Genetics research

What is Biotechnology?

The term biotechnology means making use of or harnessing biological processes. Most people associate the term biotechnology with "high tech" applications but in reality the term "biotechnology" covers a wide variety of applications ranging from less technology based practices such as standard breeding programs through to very technological practices such as genetic engineering.

Links for more information:

The accompanying Glossary of Terms webpage provides definitions and a cell poster image to help further your understanding of biotechnology. You can find a definition for the bold underlined words on this "Glossary of Terms" webpage or by clicking on each hyperlinked word or phrase. If you would like to have the Glossary of Terms page come up in a separate window for easy reference as you read, hold the SHIFT key as you click the link for the Glossary of Terms.

There are many websites available with information on different aspects of biotechnology and genomics, below are two that can get you started if you want more information on this topic.

The Geee! In Genome website (Genome Canada and the Canadian Museum of Nature) http://nature.ca/genome/index_e.cfm

Scitable by Nature Education http://www.nature.com/scitable (Note: This site is only available in English)

Why does DFO use biotechnology?

Currently the biotechnology work within DFO is focussed on Genomics (Genetics), looking at the DNA (Deoxyribose Nucleic Acid) and/or RNA (Ribose Nucleic Acid). DNA and RNA are common to all biological organisms. DNA is the "blueprint" for the organism (passed on from parent to offspring). By looking at the DNA we can look at some of the fundamental similarities and differences between organisms − within and between species, within and between populations or within and between individuals. Beyond looking at DNA, RNA is the first level of how that blueprint is used. When we look at the RNA, we are looking at gene expression.

Researchers in DFO use biotechnology in two ways:

  1. As part of studies on aquatic organisms or;
  2. To provide information to support its mandate to regulate the products of aquatic biotechnology.

Link for more information:

For more information on the National Aquatic Biotechnology and Genomics Research and Development Program and the Aquatic Biotechnology Regulatory Program, please visit the Aquatic Biotechnology site at http://www.dfo-mpo.gc.ca/science/biotech-genom/index-eng.htm

How is biotechnology used at BIO?

In the Maritimes region the biotechnology program currently makes use of molecular biology techniques and technologies to investigate the genetics and genomics of a variety of aquatic organisms. Currently this means primarily looking at the DNA from the sample. These same technologies and techniques can (and are) applied to a wide variety of organisms ranging from microorganisms, aquatic invertebrates and vertebrates. The type of questions being addressed by looking at their DNA depends on the organism but include:

  • Species identification:
    Not all species can easily be distinguished based on their appearance. In some cases, the entire organism is not available for identification. Using DNA based methods species identification can be done from small pieces of tissue such as muscle, fin clip, body mucus, scales, blood or hemolymph etc. Species identification is also very important so researchers can measure biodiversity.
  • Parentage:
    Using DNA based tests we can trace an individual back to its parents. This is important in aquaculture or other breeding programs where fish (or invertebrates) are raised in a group. This information can then be used to minimize inbreeding.
  • Population structure:
    Population genetics is an area of genetics that looks at the frequency of alleles between groups of individuals to see if there are differences. The results of these studies provide information important for management and/or conservation of populations or species. For these types of studies we use microsatellites (also known as Short Sequence Repeat (SSR)) loci or Amplified Fragment Length Polymorphisms (AFLP) products.
  • Ecosystem health:
    A newer challenge for DFO is how to determine if a whole ecosystem is healthy or not and how it changes over time. One indicator being investigated to help address this issue is looking at microbial ecology using metagenomics. For this we can look at a piece of the DNA from all the bacteria in a sample of water and see what bacteria are there and how they change. Bacteria respond quickly to changes in the environment as well as being a food source for many microscopic animals.
  • Development of molecular biology tools:
    Before the types of studies described above can be undertaken the tools have to be available. While the scientific literature is an important source of information, there are many species for which the required information is not available or is insufficient. In that situation the first step is to obtain the information ourselves. This can include isolating the loci or adapting procedures for the specific species or research question.

