Sequence #6: Tapping our ocean potential, recruiting talent, and a new genetics institute

In October, scientists, environmental and policy experts, and graduate students converged in St. John’s NL for the inaugural Ocean Frontier 2018: North Atlantic Opportunities conference, organized by the Ocean Frontier Institute to explore the enormous potential of the North Atlantic.  Genome Atlantic was pleased to attend and proud to be a partner.   

Genomics is a critical technology for tapping our ocean potential and is a key pillar of the Ocean Supercluster.  Genomics is transforming ocean industries like aquaculture, offshore exploration and tidal energy, enhancing environmental monitoring and providing clean tech solutions for addressing the effects of climate change.  A good example of the latter is a Genome Atlantic-supported research project led by Memorial University’s Dr. Kurt Gamperl, who presented his work at the conference.

Just a few degrees of ocean temperature warming can increase the incidence of disease and mortalities in farmed salmon – and Gamperl and his colleagues at the University of Prince Edward Island, University of Waterloo, Guelph University, Huntsman Marine Science Centre, Somru BioScience and the Centre for Aquaculture Technologies Canada are using genomics and genetic sequencing to help the east coast aquaculture industry adapt its production to rising sea temperatures and breed more disease-resistant fish.  Here’s an update on the project and the team’s latest findings.

From oceans to human health, Genome Atlantic attended the recent launch of the CIHR Institute of Genetics at Dalhousie University’s medical school.  The Tupper Foyer was packed to the gills in celebration of Atlantic Canada’s first-ever CIHR Institute and to offer congratulations to Dalhousie’s own Dr. Christopher McMaster who was appointed Institute Director over the summer. Far from basking in the glory, McMaster was tasked the role of emceeing the event (for which he was rewarded with a giant, iced CIHR cookie). Cookies aside, we asked McMaster about his plans for the Institute and how genomics is revolutionizing medicine

Genomics and other ‘omics technologies are creating other opportunities for Atlantic Canada, including recruiting and retaining top talent. Dr. Carl Peters is a perfect example. A native of Breman, Germany, Peters is a Postdoc who specializes in lipidomics, the analysis of lipid species found in organisms. He was recruited in 2017 by Dr. Todd Ventura’s organic geochemistry lab team at Saint Mary’s University as a Mitacs-funded intern to work on a national microbial genomics project to de-risk oil and gas exploration in Nova Scotia’s offshore.  Peters talks about his work, why it’s important, and how he hopes his current project will lead to a longer-term career in Halifax in our Young Scientist Profile.   

Université de Moncton partners with the Government of Canada, Genome Atlantic, Genome Canada, New Brunswick Innovation Foundation, and Organigram to advance cannabis research and increase productivity

Research to support growth of the cannabis industry in Atlantic Canada through the application and adaptation of novel biotechnologies

L to R: Dr. Martin Filion, Université de Moncton; Jeff Purcell, Organigram; Dr. David Joly, Université de Moncton

MONCTON, NEW BRUNSWICK – (November 13, 2018):  The Université de Moncton, in partnership with the Government of Canada, Genome Atlantic, Genome Canada, New Brunswick Innovation Foundation (NBIF) and Organigram Holdings Inc. (TSX VENTURE:OGI) (OTCQB:OGRMF), today announced the creation of an institutional research project focused on cannabis at the Université de Moncton.

Supplying cannabis and cannabis products to a legalized adult use recreational market represents a major economic opportunity in New Brunswick and across the country. Indeed, the retail market value for recreational cannabis in Canada is expected to reach $8.7 billion annually. However, current production capacity will not meet the anticipated demand.

To date, cannabis has not benefitted from the application of biotechnologies (particularly genomics) that have led to massive increases in yields and the sustainability of other agricultural production systems. The innovative, research-driven approach supported by this partnership will explore how these novel approaches can help improve the productivity and quality of cannabis products.

Genome Atlantic was the catalyst for the project, to which the project partners will contribute more than $1.1 million over three years. The research will be led by Dr. David Joly and Dr. Martin Filion, both professors from the Department of Biology, Faculty of Science, Université de Moncton. Organigram will provide working space, raw material and expert resources in collaboration with the Université de Moncton research team. Genome Atlantic’s contribution is made through Genome Canada’s new Regional Priorities Partnership Program (RP3), which allocates funding for projects that reflect regional priorities.

Specifically, the research will seek to:

  • Improve the quality of the product by identifying specific traits through genetic mapping, which will result in healthier, more resistant plants and improved growing techniques
  • Improve productivity and lower costs by introducing beneficial microbial inoculants and developing strains with improved traits
  • Conduct genetic research to identify specific markers which will allow specific strains to be protected if necessary

The expected results from this project are closely aligned with New Brunswick’s Economic Growth Plan and will contribute to an economically-viable cannabis industry by increasing production and potential revenue.

This project also builds on commitments made by the Government of Canada and the four Atlantic provinces to drive economic growth in the region through the Atlantic Growth Strategy. This Strategy supports strategic investments in initiatives that build on Atlantic Canada’s competitive advantages, such as its growing innovation ecosystem and skilled workforce, and position the region to capitalize on emerging opportunities.

Other benefits include training of highly qualified personnel required to support the growth of this industry; developing proprietary technologies that can be marketed to other jurisdictions; and enhancing New Brunswick’s and Atlantic Canada’s role as a world leader in cannabis science.

