Improving treatment & diagnosis of rare diseases in Atlantic Canada

Q&A with Dr. Victor Martinez, Clinical Genomics Specialist, IWK Health Centre; Assistant Professor, Department of Pathology, Dalhousie University

The Genome Canada-led All for One initiative is advancing precision health across the country, increasing equitable and timely access to accurate, genomics-enabled clinical diagnosis for Canadians with serious genetic diseases.

At the heart of the initiative are six implementation projects located across Canada. We asked Dr. Victor Martinez from the project team in Atlantic Canada about how All for One will have an impact in his region.

“Currently, if a patient needs to have their whole exome or genome analyzed, those tests are being sent out mainly to private US companies. Our objective is to bring all those tests in-house and increase the diagnostic rate and speed of results, which will have significant benefit for patients.”

– Dr. Victor Martinez

Can you tell us a bit about the work you’re engaged in?

My role is focused on interpreting and trying to find the biological consequences of genetic variants in patients affected by rare diseases or other hereditary conditions. This work is also linked with the research side of things, as we create the systems necessary to analyze genetic data and develop solutions to the challenges associated with new sequencing technologies.

The All for One initiative was launched to provide a new, and more consistent, standard of care for Canadians by increasing clinical genomic testing capacity across Canada. How would you describe the availability of this testing in Halifax and Atlantic Canada?

In Atlantic Canada, and specifically Halifax, it’s a little bit different than other provinces in Canada. The IWK Health Center is a publicly funded Women’s and Children’s Hospital, and it’s also a Health Authority that serves all the Maritimes provinces. This situation put us in an excellent position to take this specific All for One project and have a big impact on the diagnosis of rare diseases in the region.

Currently, we offer sequencing analysis for some patients, and this is funded by the province. Each case is reviewed, and if the patient might benefit from genetic analysis, we offer that to the patient. However, this analysis looks at a limited number of genes compared to what will be available with All for One. We currently analyze around 300 genes and look for a limited number of diseases. With expanded genomic sequencing capacity through All for One, we expect to be able to sequence whole genomes, or whole exomes [the collection of pieces of an individual’s DNA that provide instructions for making proteins], for patients. This will generate a lot more information, allowing us to increase the number of diseases we can look for.

Currently, if a patient needs to have their whole exome or genome analyzed, those tests are being sent out mainly to private US companies. That information remains outside Canada and cannot be used to improve future diagnoses locally. Our objective is to bring all those tests in-house and increase the diagnostic rate and speed of results, which will have significant benefit for patients.

How long does it typically take to diagnose a child with a rare disease? How can these wait times be reduced?

It is very difficult to estimate, but it could take seven to eight years to diagnose a rare case without sequencing. One of the milestones for our project is improving the time it takes to make a diagnosis. One of the most significant benefits of increasing sequencing capacity in Canada is being able to share that data across Canada. With rare diseases, we might have only one patient in our area with the condition.  If we can identify additional patients in other provinces, we will be able to share genetic and  clinical information about our patients and thus, significantly improve the diagnosis of these cases.

All for One is being deployed through six related projects across Canada. What is the focus of your research team in Halifax?

Our main aim is to develop and implement clinical and laboratory systems for whole exome and whole genome sequencing for pediatric patients in Atlantic Canada. We are implementing the systems needed to analyze the whole genome of a patient, which is new for us. But there is a lot of experience across Canada, so we are also harnessing that existing experience to ensure our work is compatible with other centres across Canada.

We are also working to assess the clinical utility and cost of sequencing. For example, we are looking to identify whether using exomes or whole genomes can reduce the time to diagnosis or improve other key aspects of patient care and healthcare services.

Could the work you are doing also help bring down the cost of diagnosing and treating rare diseases in children?

Cost savings should come if we can diagnose patients faster. I don’t want to overpromise, but if we can reduce the number of years it takes for a patient to be diagnosed using more sequencing-based tests, it can significantly reduce the costs associated with treatment and monitoring of patients. Whole genome sequencing technologies can also replace other tests that we offer now in the lab, such as microarrays. For example, instead doing two tests for the same patient, we could do one test via sequencing that produces a lot more information.

As we envision a future where precision health is a standard of care available to people across the country, can you describe the major barriers Canada needs to address?

The sharing of genetic data is a completely new challenge for regulatory agencies in each of Canada’s provinces and territories, which means there will always be concerns about data privacy and security. We are committed to ensuring proper privacy protocols are followed and that we have the cybersecurity mechanisms in place to protect patient data. Communicating effectively to hospitals, patients and regulators about how we are protecting patient data will be a key component of our success.

Learn more about the All for One rare diseases project Dr. Martinez is working on.

Climate Action Genomics Initiative: Climate-Smart Agriculture and Food Systems

Climate change poses a significant risk to our agriculture, aquaculture, and food production systems and will increasingly impact availability of food and other vital resources.   Innovative new technologies, products and approaches are required to reduce emissions, maintain productivity and competitiveness, and ensure food security at home and abroad. 

