the sustainability of commercially important fisheries
establish new emerging fisheries for traditionally un-exploited and often poorly understood species

New information allows scientists to assess the impacts on fish from:

human activities
climate changes
other environmental changes

This includes applying innovative approaches to issues, such as:

enhancing aquaculture broodstock productivity
developing vaccines for aquatic animal diseases by using the pathogen's own genome
learning about the changes in stock structure and genetic diversity using molecular markers to analyze archived material, including:
- scales and otoliths
- a calcareous structure from the inner ear that's traditionally sampled to determine age

Current genomics research projects

DFO completed a competitive process to allocate funding for genomics research projects for the fifth phase of the Genomics Research and Development Initiative. This phase lasted from April 2011 to March 2014.

The competitive process resulted in the establishment of 8 projects, including:

Jean-Marie Sévigny:
- stock delineation of redfish (Sebastes mentella) straddling North Atlantic Fisheries Organization (Subareas 0, 1, 2+3KLMNO) and North East Atlantic Fisheries Commission (International Council for the Exploration of the Sea Subareas XII and XIV) areas based on genetic analyses of archived otoliths
Ian Bradbury and Claudio DiBacco:
- rapid single nucleotide polymorphisms discovery and genetic mapping using next-generation restriction-site associated DNA sequencing: fostering the tools and expertise for genomic based management in model and non-model marine organisms
Ian Bradbury and Patrick O'Reilly:
- development of molecular genetic markers for investigations into climate induced selection and usage in genetic mixed stock analysis of Atlantic salmon in the Northwest Atlantic
Corey Morris, John Brattey, Robert Gregory and Ian Bradbury:
- a genomic and telemetric approach to measure Atlantic cod population structure and its application to marine protected area effectiveness
Kyle Garver:
- characterization of infectious hematopoietic necrosis virus carrier state in sockeye salmon using genomic tools
Kristi Miller:
- genomic characterization of physiologically compromised wild salmon
Jim Reist:
- Arctic fish genomics as 'sentinels' of ecosystem integrity and change
Nellie Gagné, Mark Laflamme, Francis Leblanc and Brian Glebe:
- Highly polymorphic region 0 non-pathogenic infectious salmon anemia virus in vivo: a comparative genomic study

Genomics research is being actively conducted in 6 regions, with 2 collaborative projects between the Maritimes, and Newfoundland and Labrador Regions.

These projects include extensive collaborations with researchers from:

DFO
universities
other governments

Projects were successful in leveraging both departmental and external resources, essentially matching DFO's contribution to the initiative.

High impact solutions projects

The Genomics Research and Development Initiative is delivering high impact solutions to shared priority issues through:

horizontal integration
effective collaborations among federal departments and agencies

We're contributing to interdepartmental research for the protection of Canadian biodiversity and trade from the impacts of global change. This is done through an improved ability to monitor invasive alien and quarantine species.

These 4 projects include:

Sub-project 1: Optimization and standardization of nucleic acid extractions
- Mark Laflamme
- Theme 1.1: Mining preserved specimens in reference collections
Sub-project 2: Barcoding of aquatic invasive species of highest risk to Canadian native fauna and trade (Cathryn Abbott, Sub-project Leader)
- Nellie Gagné and Nicholas Mandrak
  - Theme 2.1: Highest risk invaders in live food and aquarium trade
- Cathryn Abbott and Tom Therriault
  - Theme 2.2: Highest risk invasive aquatic invertebrates in shipping pathway
- Gary McClelland
  - Theme 2.3: Highest risk aquatic invasive parasites