The project partners each echoed their support for the goals of the project and the value of the unprecedented collaboration:

  • “Together with its partners, the Government of Canada makes transformative investments to build smart, strong and sustainable communities that meet today’s unique challenges and prepare us all for a prosperous future. I am pleased that our government, through the Atlantic Canada Opportunities Agency’s Business Development Program, is investing $353,000 in this project that will enhance Atlantic Canada’s role as a cannabis research and development leader and cannabis genomics centre of expertise.” – The Honourable Navdeep Bains, Minister of Innovation, Science and Economic Development and Minister responsible for the Atlantic Canada Opportunities Agency
  • “Our partnership with Organigram combines some of the most promising technologies with a unique access to state-of-the-art cultivation facilities and some of the most popular strains of cannabis. Such collaboration is vital to ensure that discoveries made in our lab can lead to innovations that will prevent losses, promote productivity and allow the development of novel markets.” – David L. Joly, Assistant Professor, Université de Moncton
  • “The cannabis sector is an area of strategic importance for New Brunswick and genomics is critical to many high-value components of the cannabis value chain.  Building local research capacity in cannabis genomics will give New Brunswick companies a competitive advantage in this rapidly evolving marketplace.” – Andy Stone, Director of Business Development, Genome Atlantic
  • “Cannabis holds tremendous potential for those parts of Canada and the world ready to take advantage of it. The NBIF is pleased to support a project that increases New Brunswick’s competitive advantage in this burgeoning sector by bringing together experts in industry and academia to use genomics in new ways that improve the quality of cannabis products.” – Dr. Laura Richard, Director of Research, New Brunswick Innovation Foundation.
  • “We have been working with the Université de Moncton almost since our inception and look forward to strengthening the collaboration through this project. It is a tremendous example of local, provincial and federal support for the cannabis industry and solidifies Moncton as a world leader in cannabis genetic research.  The Organigram team is excited to continue to work with Dr. Joly and Dr. Filion and to get started on this very important project.” – Greg Engel, CEO, Organigram

About Université de Moncton

The Université de Moncton is Canada’s largest French-language university outside Quebec. Founded in 1963, it is an institution with three constituents (campuses) located in Edmundston, Moncton and Shippagan, in New Brunswick. It offers a range of programs in the three study cycles to meet the training needs of the popu­lation it serves. It provides its services to the vast Francophone diaspora throughout the country, thus becoming the ideal symbol of the linguistic and cultural vitality of Francophones living outside Quebec.

About Genome Atlantic

Genome Atlantic is a not-for-profit corporation with a mission to help Atlantic Canada reap the economic and social benefits of genomics and other ‘omics technologies. Since its inception in 2000, the corporation has worked with a range of private and public-sector partners to enable more than $100 million in new genomics R&D.

About Atlantic Canada Opportunities Agency

The Atlantic Canada Opportunities Agency works to create opportunities for economic growth in Atlantic Canada by helping small and medium-sized businesses become more innovative, productive and competitive, by working with diverse communities to develop and diversify local economies, and by championing the strengths of Atlantic Canada.

About New Brunswick Innovation Foundation

Since its launch 15 years ago, the New Brunswick Innovation Foundation, an independent, non-profit corporation, has invested over $100 million in New Brunswick startups and researchers and leveraged $457 million more from other private and public sources. Those strategic investments have helped launch over 100 companies and funded nearly 500 applied research projects. Profits from NBIF’s investments go back into the foundation for reinvestment in other startups and research initiatives that drive innovation, attract investment and create jobs in New Brunswick. Find out more at

About Organigram 

Organigram Holdings Inc. is a TSX Venture Exchange listed company whose wholly owned subsidiary, Organigram Inc., is a licensed producer of cannabis and cannabis-derived products in Canada.

Organigram is focused on producing the highest-quality, indoor-grown cannabis for patients and adult recreational consumers in Canada, as well as developing international business partnerships to extend the company’s global footprint. In anticipation of the legal adult use recreational cannabis in Canada, Organigram has developed a portfolio of brands including The Edison Cannabis Company, Ankr Organics Trailer Park Buds and Trailblazer. Organigram’s primary facility is located in Moncton, New Brunswick and the Company is regulated by the Access to Cannabis for Medical Purposes Regulations (“ACMPR”).

For more information, please contact:

Communications, public affairs and marketing department


Young Scientist Profile: Dr. Carl Peters, Postdoctoral Fellow “We want to map go and no go areas for offshore drilling.”

Dr. Carl Peters, Saint Mary’s University. Photo Credit: Betsy Chambers

Field: Marine Biogeochemistry, specializing in lipidomics, the analysis of lipid species found in organisms.

A native of Bremen, Germany, Dr. Carl Peters has been in Halifax since 2017. He arrived by way of Sydney, Australia, after doing a PhD in organic geochemistry at Macquarie University and research at Australia’s Commonwealth Scientific and Industrial Research Organisation. His five-year stay Down Under followed studies in geochemistry and marine geoscience at the University of Bremen where he obtained his BSc and MSc, and worked in one of the world’s pre-eminent organic chemistry labs in environmental lipidomics at the Centre for Marine Environmental Sciences.

Peters is part of Dr. G. Todd Ventura’s organic geochemistry lab team, in the Department of Geology, Saint Mary’s University. Ventura, a Tier II Canada Research Chair, recruited Peters as a Mitacs-funded intern for his lipidomic expertise in a national microbial genomics project aimed at helping the province’s off-shore oil and gas industry reduce its exploration costs and improve its discovery rate.

Current Project: a $4.9 million, three-year study, Microbial Genomics for De-risking Offshore Oil and Gas Exploration in Nova Scotia. It mixes genomics technologies and several geoscience disciplines to provide a more accurate picture of Nova Scotia’s offshore petroleum resources. The project, funded under Genome Canada’s Genomic Applications Partnership Program (GAPP), is a national collaboration that includes Genome Atlantic, Genome Alberta, the Offshore Energy Research Association of Nova Scotia, the Nova Scotia Department of Energy and Mines, the Geological Survey of Canada, the University of Calgary, Saint Mary’s University and Mitacs.

The Challenge: For Peters it is analyzing the species of lipids found in lipid extracts made from marine sediment samples taken off the Nova Scotia coast. The samples are collected around seeps where petroleum naturally bubbles through the ocean floor, and he uses liquid chromatography, a method of separating lipids in the extracts, to do the analysis. Specifically, he hunts for intact polar lipids from bacteria associated with oil and gas deposits.

