Biotechnology and aquaculture profiling

Learn how we run programs under the biotechnology and aquaculture profiling theme.

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Theme priorities

Under the biotechnology and aquaculture profiling theme, we develop biotechnology tools for:

  • genetic profiling of aquatic species
  • widespread application in Canada and abroad
  • contributing to the sustainable use of aquatic resources

This research theme encompasses all activities related to understanding the genetic makeup of our aquatic resources. Biotechnology and genomics in this area include studying the:

  • genomes of some aquatic species
  • genetic population structure of many species
  • genetics and functional genomics underlying interactions between aquatic species and their environment.

Aquatic resource profiling directly supports:

  • sustainable:
    • fisheries
    • aquaculture
  • protection of biodiversity
  • recovery of species at risk

Our goal is to optimize the productivity of the aquatic environment (from wild capture and aquaculture) while maintaining environmental health and biodiversity.

By analyzing each species, population by population, scientists can better assess:

  • which populations:
    • can support fisheries
    • are in need of protection
  • how to prevent the loss of genetic diversity when designing breeding programs

We can also identify and monitor endangered populations for conservation. Molecular genetic methods can inform management decisions intended to support recovery efforts. Genetic databases for endangered populations can be used to establish a clearer understanding of changes in biodiversity within and among populations at risk.

On the enforcement side, the development of forensic DNA capability has:

  • expanded the scope of enforcement actions
  • reduced expenditures associated with prosecutions for illegal:
    • harvest
    • sale of fish and shellfish

About biotechnology and aquaculture



Aquaculture production is on the rise, and involves the farming of:

  • finfish
  • shellfish
  • aquatic plants

Fish are typically raised in hatcheries and retained in captivity through the whole life cycle until harvested for market.

Aquaculture emerged in Canada during the 1970s, a time marked by:

  • heightened public awareness of the potential impacts of industrial activity on the environment
  • increased public scrutiny of industry and government actions to reduce such impacts

There are challenges to farming fish and seafood, just as there are with any kind of land-based farming. Intense environmental scrutiny has ensured that both industry and government have taken action to reduce possible environmental impacts.

Fisheries and Oceans Canada (DFO) has an important role to play in aquaculture. We're responsible for the sustainable development of our fishery and aquaculture resources. We've committed to:

  • regulate the industry
  • seek opportunities to create the conditions for the development of an aquaculture industry that's:
    • environmentally sustainable
    • internationally competitive

We aim to achieve this with our innovative biotechnology and genomics tools.

Aquaculture species

Canadian aquaculture production is dominated by 5 main categories by volume:

  • salmon (69%)
  • blue mussels (14.2%)
  • oysters (7%)
  • trout (4.3%)
  • steelhead (3.1%)

The main commercial salmon species are:

  • Atlantic salmon
  • the Pacific salmon species:
    • coho, also called silver salmon
    • chinook, also known as spring or king salmon

Rainbow trout and Arctic char, other members of the salmonid family, are also farmed widely on a commercial basis.

In 2004, the aquaculture industry reported operating revenues of $668.9 million. Finfish sales, which accounted for almost 87% of total operating revenues was $754.4 million. The value of aquaculture exports was $424.9 million.

For some species of salmon, aquaculture production far exceeds wild harvest. In 2004, 71,300 tonnes of farmed salmon were produced in British Columbia marine salmon farms. Atlantic salmon made up 75%, chinook 24% and coho for the remaining 1%.

Revenue from mollusks was $67.5 million, with 44% of mollusc production from Prince Edward Island.

New species are in the experimental stages of aquaculture development in Canada, such as:

  • cod
  • eels
  • halibut
  • wolffish
  • abalone
  • haddock
  • blackcod
  • quahaugs
  • geoducks
  • sea urchins
  • striped bass

Developing broodstock

Atlantic salmon

Atlantic salmon

Traditional selective breeding programs have been used to develop broodstock strains with desirable characteristics, such as faster growth and disease resistance. DNA analyses will help us identify the fish with the most desirable performance traits so that only the best are used to create the next generation.

Scientists at DFO work with researchers in the aquaculture industry to decide which fish or shellfish to breed using DNA analysis to identify and grow the best performing fish or shellfish.

The application of cost-effective DNA fingerprinting techniques helps broodstock management and selective breeding by providing rapid family identification.

In salmon, current research to link genetic markers with quantitative traits such as growth and disease resistance will help to identify the best broodstock fish in the future.

Additional genetic markers are being developed at DFO and in large genome projects. These will let us identify fish carrying superior quantitative trait loci (QTLs) before we transfer them to saltwater. QTLs are genes controlling traits such as disease resistance and rapid growth.

Preserving genetic diversity

Genetic analysis makes it possible to determine the success of different enhancement (specialized breeding) strategies by tracing:

  • adults
  • progeny (their young)
  • returnees

We use DNA analysis in Pacific and Atlantic salmon aquaculture to:

  • monitor any genetic diversity loss in aquaculture strains from breeding
  • distinguish wild from cultured salmon found in the same waterway

Producing bigger fish and shellfish

Cultured oysters

Cultured oysters

Through biotechnology, we can enhance some fish and shellfish traits, such as:

  • growth speed
  • disease resistance
  • reproductive potential
  • ability to endure adverse environmental conditions

Atlantic coast aquaculture has grown quickly in the last 30 years, particularly for salmon and mussels. We're using molecular genetics to produce bigger shellfish at a faster rate and with more reliable quality.

As with salmon, we're developing additional sets of genetic markers to identify fish carrying superior QTLs before we transfer them to saltwater.

Y-chromosome DNA markers

Producing and maintaining monosex salmon strains for aquaculture is easier now that we use Y-chromosome DNA markers associated with male sexual development.

Aquaculture production is more efficient when we use monosex salmon strains. This method has been critical for the survival of the entire chinook salmon industry for more than 20 years.

More recently, we've been successful in using Y-marker technology to develop new monosex strains. We've also used these Y-chromosome DNA markers to identify genetic sex. This allows us to identify pollution effects from industrial and urban waste that causes salmon stress and sex reversal.

Interactions between wild and farmed fish

Since the beginning of modern aquaculture, DFO scientists and stakeholders have studied potential impacts of farmed fish on wild fish populations.

Potential impacts include:

  • nutrient enrichment
  • competition for habitat and food
  • possibility of interbreeding leading to endangerment of native populations

We can use biotechnology to prevent interactions between farmed and wild fish. In addition, we can use molecular genetic analyses to assess the presence and extent of interbreeding between aquaculture salmon and wild salmon.

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