In response to this major challenge, Genome Canada is launching the Climate-Smart Agriculture and Food Systems genomics initiative which is investing $30M in interdisciplinary, collaborative, and cutting-edge genomic research and innovation to reduce the carbon footprint of Canada’s food production systems.

This large-scale initiative will fund a portfolio of interdisciplinary genomics research and innovation projects while connecting these efforts with cross-cutting programs to support knowledge mobilization, data coordination and solution implementation across Canada.  This portfolio approach allows benefits from one solution to translate into other production systems or supply chains and cascade impact throughout the broader national food system. 

The Interdisciplinary Challenge Team Funding Opportunity ($24M) is the first of the programs to be launched under the Climate-Smart Agriculture and Food Systems Initiative.   Projects should involve multidisciplinary teams including GE3LS* researchers, must focus on the use of genomic approaches to develop tools and technologies, and demonstrate significant potential to achieve impact in reduction the footprint of Canada’s food systems.  The funding process will involve three stages: Registration, Letter of Intent, and Full Application.   Co-funding will be required.    

Eligible research themes include, but are not limited to:

  • Increasing production efficiencies to existing food systems while reducing environmental footprints
  • Carbon sequestration (cultivars, soil microbial communities etc.)
  • Sustainability in food production systems e.g., with decreased use of water, fertilizers, and pesticides; improving fish feed
  • Cellular agriculture (e.g., tissue engineering, precision fermentation techniques, etc.)
  • Controlled environment agriculture

Please see for more information on this funding opportunity. 

Interested researchers should contact Genome Atlantic as soon as possible for more information on deadlines and proposal development support.  

For more information or to apply, please contact Kristin Tweel ( and/or Andrew Yoshioka (  

*The acronym GE3LS stands for genomics and its ethical, environmental, economic, legal and social aspects. However, it should be understood broadly as research into the implications of genomics in society from the perspective of the social sciences and humanities. Therefore, it is not strictly limited to the disciplines that comprise the acronym, but rather encompasses all those that rely on quantitative and qualitative methodologies to investigate the implications of genomics in society and to inform applications, practices and policies.

Eight Genomics-Based Climate Change Projects Receive Small-Scale Climate Change Funding


HALIFAX, N.S. – Eight climate change research projects were announced today by Genome Atlantic, in partnership with Research Nova Scotia. The projects bring genomics problem-solving capabilities to wide-ranging areas of Atlantic Canada’s economy, from the lobster fishery to soil management.

The initiative was made possible through a new $124,530 Small-Scale Climate Change Fund (SSCCF) set up by Genome Atlantic, with support from Research Nova Scotia.

Each approved project received an award ranging from $5,000-$20,000. Projects were eligible for funding in excess of $5,000 if they had co-funding partners.

“We were very impressed by the number and quality of applications we received for these relatively small, but potentially important, genomic research projects aimed at alleviating the effects of climate change,” said Dr. Kristin Tweel, Genome Atlantic’s Director of Sector Innovation. “Having Research Nova Scotia as a partner meant we were able to fund twice as many awards as we could have done alone, so we are very grateful for Research Nova Scotia’s visionary outlook and support,” she said.

“Climate change poses serious and far-reaching challenges for Nova Scotia,” said Stefan Leslie, CEO of Research Nova Scotia. “That’s why Research Nova Scotia is proud to partner with Genome Atlantic on the Small-Scale Climate Change Fund. These research projects will help mitigate the effects of climate change on our region and promote sustainability and resilience in our traditional industries.”

The SSCCF is designed to kick-start short-term, proof of concept research, with preliminary results expected by May 31. The purpose is to test potential genomic-based solutions to problems affecting businesses, industries, organizations or governments in Atlantic Canada and to provide the basis for larger future scientific investigations.

The successful projects include initiatives that relate to potato wart, sampling for harmful algal blooms in freshwater, the genetic value of the Milking Shorthorn Dairy breed, the heat threshold of Prince Edward Island and Nova Scotia mussels, invasive earthworm identification, detection for the impending arrival of a new oyster parasite, the affordability of livestock forage grown with rejuvenated soil microbiomes, and the risk to the Maritime lobster fishery from a disease decimating lobster landings, south of Boston, Mass.

Applicants had to ensure their research would be applied by engaging an end-user – an industry/association or government partner – to be part of the application. They also had to show how their initiative could impact climate change and lead to a larger funded research project.

Brief descriptions of the successful projects are below.


For more information contact:

Charmaine Gaudet, APR, Director of Communications, Genome Atlantic| 902-488-7837 (Halifax, N.S.)

Stephanie Reid MA, Director, Marketing & Communications, Research Nova Scotia, | 902-223-9450 (Halifax, N.S.)

Approved Small-Scale Climate Change Projects

Milking Shorthorn Dairy Cattle in the Maritimes

Growing domestic interest in Canada’s relatively small population of Milking Shorthorn dairy cattle has sparked the need for genomic evaluations in the breed. The moderate-sized breed has gained a reputation for its high efficiency in converting forage to milk containing high-valued fat and protein. The Canadian Milking Shorthorn Society, headquartered in Kensington P.E.I., wants to start the evaluation process by building a reference population of genotypes – a compilation of the genetic makeup of individual members of the dairy breed in Canada. As a first step, the society wants to work with Milking Shorthorn breeders in Prince Edward Island, Nova Scotia and New Brunswick to genotype most of the cattle resident in those provinces. The work will also provide a template for additional genotyping of other Milking Shorthorn dairy cattle across the country as well as for testing genetic material from existing gene banks.