The Objective:  To develop new screening techniques, including profiles of the lipid clusters in marine sediment, that could help confirm the presence of offshore oil and gas reserves. Put another way, the project aims to develop an array of genomics-based tools to identify the aerobic, anaerobic and thermophilic bacteria that thrive on hydrocarbons and indicate nearby undersea stores of oil and gas. The achievement could shave millions of dollars from oil and gas exploration costs and bring more certainty to the risky business of exploratory well drilling in marine environments.

The Project’s Importance: Peters explains reliable tools to map “go and no-go areas,” for offshore drilling could help revive oil and gas exploration off Nova Scotia’s east coast. New offshore commercial reserves would mean new royalty and tax revenue for the government as well as significant new employment and investment. While Nova Scotia is the focus, offshore drilling in other jurisdictions with similar marine environments could also benefit.

The Exciting Part: “The integrative aspects” says Peters. “We’re going to put a huge dataset together that consists of genomics, proteomics and lipidomics.” The plan is for Ventura, who manages the overall lipidomics and integration components, to fold Peters’ lipidomics data into the results from the University of Calgary’s genomic and proteomic (protein) analyses of the marine sediment samples. “That’s really exciting because that has never been done before in this detail and with this kind of effort.” He is eager to see how the data from the different sources dovetail and what the comparisons will reveal. Only then will they know how close they have come to their objective.

Project’s Significance for Your Career Path: Like most postdocs, Peters doesn’t know whether he will ultimately land in academe or the private sector, so he has to keep his skill set sharp and versatile. In this project, he said, “I’ve learned a lot that’s helpful. The networking is really fantastic.” It provided good counterpoint to the solo endeavor of his PhD.  “I have never worked in such a big project and one that was so collaborative and multi-disciplinary.” He now has contacts from the University of Calgary to the Bedford Institute of Oceanography and from the Offshore Energy Research Organization of Nova Scotia to the Nova Scotia Department of Energy and Mines. In the near term he hopes the experience leads to a projected follow up investigation he helped design that would keep him in Halifax for another three years, this time as a research associate. Peters would like to extend his stay in the city; his partner, a data scientist who holds a PhD in geology, has settled in at Dalhousie University as a senior data manager, and a few months ago they welcomed their first child.

DNAbling the Healthcare Revolution

Dr. Christopher McMaster, Dalhousie University. Photo Credit: Danny Abriel

Dr. Christopher McMaster, Canada’s newest scientific director of the Institute for Genetics, is excited about the potential of genomics to help people stay healthier longer. “I think over the next decade genomics and other ‘omics fields will revolutionize how medicine is practiced,” he said.  

In 2000, the Canadian Institutes of Health Research (CIHR) established the Institute for Genetics – along with 12 other institutes – to support research discovery and its translation into improving health and strengthening our health care system.  At the same time, scientists were racing to complete the mapping of the human genome.

By 2003 the first human genome was sequenced. It cost $1 billion and took 13 years to complete. Now a human genome can be sequenced in a few days for less than a thousand dollars.  McMaster uses the analogy of purchasing a Ferrari to reference how incredible technology advances have rapidly reduced the cost of DNA sequencing. “It’s the equivalent of purchasing a Ferrari for $394,000 in 2003 and selling that same Ferrari to me today for 40 cents,” he said. 

More Analysis Needed

Unfortunately, the ability to rapidly acquire genetic data has significantly outpaced our capacity to interpret and use it. In his role as scientific director, McMaster explains, “We will need to increase our capacity to analyze genomic data if we are to determine what keeps us healthy and what makes us sick.”

But analyzing genomic data is not a simple task. Scientists searching for genetic mutations tend to look in protein-coding DNA, which comprises the exons of known genes, but that only makes up two per cent of the human genome. More recently, researchers have uncovered ‘dark DNA’ in the remaining 98 per cent of the human genome where the function of the DNA sequence is not clear and interpreting its effect is a challenge. “We don’t understand what every gene does or how it’s regulated,” said McMaster. “There’s a lot more basic science that needs to happen if we’re going to make the most of the millions of genomes being sequenced.”

Opening Doors Internationally

McMaster explains that in order to improve our capacity to decipher the meaning of genetic variants, especially those that cause rare inherited diseases, large amounts of data must be collected and shared by clinicians and researchers. The more genomes sequenced and aggregated in databases, the better we will get at predicting a person’s health and potential for disease. “It means clinicians can be prognostic and help patients stay healthy, whether it’s making sure they change behaviors, change diets, or get on medications prior to symptoms kicking in,” he said.

This is where the CIHR Institute of Genetics plays a vital role. McMaster is planning on strengthening Canada’s genetic community by furthering the Institute’s collaborations with Europe, United States, China, Japan, Australia and the world. “We are looking to leverage our partnerships so genomics data can be integrated, harmonized, and accessed across international boundaries for the betterment of health, worldwide,” he said.

Addressing Patient Privacy

While pooling genomic data will be better for patients in the long run, sharing data is not how medicine is traditionally practiced. “Protecting patient privacy, by addressing policy and legal challenges, is a priority as we begin to access, analyze, and manage more data,” he said.

Model for Success

The ease with which the human genome can be sequenced and the potential for genomics to become a routine part of medicine, makes it fitting to have the CIHR Institute of Genetics housed in the Sir Charles Tupper Medical Building of Dalhousie University’s medical school. “Dalhousie University has provided us with institutional support and first-class space,” said McMaster. “Plus being on the ground floor makes us accessible so researchers, clinicians and scientists working in genetics can drop by anytime to find out what’s happening and ask for advice. It’s an ideal model for success.” 

This is the first CIHR Institute to be located in Atlantic Canada and McMaster and his team look forward to having national and international leaders in genomics come to Halifax.  Not only will these leaders meet with Institute staff but it presents an opportunity to showcase the unparalleled success Atlantic Canadian researchers have had, particularly in the areas of inherited disease and the microbiome, from discovering genes linked to orphan diseases to developing new therapies. “There’s an opportunity to exchange ideas and learn from the expertise of these leaders in genomics,” he said.