Who is working on Biotechnology and Genomics (Genetics) at BIO?

Biotechnology is a tool that can be used by many DFO scientists, but it requires specialized equipment and training. As a result there are a couple of groups that specialize in this area.

The Aquatic Biotechnology Lab (ABL)

The Aquatic Biotechnology Lab (ABL)

Biotechnology is a rapidly evolving and technology driven area of biology. The Aquatic Biotechnology Laboratory is as a core facility to provide the equipment, personnel and expertise in the area of molecular biology to DFO scientists and collaborators in a cost effective manner.

The major equipment in the lab includes:

  • AB3130xl capillary electrophoresis system (Applied Biosystems)
  • FMBIOIII fluorescence scanner (Miraibio)
  • EDAS 200 gel documentation system (Kodak)
  • Six Eppendorf ep Mastercycler gradient thermocyclers, two Eppendorf Mastercyclers and one Applied Biosystems 9700 dual block thermocycler
  • StepONE and StepONE Plus real-time instruments
  • C.B.S. Scientific vertical gel electrophoresis rig (55cm width)
  • DCode DGGE gel rig (BioRad)
  • workstation (AirClean)
  • QIAXcel (Qiagen)
  • QIACube (Qiagen)

Contact Person: Lorraine Hamilton (Laboratory Manager)
e-mail:  Lorraine.Hamilton@dfo-mpo.gc.ca

Genetics of Atlantic salmon and other finfish species

Genetics of Atlantic salmon and other finfish species

Participants: Manon Cassista-Da Ros (Molecular biologist), Carolyn Harvie (Assessment biostatistician), Louise de Mestral Bezanson (Biological Technician) and Patrick O'Reilly (Research Scientist)

Molecular genetic, parentage, kinship and population analyses in support of conservation and management of Atlantic salmon and other finfish species.

Genetic variation and fitness in Atlantic Salmon

Wild anadromous Atlantic salmon (Salmo salar) populations are rapidly declining throughout the southern half of the species freshwater distribution. Our group is involved in analyses directed at minimizing the loss of both genetic variation and fitness in small semi-captive populations in Nova Scotia and New Brunswick. Using pedigree information obtained through molecular genetic data and subsequent kinship and parentage analyses, we are attempting to maximize retention of founder genetic variation, and to minimize loss of genetic variation in subsequent generations due to genetic drift. In collaboration with researchers from several universities, we are also investigating the efficacy of these programs in minimizing adaptation to captive conditions and loss of fitness in the wild. Information on rates of loss of genetic variation, and changes in behaviour, morphology, and survival associated with specific management practices, will be used to adapt existing strategies, with the ultimate goal of maintaining salmon that can successfully survive and reproduce in native river habitat and that retain sufficient genetic variation to enable populations to adapt to future environmental challenges.

Population and genetic structure

Resolution of genetic structuring in fishes can be useful both in the identification of fish stocks, groups of individuals demographically independent of other such groups, and in delineating important components of a species' biodiversity for broader conservation purposes. Our group is engaged in analyses of microsatellite, SNP (Single Nucleotide Polymorphism), and MHC (Major Histocompatiblity Complex) variation in anadromous and marine finfish species, for these purposes. Our primary focus is on Atlantic salmon, were we have accumulated genotypic data on over 18,000 individuals from over 40 populations in the Maritimes, but we are also carrying out research on Atlantic cod (Gadus morhua).

Investigations into interactions between wild and aquaculture salmon in North America

The Bay of Fundy/Gulf of Maine is home to some of the most intensive culturing of Atlantic salmon on the east coast of North America, but also to many numerically depressed and endangered wild populations. Our group is also interested in whether aquaculture escapes have impacted depressed wild populations either directly through introgression, or indirectly via the introduction and transmission of pathogens. One of our projects involves analyses of MHC variation in wild populations prior to and after the introduction of aquaculture to the region, and in populations near and distant to Passamoquoddy/Cobscook Bay, areas of high concentrations salmon farming.

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