The project: Pursuing Genomic Evaluation for Milking Shorthorn Dairy Cattle to Improve on-Farm Efficiency and Climate Friendly Milk Production.

Principal Investigator:
Ryan Barrett, Secretary-Manager, Canadian Milking Shorthorn Society, Kensington, P.E.I.

Nova Scotia Oyster Industry

Building on ongoing research to develop protocols for two- to three-hour field-based detection of the oyster parasite, Haplospordium nelsoni, a Cape Breton research group will expand its work to add rapid detection for another oyster parasite, Perkinsus marinus.  The oyster industry is a multi-million dollar industry in Atlantic Canada. While H. nelsoni devastated the Bras d’Or Lake industry early this century, P. marinus is an impending threat for oyster growers, starting in southern Nova Scotia. The protozoan parasite has spread northward along the U.S. eastern seaboard over the past 20 years due to increasing water temperatures, which are now affecting Atlantic Canada. Southern Nova Scotia’s water links with the U.S. via marine and boat traffic leave that area vulnerable to the arrival of P. marinus.  Quick and early detection of this oyster pathogen, however, could mean mitigation measures could be taken to avert a commercial calamity for the industry.  

Project: Rapid detection of Perkinsus marinus to protect the Atlantic Canada oyster industry from a climate change threat.

Principal Investigator:
Dr. Rod Beresford, Research Fellow, Verschuren Centre for Sustainability.  (Associate Professor, Integrative Science, Cape Breton University)

Water Quality in Atlantic Canada

Harmful algal blooms produced by cyanobacteria have become an important priority in Atlantic Canada. As a result of climate change, these bacteria have begun to turn up with greater frequency and for longer durations in lakes across Nova Scotia. Under certain circumstances, cyanobacteria can release toxins and other compounds that affect water quality. Sampling approaches are needed to better understand, monitor, and prioritize risks associated with algae and algal toxins. A research team from Dalhousie University plans to take a state-of-the-art passive sampling approach to monitor cyanobacteria, based on its recent success in developing a passive sampling device to monitor SARS-CoV-2 in various wastewater environments.

The Project: Enhanced Climate-based Monitoring of Algae and Algal Toxins through Passive Sampling.

Principal Investigators:
Dr. Graham Gagnon, NSERC/Halifax Water Industrial Research Chair in Water Quality & Treatment and Director, Centre for Water Resources Studies,
Dr. Amina Stoddart, Assistant Professor, Centre for Water Resources Studies and Department of Civil and Resource Engineering,
Dr. Crystal Sweeney, Postdoctoral Fellow, Centre for Water Resources Studies, all at Dalhousie University, Halifax, N.S.

Blue Mussel Industry in Prince Edward Island and Nova Scotia

With Prince Edward Island’s blue mussel production coming under increasing pressure from warming coastal waters, the suspected higher thermal tolerance of mussels from Sober Island Pond, N.S. may offer a potential genetic solution. Preliminary research suggests the Sober Island Pond mussels can withstand higher water temperatures than their cousins in St. Peter’s Bay, P.E.I. Mussel grower, Atlantic Aqua Farms Ltd. of Borden-Carleton P.E.I., and a Dalhousie University researcher who specializes in an ecosystem approach to aquaculture want to compare the two populations to find their thermal thresholds and consider whether genes from the Nova Scotia mussels might improve the environmental heat tolerance of P.E.I. mussels. This research could be important for the future of the island industry, which currently supplies 80 per cent of the North American mussel market.

The Project: Exploring adaptation and plasticity to ocean warming in blue mussels. 

Principal Investigators: 
Dr. Ramon Filgueira, Associate Professor, Marine Affairs Program, Dalhousie University, Halifax, N.S.; 
Dr. Tiago Hori, Director of Innovation, Atlantic Aqua Farms, Vernon Bridge, P.E.I.

Agricultural Soil Management

One way to step up carbon sequestration is to enhance the soil microbiome – the mixture of organisms in the soil- with essential microbes and fungi so the soil can hold more carbon dioxide from the atmosphere. NL Marine Organics, an enriched fish-based fertilizer producer, in Portugal Cove St. Phillips, N.L. wants to determine how growing livestock forage with rejuvenated soil microbiomes could be made more affordable for agriculture. The project plans to collect baseline data from soil samples on farms using different soil management practices; consult farmers to identify change management issues; denote practices that impact the soil microbiome and the economic factors that could persuade the agricultural sector to adopt a new, environmentally friendly approach to soil management. 

Project: Carbon Sequestration and Food Security through Metabolomic Approaches to Soil Microbiomes.

Principal Investigator:
Diane Hollett, co-founder of NL Marine Organics, Portugal Cove St. Phillips, N.L. 