McMaster’s first order of business is to set the strategic direction for the Institute of Genetics. “This is the fastest moving medical field out there, so as we plan for the future, it’s important to get our priorities right because the impact on the healthcare system will be massive,” he said. The newly appointed scientific director is already working with an institute advisory board and consulting with patients, doctors, and scientists about what directions are most important for the Institute to pursue and discussing ways to translate research evidence into policy and practice to improve the health of Canadians and people around the world.

Saving farmed Atlantic salmon from climate change

Dr. Kurt Gamperl, Memorial University. Photo credit: Memorial University

Dr. Kurt Gamperl, Memorial University. Photo credit: Memorial University

Warming sea temperatures in the North Atlantic are a big concern for Atlantic Canada’s aquaculture industry.  Rising summer water temperatures of even a few degrees, especially in combination with low water oxygen levels, can pose a number of challenges to salmon aquaculture including an increase in the incidence of disease and mortalities.  But help is on the way, thanks to a $4.4 million Atlantic regional research project called Mitigating the Impact of Climate-Related Challenges on Salmon Aquaculture (MICCSA).

The project is using genomics and genetic sequencing to provide the east coast salmon aquaculture industry with tools and knowledge that can be used to adapt its production to rising ocean temperatures and to select more disease-resistant broodstock.

Announced last year in St. John’s, NL, MICCSA was enabled by Genome Atlantic and funded by $3 million from the Atlantic Canada Opportunities Agency (ACOA)’s Atlantic Innovation Fund, $0.5 million from Innovate NL and another $0.5 million from industry and national academic partners. The project is co-led by researchers at Memorial University and the University of Prince Edward Island.  

There’s a lot riding on the MICCSA project.  The aquaculture industry is growing in economic importance to Canada, accounting for 14 percent of total Canadian fisheries production and 33 percent of its value – or more than $2.1 billion. The Canadian aquaculture industry provides 15,000 jobs (direct and indirect) and is a significant economic contributor to coastal, rural and aboriginal communities on Canada’s east and west coasts.   The Atlantic salmon is the main species produced by Canada’s aquaculture industry and is Canada’s third-largest seafood export by value. 

Water temperatures are expected to rise 2-4 degrees Celsius in the next two-three decades, and these higher temperatures are likely to be associated with oxygen levels that are lower than normal (a condition termed hypoxia). Without counter measures, these shifts could make the culture of Atlantic salmon in some locations untenable and result in more disease, exacerbating proclivities for known chronic conditions and destabilizing the industry.

Dr. Kurt Gamperl, a fish physiologist in the Department of Ocean Sciences at Memorial University, and one of two principal investigators for the project, says that “fish are already experiencing temperatures in the 18-20º degrees Celsius range at some sites during the summer, sometimes in combination with hypoxia. Anecdotally, it is believed that diseases have become more prevalent and that treatments for some disease are less efficacious at high temperatures.”

A genomics solution

MICCSA aims to help safeguard the region’s economically important salmon aquaculture industry and contribute to its sustainability and continued growth. Gamperl explains that through the MICCSA project, researchers are using genomics to examine the response of Atlantic salmon families from the Huntsman Marine Science Centre in St. Andrews, New Brunswick, to conditions of elevated temperature and hypoxia, and to evaluate their susceptibility to infectious salmon anaemia (ISA) and sea lice. Researchers are also looking for gene expression biomarkers of fish health, stress and disease status that can be developed into diagnostic tools known as Enzyme-Linked Immunosorbent Assays (ELISAs). Genetic markers for improved physiological and immunological traits are also being developed, and these will help the industry select Atlantic salmon that can survive higher temperatures and hypoxia, and resist disease.  Finally, the project is expected to yield information to improve vaccines for salmon.

“This research,” Gamperl says, “should provide the industry with much needed information on the environmental conditions where their fish grow best, what fish to select – breed – for such conditions, and where to site sea-cages so that the fish are not exposed to unfavourable environmental conditions. Overall, this will increase the profitability and sustainability of the industry,” he says, adding, “if the research can improve cultured salmon health and decrease antibiotic usage, consumer demand and acceptance for cultured salmon are likely to grow.”

MICCSA project industry partner the Centre for Aquaculture Technologies (CATC) based in Souris, Prince Edward Island, agrees that this research is critical to the aquaculture industry.  “The ability to predict what strains of Atlantic salmon perform better under elevated temperatures could soon become an urgent need for commercial breeding programs,” said Debbie Plouffe, the company’s executive vice president of research. 

Plouffe believes that aquaculture will play a key role in supplying economical, high-quality and sustainably produced protein for human consumption in the coming years. “In order for the industry to reach its maximum potential, the application of state-of-the-art approaches to breeding are going to be essential.  CATC’s participation in this collaborative project is one of the many ways that our company is working with Genome Atlantic and Canadian public and private sector partners to drive innovation in the aquaculture sector.”

Project already yielding significant results

Gamperl says that the MICCSA project is already yielding significant results. “We’ve made tremendous progress towards reaching the program’s goals,” he says, outlining several important findings. 

So far, researchers have validated the use of data loggers that simultaneously record several physiological variables such as heart rate, activity/swimming speed and body temperature that can be used to monitor free-swimming Atlantic salmon in sea cages. The project is providing researchers with a better understanding of the salmon’s stress physiology including how high temperatures (20-23ºC) alone, or in combination with moderate hypoxia, impact production characteristics and the salmon’s innate immune response to viral and bacterial antigens (i.e., vaccination). 

Researchers have also identified several key immune- and stress-related genes (biomarkers) that are responsive to environmental temperature challenges and have produced antibodies and ELISAs to several biomarkers so that their protein levels can be quantified and monitored.