Invasive Earthworms in Atlantic Canada

Researchers at Saint Mary’s University in Nova Scotia and the Canadian Forest Service in New Brunswick and Quebec, want to get a handle on the variety of earthworms in Atlantic Canada, about which little is known, by using environmental DNA. The technique involves using soil samples to analyze tell-tale genetic material left behind by the worms, to indicate the species present. If it proves practicable, the methodology could be time saving, cost efficient and more accurate than conventional searches for species identification. The technique could also fill a major information gap on earthworm distribution in Atlantic Canada. Without the data government and researchers cannot model or understand the effects of large-scale earthworm invasions, which are likely to increase with climate change. Earthworms, because of their ability to change soil properties can either increase or decrease soil carbon storage. They have been found to reduce the amount of carbon stored in the soil organic layer by more than 50 per cent, but they can also increase storage by mixing carbon into deeper layers of soil. The differing effects are believed to be related to the earthworm species, their habitat and the surrounding climate.

The Project: Tracking invasive earthworms through eDNA: a proof of concept.

Principal Investigator:
Dr. Erin Cameron, Assistant Professor, Department of Environmental Science, Saint Mary’s University, Halifax.

The Maritime Lobster Fishery

This project will look at establishing the risk of epizootic shell disease (ESD) and its potential for damage to Canada’s east coast lobster industry. There are concerns the warmer, more acid waters created by climate change that have facilitated the prevalence of ESD in the Gulf of Maine could creep north into Canadian waters. Landings from the once lucrative lobster fishery, south of Boston Mass., are down by more than 85 per cent since 1997. While poorly understood, ESD is believed to be caused by chitinolytic bacteria, which produces lesions in lobster shells. Once the risk is known, Canadian management practices may be better able to minimize the potential impact here.

The Project: Baseline Molecular Epidemiologic Risk Assessment for Shell Disease in the Atlantic Canadian Lobster Fishery. 

Principal Investigator: Dr. Fraser Clark, molecular immunologist, Department of Animal Science and Aquaculture, Dalhousie University.

Prince Edward Island Potato Industry

A multidisciplinary team versed in climate change, gene sequencing, agriculture diseases and precision agriculture will comb the scientific literature to collect potato gene-sequencing data that could make P.E.I. potatoes more resilient to climate change and resistant to potato wart. Last year, the disease caused significant economic loss to the island’s potato industry after it was found in potatoes on two P.E.I. farms. The discovery prompted suspension of all shipments of P.E.I. seed, table and processing potatoes to the U.S. for about three months.

The project: Identification of Climate-Resilient and Wart-Resistant Potato Varieties for P.E.I.

Principal Investigator:
Dr. Xander Wang, Associate Professor, School of Climate Change and Adaptation, University of Prince Edward Island.

New research approved for Atlantic salmon aquaculture and forestry


New research approved for Atlantic salmon aquaculture and forestry

Halifax, NS – Two multi-million-dollar research and innovation projects, one to benefit Atlantic Canada’s salmon aquaculture industry and the other to aid the sustainability of the Maritimes’ forestry sector, were announced today by the federal Minister of Innovation, Science and Industry, the Honourable François-Philippe Champagne.

The two ventures were among 10 research initiatives included in the Minister’s announcement of approved projects from the latest competition round of Genome Canada’s Genomic Applications Partnership Program, known as GAPP.

The aquaculture project, to be managed by Genome Atlantic, is a four-year $4.7 million initiative to improve commercial Atlantic salmon broodstock.

The forestry project is a three-year $6.2 million venture to speed up development of new varieties of red and black spruce that can withstand climate change. The tree species are widely used in Eastern Canada’s forest industry. The project will be managed by Génome Québec and supported by Genome Atlantic.

Improving Atlantic salmon broodstock

Salmon aquaculture is a significant food producer and economic contributor in Atlantic Canada, providing the main protein served in at least 232 million meals each year and more than 8,000 jobs. Improvements in the biological performance of salmon grown in waters of Canada’s east coast will also protect animal welfare and bolster the sector’s success in domestic and international markets.

Mowi Canada East, part of the of Mowi ASA group headquartered in Norway, has salmon aquaculture operations in New Brunswick, Newfoundland and Labrador, and Prince Edward Island. The company will be collaborating with the Huntsman Marine Science Centre, St. Andrews, N.B. to map the genomic markers for North American Atlantic salmon that positively influence general fish performance, resistance to sea lice, and tolerance to changing water temperatures. Dean Guest, Freshwater Director for Mowi Canada East will lead the project with academic counterpart, Dr. Amber Garber, Research Scientist at Huntsman Marine Science Centre.

FastTRAC-ing breeding of commercial spruce

The forestry project called FastTRAC2 is the sequel to FastTRAC1 that focused on developing new varieties of Norway spruce and white spruce. The new project will use genetic selection to speed up the participants’ advanced breeding programs for black spruce and red spruce.

Dr. Patrick Lenz, Research Scientist with the Canadian Wood Fibre Centre, part of the Canadian Forest Service at Ste Foy, Québec is co-leading the project with Dr. Jean Bousquet, at Université Laval, Québec City, and with Bruce Stewart, Director of Forestry, Nova Scotia Department of Natural Resources and Renewables. He is overseeing the project for the Maritimes and its implementation in the Nova Scotia Tree Improvement Working Group’s red spruce breeding program. Other project partners include the New Brunswick Department of Natural Resources and Energy Development, the New Brunswick Tree Improvement Council and the Woodlands Division, J.D. Irving Ltd.

Read the Genome Canada release about all GAPP projects announced today:



“Genomics research and development plays a pivotal role in improving the lives of Canadians and advancing our post-pandemic economic recovery. Investments, like the one announced today by our government, allow scientists and researchers to take their work beyond the walls of the lab and bring real-world benefits to Canadians in key sectors, including solutions to fight climate change and to keep our industries productive, sustainable and competitive globally.”

– The Honourable François-Philippe Champagne,
Minister of Innovation, Science and Industry

“DNA-based solutions are an important part of the innovation toolkit for many industries in Atlantic Canada, and the demand for these technologies has never been greater. The projects announced today represent custom-fit solutions to significant industry challenges, with the ultimate goal of helping those industries achieve increased and more sustainable production.”

—Britta Fiander, Director of Innovation Programs,
Genome Atlantic, Halifax, N.S.

“We have been working with this specific broodstock since 2010, collecting thousands of data points and fin clips following numerous challenges and assessments, to support a family-based selection program. We are very excited for the opportunity that this project will provide to Mowi Canada East and Huntsman Marine Science Centre to now also select broodstock on an individual basis.”

—Dr. Amber Garber, project co-lead and Research Scientist,
Huntsman Marine Science Centre, St. Andrews, N.B.

“FastTRAC2 is very important for Atlantic Canada and, given that our provincial tree, the red spruce, will be a major focus of the project, it’s especially important to Nova Scotia. Quite possibly this venture is going to make the tree breeding programs in our region the most advanced in the country.” He noted “Nova Scotia is uniquely positioned to partner in this genomic research because of its 50-year-old tree breeding program which has amassed all the necessary test sites and, crucially, a trove of useful data.”

– Bruce Stewart, project co-lead, Director of Forestry,
Nova Scotia Department of Natural Resources and Renewables, Truro, N.S.

For more information contact:

Charmaine Gaudet, APR, Director of Communications, Genome Atlantic | 902-488-7837 (Halifax, N.S.)

Ian Roberts, Director of Communications, Mowi (Scotland, Ireland, Canada) | 506-754-6019 (New Brunswick)

Bruce Stewart, project co-leader, Director of Forestry, Nova Scotia Department of Natural Resources
and | 902-956-0462 (Truro, N.S.)

Antoine Gascon, Communications and Public Affairs Specialist, Génome Québec | 514-377-5613

Genome Atlantic launches Small-Scale Climate Change Fund

applications are now closed

Atlantic Canada faces unique and difficult challenges as climate change progresses. This targeted funding opportunity is intended to support short term, rapid initiatives which will advance identification, development and/or adoption of genomics tools that lead to solutions that help to combat climate change.

The goal for this program is to provide a foundation for Atlantic Canadian stakeholders to pursue subsequent larger scale Climate Change funding initiatives, such as Genome Canada’s anticipated flagship mission.

The Small-Scale Climate Change Fund is led by Genome Atlantic, in partnership with Research Nova Scotia.

Download the application form (NOW CLOSED) for more information on topic eligibility. If you are unsure if your proposed project is a fit, please reach out with questions to the address below.

Please note:
• Project contributions can range from $5,000 to $20,000
• Applications are due February 14th, 2022
• Projects must be completed or at least be able to demonstrate preliminary results by May 31st, 2022

For more information or to apply, please contact Kristin Tweel (

Atlantic Business Magazine Feature

Genome Atlantic: Writing the code for regional innovation and commercial success

In a region the rest of the world often appreciates only for its coastal vistas and pastoral beauty, the virtuous marriage of hard science and bold business is transforming the way people live and work, one extraordinary innovation at a time.

This is Genome Atlantic, a not-for-profit corporation with a mission to help Atlantic Canada reap the economic and social benefits of genomics and associated technologies in everything from agriculture, fisheries and aquaculture to energy, the environment, forestry, mining, and human health.

Says Steve Armstrong, Genome Atlantic’s President and CEO: “Delivering meaningful socio-economic impact requires innovation-friendly companies, creative academic experts, and a mix of private and public sector investment. That means exploring opportunities, finding partners and developing proposals. We are the connective tissue that has been bringing those key success factors together for 21 years.”

Since its inception in 2000, Genome Atlantic has been instrumental in putting together approximately $150 million in client-led projects focused on delivering tangible economic and health benefits. Now, says Armstrong, the region’s demand for genomics-based solutions has never been greater.

“Increasingly DNA-based or genomic technologies are an essential element of the innovation toolkit for companies and select public sector entities spanning just about any sector you can imagine,” he notes. “Many companies simply will not remain competitive if they do not continue – or in some cases, start – using genomics technologies. From optimizing agri-food and aquaculture production, to growing trees with the desired traits, to effectively monitoring their environmental footprint, to adapting to climate change: Genomics is key to all of that.”