Gamperl says the project team is now looking forward to another important phase of the work.  “We’ll be receiving salmon from the Huntsman Marine Science Centre in the summer of 2019.  This will allow us to embark on family-based experiments, this phase of the project that is critical to identifying Atlantic salmon families that have an enhanced capacity to adapt to environmental challenges and mount robust pathogen-specific immune responses.”

The back story

Large-scale research projects like MICCSA are the product of leading-edge science, strong collaborations, solid investments and help from the local Genome Centre. 

It was the genomics potential that brought Genome Atlantic to the table for this research initiative. Genome Atlantic played a significant role in enabling the project, shepherding it through its final stages of proposal development to ultimate success.

First developed as a potential Genome Canada Large-Scale Applied Research Project (LSARP), the project came up short given the level of stiff nationwide competition for major Genome Canada funding programs.  However, Genome Atlantic and the research team knew that the project was strong and had regional significance.  So, they carefully considered the feedback provided through the LSARP evaluation process and refocused the proposal for ACOA’s Atlantic Innovation Fund.  The proposal was ultimately successful, scoring a big win for the future of Canada’s Atlantic salmon aquaculture industry.

The feeling when the funding was announced was “fantastic” says Andy Stone, Genome Atlantic’s director of business development. “We worked quite closely with the researchers and the industry partners and we became part of the team when the proposal was being developed, so there is certainly an emotional attachment.”

Beyond that, he says, there is another level of satisfaction, “especially given the gravity of the challenge for climate change, you know that you are part of something that has potential impact.”

Kurt Gamperl praises Genome Atlantic for its advice and persistence. He maintains that the organization’s decision to hire a consultant to write and improve the commercial and intellectual property sections of the funding proposal was decisive for the outcome. “These sections were key to our successful grant application,” he says.  “We continue to ask advice from Genome Atlantic staff with regards to the project and how to ensure that it has maximum impact,” says Gamperl.

The MICCSA project is a collaboration between Memorial University (Drs. Camperl and Matt Rise) and the universities of Prince Edward Island (Dr. Mark Fast), Guelph (Dr. Roy Danzmann) and Waterloo (Dr. Brian Dixon) along with Huntsman Marine Science Centre and industry partners Somru BioScience and CATC. Along with Dr. Gamperl, Dr. Mark Fast, an associate professor at the University of Prince Edward Island’s Atlantic Veterinary College, co-leads the project.  The MICCSA project compliments ongoing aquaculture research at Memorial University and the University of Prince Edward Island, including work that Dr. Fast and Dr. Matt Rise of Memorial University are doing as part of another large-scale collaborative research initiative, funded by Genome Canada and managed by Genome Atlantic, aimed at developing therapeutic feeds to combat co-infection in Atlantic salmon.

Sidebar:  A customized approach to genomic solutions 

The MICCSA project is one of many examples of how Genome Atlantic works with clients, partners and research teams to find the right solution.  Andy Stone, Director of Business Development, says that a “customized approach” is needed with each opportunity to help Atlantic Canadian business and industry access the potential of genomics. 

Genome Atlantic’s “small but mighty” business development team manages a portfolio of opportunities across seven different sectors including human health and environment, along with the resource sectors of agriculture, fisheries and aquaculture, energy, the environment, forestry and mining.  The team helps clients to explore opportunities, find potential partners and develop proposals. “We get involved in every stage of development and the service we offer is very unique,” said Stone. 

“These are all competitive processes and we want to make sure our proposals have a  peer review in advance to identify any potential weaknesses or challenges with the science and address those,” said Stone. “But also, we will run a copy edit type of review to make sure it reads well. So ultimately, we’re packaging proposals and putting a bow on them, and after they are successful, we offer project management services as well.”

Sequence #5: Yes, Genomics Can Help With That

Genomics is proving to be a game changer for many resource industries critical to Atlantic Canada’s economic growth.

Nova Scotia’s Minister of Energy Geoff MacLellan recently announced details of his department’s $11.8-million commitment to Phase Two of Nova Scotia’s offshore growth strategy.

MacLellan acknowledged the important role of innovative technologies like genomics in helping to ‘de-risk’ offshore exploration and showed Genome Atlantic’s newly-produced video “Reducing the Risk”, about how genomics is contributing to a better picture of Nova Scotia’s offshore petroleum deposits.

Genomics is helping to tackle another big offshore challenge – microbiologically-influenced corrosion (MIC), which costs the oil and gas industry tens of millions of dollars a year.  Genome Atlantic joined international experts in St. John’s, NL recently for a workshop and research symposium dedicated to better understanding and managing MIC.  Check out Memorial University’s story on the event and the $7.8 million research project managed by Genome Atlantic and Genome Alberta aimed at improving pipeline integrity.  Click here for more information about the MIC research project.

Cannabis is an important emerging industry for Canada, and genomics plays an important role here too. Cultivars and breeders are using genomics to identify desired traits, accelerate breeding and unlock high-value opportunities for developing specialized strains. The Province of New Brunswick has identified cannabis as a major economic driver, and this spring, Genome Atlantic partnered with Opportunities New Brunswick and BioNB to host a panel discussion in Fredericton focused on maximizing cannabis opportunities along the entire value chain, including through genomics technologies.

In aquaculture, another important emerging industry for Atlantic Canada, genomics is driving growth by helping to boost breeding programs, reduce loss from disease and pests, and optimize feed formulas. Better feeds help keep farmed fish healthy, and Genome Atlantic spoke with two leading Ocean scientists at Memorial University who are working with researchers at Cargill Aqua Nutrition and UPEI to develop therapeutic feeds that optimize growth and disease resistance in farmed salmon.

Genomics is also bearing fruit for agricultural researchers like Dalhousie University’s Dr. Sean Myles.  Myles wrote the book – literally – on grapevine breeding programs for the wine industry and was instrumental in leading the development of Canada’s National Apple Breeding Consortium. Check out our conversation with him about the role of genomics in value-added agricultural products, particularly here in Atlantic Canada.

Five Questions for two East Coast Ocean Scientists revolutionizing disease prevention in farmed salmon

Drs. Matthew Rise (L) and  Chris Parrish.  Photo credit: Chris Hammond, Memorial University

Aquaculture is an important and emerging industry in Canada, generating approximately $1.35 billion in revenue and employing 25,000 people*. With regard to farmed salmon in particular, one of the biggest threats is infectious diseases caused by sea lice, pathogenic viruses and bacteria. High-quality, therapeutic feeds can play a big role in helping salmon to resist infectious diseases and stay healthy.


Using genomics, East coast scientists are partnering with international aqua food giant, Cargill Aqua Nutrition, to revolutionize its feed formulas to shield farmed salmon and their investors from the costly scourges of sea lice, and microbial pathogens. The Canadian division of Cargill Aqua Nutrition sources approximately 80 percent of their feed ingredients from Canada and sells feeds to aquaculture operators in Canada, the U.S., Mexico and Asia.


For insight into this pioneering endeavour, Genome Atlantic contacted two of the leading scientists involved: Dr. Matt Rise, a functional genomics specialist who investigates fish immunology and aquaculture nutrigenomics, and Dr. Chris Parrish, a lipids researcher who probes nutritional and biomarker lipids in marine food webs. Both of these scientists are faculty members with the Department of Ocean Sciences at Memorial University, where Rise also heads a sustainable aquaculture module at the Ocean Frontier Institute. He was also recently appointed to a federal government Independent Expert Panel on Aquaculture Science led by Dr. Mona Nemer, Canada’s Chief Scientific Advisor.


Drs. Rise and Parrish, along with colleagues Dr. Mark Fast at the University of Prince Edward Island and Dr. Javier Santander of Memorial University, have been working with Cargill Aqua Nutrition on applying genomics to nutritional science.


The pair’s large-scale collaboration with Cargill actually consists of two large-scale research projects  sponsored by Genome Atlantic and Genome Canada, funded in part under Genome Canada’s Genomic Applications Partnership Program (GAPP): a completed $3.8 million investigation into single pathogen infections to produce a Biomarker Platform for Commercial Aquaculture Feed Development; and an ongoing second project, worth $4.5 million, dealing with the development of diets to combat co-infections from multiple pathogens and tagged as Integrated Pathogen Management of Co-infection in Atlantic Salmon.


The first project produced a new method to evaluate how diet affects farmed salmon’s growth and immune response at the gene and cellular levels. While it remains important to measure fish weight and growth, the new biomarker gene expression platforms developed by the scientists and their collaborators provide more detailed information on the impact of diets and feed ingredients on fish metabolism and immune response. This is needed in order to gain a more complete picture of the impact of novel diets on fish health and growth performance.


From individual salmon, the researchers use “gene chips” (also DNA microarrays) representing 44,000 different genes, as well as lipid biochemistry, to screen for diet-responsive biomarkers of fish health. The research team, including graduate students, post-doctoral fellows and technicians, use the genomic data to develop and use smaller panels of biomarker genes in a technique called “multiplex qPCR”. These panels of about 30 genes allow the researchers to rapidly collect detailed information on how novel diets and feed ingredients affect growth, metabolism and immune responses.


It is estimated that the use of therapeutic feeds could save the Canadian aquaculture industry approximately $60 million annually, while decreasing the use of chemical treatments and minimizing the risk of disease in aquaculture salmon.


Drs. Rise and Parrish also worked together on a highly successful project with fellow researchers at Memorial and Dalhousie universities that validated Camelina sativa, a plant commonly known as camelina or false flax, as a cost-effective, sustainable substitute for wild-sourced fish meal and especially fish oil.


The harvest of foraged fish used for animal feed has been stable during the past 30 years (FAO), but the animal feed industry increases at about three percent annually so the percentage use of fish products in feed must decrease. Plant oils and plant protein concentrates are viable alternatives to animal ingredients, and camelina has potential health benefits for fish in addition to growth support.


The $6.1 million camelina research project managed by Genome Atlantic, was done with principal support from the Atlantic Canada Opportunities Agency’s Atlantic Innovation Fund. The results enabled the Canadian Food Inspection Agency to approve a Genome Atlantic application to allow mechanically extracted camelina oil as a feed ingredient for farmed salmon and trout.


*Sources:Canadian Aquaculture Association and Statistics Canada (2016)



The Questions


Genome Atlantic: How did you come up with the idea of applying genomics and nutrition to prevent disease in farmed salmon?

Drs. Matt Rise and Chris Parrish:  It has become self-evident for humans that eating healthily can help prevent disease. We know that dietary ingredients such as the types of fats we eat have important health implications. So extending work on salmon nutrition from a focus on uniform weight gain to reducing dependence on antibiotics and other interventions was a natural next step. Not only did we want to look at disease prevention through the use of safe and sustainable dietary ingredients, but also to understand the mechanisms that underlie these processes.


Nutrigenomics, the use of genomics tools and techniques to study how nutrients influence gene expression, is a rapidly growing area of both human and animal (including fish) health related research. At the Ocean Sciences Centre of Memorial University, we are fortunate to have excellent research infrastructure and collaborations (e.g., with Cargill) for aquaculture nutrigenomics research.


GA: Can you briefly describe how genomics has been used in your two recent research projects: first with single pathogen infections and now with co-infections from multiple pathogens in farmed salmon.

MR &CP: Both of our GAPP (Genomic Applications Partnership Program) projects involve close collaboration between our lab groups (with the Rise lab focusing on genomics and the Parrish lab focusing on lipidomics), Dr. Richard Taylor (Cargill Aqua Nutrition) and many other collaborators with the goal of using functional genomics tools and techniques to accelerate development of novel grower and clinical diets for farmed salmon.