The numbers are, indeed, convincing. Over the past five years alone, Genome Atlantic has seen a three-fold growth in R&D investment, almost all driven by end-user need and much of that from the private sector. In fact, business expenditure on R&D (BERD) represents about 25 per cent of the corporation’s project portfolio, compared with eight per cent in 2008. That portfolio consists of 23 current active projects valued at close to $60 million, in partnership with 25 companies and 15 universities.

Sequence #13

In this issue of sequence

Jay Woodworth, Perennia Food and Agriculture Inc’s Christmas Tree specialist with one of the SMART Balsam Fir seedlings. She oversees the Christmas Tree Council of Nova Scotia’s research program. Photo: John Hillis, Truefaux Films
An aerial view of Marbase, home of North America's first commercial lumpfish hatchery now in development. Photo, Marbase Marystown Inc.
Photo, New England Aquarium

International team to meet in Halifax next month

The international research team, assembled to explore the potential role of genetic factors in the problematic recovery of the North Atlantic right whale, is meeting in Halifax in January to discuss their approach.

Saint Mary’s University and the New England Aquarium are collaborating on a $6 million research study announced in July by Genome Atlantic.

They are using extensive data about whale health and reproduction collected in Canada, the United States and elsewhere to further their research. The team’s findings could have implications for marine management, policies, practices and conservation plans.

Dr. Mark Fast, Professor of Fish Health and Immunology, Atlantic Veterinary College, UPEI, is helping develop tools to pinpoint the risk factors for Complex Gill Disease, the cause of staggering losses for salmon fish farmers outside Atlantic Canada. Photo, UPEI Marketing and Communications
Dr. Scott Pavey in his CRI Genomics lab at the Canadian Rivers Institute, University of New Brunswick, Saint John, N.B. Photo, Rob Blanchard, UNB Communications

Sequence Past Issues

Atlantic Canada’s freshwater fish capture N.B. ecogenomics expert’s attention

In the face of climate change and other pressures, Dr. Scott Pavey, a rising star in the new and promising field of ecogenomics, is focused on retaining the biodiversity of New Brunswick’s and Atlantic Canada’s freshwater fish and the industries that rely on them.

He runs what he proudly calls, “the most advanced ecology-focused genomics lab in New Brunswick.”

CRI Genomics, Dr. Pavey’s lab at the Canadian Rivers Institute, University of New Brunswick, Saint John, is known for applying state-of-the-art genomic technologies and techniques to investigations into how to conserve and manage freshwater fish stocks and make aquaculture and the fisheries that depend on them more sustainable.

This is important work, he said, because “All industries that alter the environment, such as mining and forestry, or discharge into the environment, such as pulp mills etc., have a responsibility to ensure their impacts do not adversely affect the habitat and populations of freshwater fish. Freshwater fish habitat is protected by federal legislation. Every EIS [environmental impact statement] for projects near freshwater must take freshwater fish into account.”

Reduced biodiversity, he said, “weakens the entire system because species exist in food webs and are reliant on each other. If the prey go extinct, the predator starves.” Dr. Pavey pointed out, freshwater has been heavily impacted in Canada and worldwide and when these impacts cause local extinctions of species; they reduce biodiversity.

The lab of The Tier 2 Canada Research Chair in Aquatic Molecular Ecology and Ecological Genomics specializes in aquatic molecular ecology and ecological genomics. Aquatic Molecular Ecology uses molecular genetic tools for advanced DNA analysis, such as entire genome scanning and bioinformatics to identify and study communities of interdependent organisms in aquatic ecosystems. Ecological Genomics seeks to understand the genetic mechanisms that govern the way organisms respond to their natural environment. Ecology, evolution and conservation are Dr. Pavey’s watchwords.


Since 2020, he has been active in a $9.1 million Genome Canada Large-Scale Applied Research Project (LSARP) called GEN-FISH, short for Genomic Network for Fish Identification Stress and Health. It has involved a group of researchers, professionals and community members in an extensive and innovative four-year undertaking to develop toolkits that pinpoint where Canada’s more than 200 freshwater fish species can be found and in what numbers.

Accurate information on the kinds of fish and their numbers in rivers and lakes, he said means improved environmental monitoring, assessments and fish management. He explained, “Fish are under water, thus hard to see directly. It takes a huge effort to set nets. So, when there are impacts, they are often invisible. With eDNA we can more easily detect such impacts and recoveries

Also on the agenda are plans to develop a method to chart how Canada’s freshwater species are faring under increasing, mostly human-induced, stress. Project partners from Atlantic Canada include the New Brunswick Energy and Resource Department (NB ERD) and the Nova Scotia Salmon Association.

Dr. Pavey’s role is to extend the Ontario-based, but Canada-wide research to Atlantic Canada.


The project aims to produce three sophisticated toolkits, one for fish surveillance, another for fish health and a third for decision making that essentially promotes the other two toolkits for widespread general use.