The first GAPP project (which was recently completed) focused on diets to combat salmon diseases such as infectious salmon anemia (ISA, caused by a virus) and salmonid rickettsial septicemia (SRS, caused by a bacterium).  The current GAPP project uses similar genomics tools (such as DNA microarrays, also called ‘gene chips’, used to screen the expression of thousands of genes simultaneously) with the goal of developing diets to combat co-infections of salmon (for example, a primary sea lice infection with a secondary viral or bacterial infection).


We have been able to correlate gene expression with the ingredients in the diets as well as with diet-induced changes in chemical composition in tissues.


GA: Do you see other areas of aquaculture where genomics could play an important role in solving pressing problems?

MR & CP: Doing lipid nutrition and biochemistry research alongside genomics work has greatly helped us understand mechanisms involved in responses to diet and implications of dietary alterations. In turn this has helped us define minimal levels of key components of fish oil and fish meal and of maximal levels of alternatives. We have been working very hard on effects of diet ingredients on salmon generally, but a great next step would be to reverse the approach and to look at matching individual strains of salmon to make the best of available diets. This would be akin to eating based on your genetics.


In addition to the area of nutrition, genomics research will contribute to many other areas of aquaculture such as breeding (for example, the selection of broodstock with rapid growth rate, resistance to stress and disease, and other traits of interest) and the development of effective diagnosis and vaccines to combat infectious diseases.


GA: Does this line of inquiry that marries genomics and nutrition have potential applications beyond marine life?

MR & CP: Certainly. The field of nutrigenomics is an emerging science which is gaining a lot of attention in the field of human nutrition. Our work at the interface of nutrigenomics and lipidomics is showing that salmon immune responses can be manipulated by varying dietary raw materials such as plant products and functional ingredients.  The research on salmon may provide hints regarding how immune system function in other vertebrates (such as humans) may be influenced by nutrition.


GA: In your experience, how important are academic-industry partnerships in advancing research in your fields?

MR & CP: For us this is a key component as we are completely up to date with the latest advances and challenges associated with the feed industry. We also get very quick feedback on our scientific results.


Our GAPP projects involve large research teams including graduate and undergraduate students, post-doctoral fellows, and technicians in our labs, as well as other academic collaborators (such as Dr. Mark Fast at the University of Prince Edward Island and Dr. Javier Santander at Memorial University) and industry collaborators. These academic-industry partnerships provide excellent opportunities for personnel in our labs to work closely with industry scientists to solve real-world problems.  The knowledge generated in our research translates directly to gains for the industry partner, in this case, Cargill Aqua Nutrition.  By accelerating the development of health-promoting diets for farmed salmon, our research also directly benefits aquaculture production.

New offshore research funding announced

“Combining genomics with geology has the potential to provide us with the clearest picture yet of petroleum deposits in Nova Scotia’s offshore.”

Andy Stone, Director of Business Development, Genome Atlantic


The Nova Scotia Department of Energy recently announced a four-year, $11.8-million commitment to the second phase of its Offshore Growth Strategy.  In his remarks at a press conference held to outline details of the offshore research strategy, Energy Minister Geoff MacLellan noted four main components of Phase Two of the research strategy:

  • Collecting core samples and high-resolution mapping information of the ocean bottom and sub-bottom;
  • Working with Morocco to reconstruct seismic images from 200 million years ago when Morocco and Nova Scotia separated;
  • Updating the Play Fairway Analysis with new information from offshore drilling results; and
  • Building new areas of research and strengthening existing research capacity.


Genome Atlantic’s partnership in the announcement reflected the Province’s recognition of genomics as an important continuing element in its offshore research strategy. Minister MacLellan shared the Genome Atlantic video “Reducing the Risk” as an example of a leading-edge innovative approach to offshore development.


The video documents “Microbial Genomics for De-risking Offshore Oil and Gas Exploration in Nova Scotia” (link to story )a $4.9-million, three-year project that is using genomics to help create a comprehensive snapshot of Nova Scotia’s offshore with the goal of making it more attractive to oil and gas companies.


Andy Stone, Genome Atlantic’s Director of Business Development who spoke at the event, explained that, “In simple terms, the genomics research is tracking microorganisms that eat underwater petroleum. These microorganisms cluster in petroleum seeps that originate from under the seafloor. Combining genomics with geology has the potential to provide us with the clearest picture yet of petroleum deposits in Nova Scotia’s offshore.”


Stone noted that the genomics work builds on the successful Play Fairway Analysis completed in 2011 which led to $2-billion in expenditure commitments for offshore exploration.  “Our genomics work will contribute to further reduce investment risk for prospective petroleum exploration companies in Nova Scotia’s frontier basin.”


He thanked the Department of Energy for their support and acknowledged the many partners in the current genomics research project including the Nova Scotia Department of Energy, the Offshore Energy Research Association (OERA), Genome Canada, Genome Alberta, University of Calgary, Saint Mary’s University, Mitacs Canada, and NRCan/Geological Survey of Canada who contributed to the overall research program.

He added that Genome Atlantic is currently building additional partnerships with OERA, Stantec and Dalhousie University on an offshore tidal energy project that will use environmental genomics (eDNA) to detect the presence of marine species around tidal energy installations. (Stay tuned for more information on this project in a future issue of Sequence e-bulletin.)

Five questions for a top Canadian genomics expert in apple and grape breeding


When it comes to new apple and grape varieties, you could say Dr. Sean Myles’ work with genomics has born enough fruit to make him one of the country’s leading plant genetics researchers.


Using genomics, Myles can detect and track desired traits in seedlings, which can help those developing new cultivars be certain of some fruit attributes as soon as the seeds germinate – in other words, much more rapidly than the many years needed to grow a tree and wait for it to bear fruit.  The genomic-based process is also acknowledged to be cheaper and it could also be more efficient.


A Fredericton, N.B. native, Myles holds the Faculty Research Chair in Agriculture at Dalhousie University.


Through his Apple Diversity Group in Kentville, N.S., he has amassed a very diverse apple tree collection of more than 1,000 varieties from many parts of the world, in a collaboration between Agriculture and Agri-Food Canada and Dalhousie University. While aiming to better understand genetic apple diversity, he also hopes to learn more about fruit biology and how to breed productive cultivars with less reliance on pesticides.


Currently he is involved in a 10-year project to assess new varieties of apples for traits such as disease resistance and sweetness, sequence the genomes of the fruit, and look for relationships between DNA sequences and the traits associated with them.


The book, Grapevine Breeding Programs for the Wine Industry, credits Myles with reviving grape breeding in Nova Scotia through his work with Dr. Andrew Jamieson, an Agriculture and Agri-Food Canada fruit breeder, that has led to the development of several promising new varieties for the Nova Scotia wine industry.


Apples and grapes hold more than passing professional interest for Myles. His wife, Gina Haverstock, is a sommelier and the award-winning winemaker at Gaspereau Vineyards and in 2016 the pair opened the Annapolis Cider Company in Wolfville, N.S.


Myles’ research interests in genomics go well beyond apples and grapes, however, and he has looked into disease-resistant hops, found the gene that gives rise to blond hair in dark-skinned Melanesians, and tested commercial cannabis varieties against their marketing hype. He works with a range of industry partners, which, among others, have included the Canadian Horticulture Council, the Nova Scotia Fruit Growers Association and Anandia Labs, a Canadian cannabis research company.






The Questions:


Genome Atlantic: Five years ago in Canadian Geographic you stated, when it comes to apples, “everyone is getting out of the breeding business.” You doubted your team would ever have a breeding program for new commercial apple varieties because it was cheaper to  “buy some new chemical and go and kill the pathogens that are killing your plants than it is to grow a new apple variety that is resistant to pathogens.” Has anything changed to make you more optimistic?


It’s an exaggeration to say that “everyone” is getting out of the apple breeding business, but there has certainly been a significant reduction in the number of apple breeding programs in Canada.  What does make me optimistic is that we have successfully consolidated resources from coast to coast and have established a National Apple Breeding Consortium – essentially a unified Canadian apple breeding program in which our lab plays a role. Those who specialize in genomics, for example, no longer have to evaluate advanced breeding lines in the field, while those who have expertise in fruit quality evaluation in the field can focus on their particular strength without worrying about the genomics. What we expect is that, by bringing together a diversity of researchers, growers and other industry partners, each group can focus on what they do best and we can in fact accomplish more as a single national entity than we ever did as divided regionally focused breeding programs. I’m tremendously optimistic about what we can accomplish, but keep in mind that we’re playing the long game here: an evaluation of our impact can only be made after at least a decade of trying out this new model.



Genome Atlantic: How difficult is it to pinpoint the commercially desirable traits in apples or grapes? Is this the most challenging aspect of using genomics in plant breeding?


Growers and processors are more than happy to share with us what they feel are the commercially desirable traits that should be the targets for fruit breeding.  Unfortunately for the geneticist and the breeder, they are numerous and sometimes elusive.  Growers want plants that require less chemical input to grow – that grow in a manner which reduces labour in the field – and that produce fruit that looks and tastes highly desirable to the consumer.  Disease resistance is fairly straightforward – we have several targets already that many breeders work on.  Growth habit and consumer desirability are trickier to tackle.  As a scientist, this makes things more interesting though – how do we measure what the consumer really wants and then rapidly breed for it using genomics?  The Canadian National Apple Breeding Consortium is particularly well equipped to tackle this, and it is precisely in this area of “fruit quality genomics” where we feel we can take the lead internationally.


Genome Atlantic: Through your connections with the U.S. Department of Agriculture you were able to duplicate its entire stockpile of apple cuttings for your Apple Biodiversity Collection. Do the Americans have any ongoing interest in your work with the collection?


Our work on apple genetic diversity is not only of interest to the US Department of Agriculture because of our strong collaborative relationship, but to apple researchers worldwide.  Our collection of over 1,000 apple varieties here in Nova Scotia is just beginning to reap its rewards in terms of scientific insights and there is intense interest around the globe in the results of our work on this unique collection of apples. We anticipate that we will continue collaborating not only with the USDA on projects that make use of the Apple Biodiversity Collection, but with researchers from other countries as well.


Genome Atlantic: How important is it for Canada and its fruit growers, particularly those in Atlantic Canada, to support using genomics in plant breeding?


Apple growers know how to take the long view.  When you establish an orchard, you make a business plan that extends 30 years into the future. Investing in genomics in apple breeding is highly similar: it will likely take at least 20 years before the insights we are gaining now will result in a benefit to a grower’s bottom line. This is not unique to Atlantic Canada – it’s the same everywhere in the world. With our newly established National Apple Breeding Consortium, communication between genomics researchers and industry members is improving dramatically, especially as it relates to the timelines of the deliverables from genomics, and I’m confident this will result in a win-win scenario for the Canadian apple industry.


Genome Atlantic: The Annapolis Cider Company that you and your wife opened in Wolfville is a new boutique beverage business built on Annapolis Valley apples. At the time, Dr. David Gray, Dalhousie’s faculty of agriculture dean, hailed the venture as “a fantastic example of science in action.”  Could this type of enterprise be a model for future business development in the region, as the dean suggested?


It is our sincere hope that our business becomes a model for future entrepreneurs in our region.  We believe strongly that new businesses producing novel value-added agricultural products are key to rural economic sustainability in Nova Scotia.  In turn, we’re trying hard to convince the public that consuming these products, and getting on the buy-local train, is part of the solution to our rural communities’ looming economic woes.  Everywhere we look we see people desperately desiring premium, value-added agricultural products – the demand is there! I’m convinced that if others follow in our footsteps and manage to build sustainable businesses based on products made from the agricultural land around us, we can all experience a net positive impact on our economy, our health and our society overall.