“We are helping with developing, lab testing, and field testing the Fish Survey Toolkit,” said Dr. Pavey. “Assays need to be separately developed for each species before they are put on the chip. My graduate students are doing this, focusing on fish important to Atlantic Canada. They are also collecting eDNA [environmental DNA] samples in the field that we are using to field validate our developed tools.”

The fish in this region, he said, “are important because they are in Atlantic Canada. They also have commercial fishing, recreational fishing and cultural importance.”

Dr. Pavey said, “Our lab is going to submit sequences for the first draft Fish Survey Toolkit in a month or so. We are focusing on 15 species important to Atlantic Canada. We expect to have several draft toolkits in year three of the grant and test them in real conditions, including rivers and lakes in New Brunswick. We will have finished products in two years.“

Interest in these products is expected to be strong, especially from the fish management and environmental sectors and from some industries too. Many of them have a need to monitor their environmental impacts on freshwater from such things as industrial effluent. “Current entities requesting my services include the federal and provincial governments, non-profits, first nations and private consulting,” he said.

The Fish Survey Toolkit, he said, will let users know whether any of the Canadian fish species included for identification on the toolkit chip is present in any particular lake or river, based on analyses of water samples collected from them.

For this project, Dr. Pavey’s lab has been working on identifying fish species from environmental DNA. He explained the process this way: “A water sample is taken from a waterbody. The water is filtered and cells from fish that were in that waterbody collect on the filter. We prepare the DNA so that we can use a chemical reaction to make copies of the segment of DNA that is unique to a single species. If the species’ specific reaction produces a product, we know that species was in the water body.”

Fish-Health Toolkit

“The Fish Health Toolkit,” he said, “is designed to answer what is causing fish to be sick or die. Is it high temperatures? Heavy metal toxicity? Etc. The latter would involve lethal sampling of the individuals in question and determining which ‘stress’ genes are turned on or upregulated to tell us the nature of the ailment.”

Dr. Pavey is certain the toolkits will bring more attention to conserving and sustaining the Atlantic region’s freshwater resources. “They absolutely will,” he said. “They will be a new tool that will allow high throughput testing.” That means high volume testing with quick results.

“We have partnered with DFO [Department of Fisheries and Oceans] and NB ERD and both organizations are very excited to use these tools. Because I’m involved with the grant, I will ensure that the tools are designed in a way it meets the needs of organizations in Atlantic Canada.”

Considering Canada has one-fifth of the earth’s freshwater resources, the need for these toolkits quickly becomes apparent.

Meanwhile the GEN-FISH project has sparked new ideas for exploration. “While GEN-FISH is primarily focused on presence/absence of species, we are experimenting with how to use similar techniques to estimate abundance,” he said.

Other Work at CRI Genomics

In other work at CRI Genomics, Dr. Pavey noted “the lab team has spent a lot of time focusing on fish such as Atlantic Cod, and looking at factors that could help their populations rebound.” Striped Bass, Bluefin Tuna and the American Eel are other species to which his team has given special attention. All these fish species are of concern under the Canadian Species at Risk Act. His team used DNA sampling from tissue to determine population interactions and environmental adaptations of these species.

His recent research on the American Eel with Dr. Louis Bernatchez at Laval University identified the genes responsible for the eels’ survival in freshwater and saltwater environments. Genetic analysis of the all-female eels in the Upper St. Lawrence River, showed they had unique adaptive genetic traits compared to counterparts reared in brackish or saltwater.

It was an important finding because that kind of knowledge can result in more nuanced fisheries management policies to protect habitat and migration routes of sub populations that need critical genetic consideration.

The considerable range of CRI Genomics’ capabilities, means Dr. Pavey’s eight-member team is kept busy, often by clients seeking customized services unavailable elsewhere in the region. The client list includes the NB Museum, Huntsman Marine Science Centre, Memorial University, the Department of Fisheries and Oceans, the University of Massachusetts and NovaEel, a Nova Scotia-based aquaculture start-up.

The lab can do genotype-by-sequencing, also known as GBS, to enable researchers to track down the genetic roots of observable traits such as size or colour in fish, for instance. It can also identify unique adaptations found in local fish species, employ sequence barcode regions in DNA to identify species in microbiomes or insect communities, and use the environmental DNA found in small tissues and cells suspended in the waters of lakes and rivers to identify species that inhabit them. In addition, the lab has the capacity to run simultaneous targeted resequencing of candidate genes from many individuals.

With these resources, Dr. Pavey has set himself an important agenda in preserving the biodiversity of Atlantic Canada’s freshwater fish.

Cleaner fish R&D at Memorial University of Newfoundland helps spawn new industry


Newfoundland’s emerging cleaner fish industry to control sea lice infestations in Atlantic Canada’s farmed salmon has direct links with ongoing genomic research on lumpfish and cunner at Memorial University of Newfoundland’s Department of Ocean Sciences.

Marbase Marystown Inc., also known as Marbase, the company building North America’s first lumpfish hatchery to anchor its aquaculture services hub at Marystown, N.L., acknowledges on its website the reason it settled on lumpfish, as its cleaner fish of choice. It was due in part, to “development work on lumpfish that has taken place at Memorial University’s Ocean Science Centre.” The OSC is home to North America’s leading cleaner fish R&D facility.

Paul Antle, Chairman and CEO of Marbase explained it this way: “Memorial University’s Ocean Science Centre has developed decades of data around lumpfish husbandry and is considered a critical library of research as we establish Canada’s first commercial lumpfish hatchery. The partnership between the OSC and Marbase is a key element of that commercialization program. Not only do we value the historical research, but the potential opportunities in further genomic research, as we grow out our facility and refine the genetic characteristics of the ideal lice-eating lumpfish.”

“Basically, cleaner fish are another tool in the tool box for the industry,” explains Danny Boyce, Facility and Business Manager of Memorial University’s Dr. Joe Brown Aquatic Research Building. He points out chemical therapeutants, mechanical delousing and sea lice skirts are also available options, for use alone or in some combination, to deal with sea lice, the widespread marine parasite now costing salmon producers up to $150 per tonne in estimated annual losses and treatments. In Canada last year that figure translated into an $18 million cost to producers. The parasite feeds on the mucus, blood and skin of salmon, with harmful or fatal results for the infected fish.

Industry interest and demand for cleaner fish – species like cunner and lumpfish that thrive on sea lice – is on the rise, as a biological and environmentally friendly component in the arsenal against the pest. The Marbase lumpfish hatchery expects to start with initial annual production of three million individuals and the potential to expand to five million.
Cleaner fish have already made their mark in farmed salmon operations in Norway, the United Kingdom, Ireland and the Faroe Islands.

In the absence of a North American commercial lumpfish hatchery, Mr. Boyce’s facility has basically market tested the fish in Atlantic Canada by supplying relatively small-sized lumpfish on a limited basis to Cooke Aquaculture in Nova Scotia, Mowi Canada East in New Brunswick and Grieg Seafood in Newfoundland and Labrador. Demand has now outstripped the facility’s capacity for supply. Commercial sales were a sideline to its main focus of cleaner fish R&D purposes, under Memorial’s Department of Ocean Sciences Research Production Program.
Here is where the research team headed by Dr. Javier Santander, a marine microbiologist and Associate Professor in the Department of Ocean Sciences at Memorial University has made its mark.

Working in partnership with Cold Ocean Salmon, a subsidiary of Cooke Aquaculture Inc., and with funding from Genome Canada, the Atlantic Canada Opportunities Agency and Newfoundland and Labrador’s Department of Industry, Energy and Technology, the team has used lumpfish and cunner from the facility to sequence their genomes. It was an achievement made possible by Genome Atlantic’s participation in Genome Canada’s Regional Priorities Partnership Program.

Now sequencing data are available to evaluate the species’ characteristics for commercial cleaner fish deployment. “We already have the information for the development of several biomarkers that will impact broodstock selection, diet formulation, and fish health,” said Dr. Santander. “This will not only impact Marbase, but the entire cleaner fish industry,” he added.

Essentially the team’s research efforts are now directed at removing obstacles that have precluded wider use of cleaner fish in farmed salmon operations. One of the biggest challenges has been bacterial infection, but Dr. Santander said “we are very near,” to solving the lumpfish’s high susceptibility to Vibrio anguillarum, the bacterial pathogen most often found in lumpfish and the cause of vibrosis, a deadly haemorrhagic septicaemic disease.

“We have an effective vaccine that has been tested several times and soon will be evaluated in the field,” he said. Furthermore, he said, plans are afoot to develop a certified vaccine unit at Memorial University of Newfoundland to complete certification requirements for the formulation.

After evaluating commercial and experimental “in house” vaccines (designed in previous research) against Vibrio anguillarum, Dr. Santander said, “we determined that one of our preparations conferred superior protection.” His research group is now processing the data for transcriptomic profiling of the lumpfish response to the effective immunization.

The team is also working on vaccines for other bacterial pathogens such as Aeromonas salmonicida, which produces furunculosis, and Piscirickettsia salmonis, a cause of significant farmed salmon mortality.

The team has published a series of discoveries from these pursuits. In July this year, the group revealed how feed-based immunization of lumpfish larvae and juveniles against Vibrio anguillarum was found to be less effective than vaccine injected through the abdominal cavity.

They also isolated a new marine pathogen, Pseudomonas sp. from wild cunner and described its genetic makeup in a paper published in April. The achievement was significant because bacterial diseases, due to natural infections in cunner, have yet to be described.

While scientific investigations and commercial interests have largely homed in on lumpish, the possibilities of cunner remain of interest. There are marked differences between the two species, but as cleaner fish, both have commercial advantages.

Mr. Boyce noted, “lumpfish are very active and like cooler waters, less than 14 degrees C, while cunner love warm waters but go torpid in the winter months. They just hunker down.”

Lumpfish are also faster growing. He said, “A 20-gram lumpfish can be produced in less than a year – six to seven months – whereas a cunner is slow growing and it starts out as a really small egg and has a very difficult larval phase with a low survival rate. So biologically, it’s a much harder species to raise than a lumpfish” said Mr. Boyce.

Still, Dr. Santander points out, “utilization of both species as cleaner fish is the ideal goal.” He said, “cunner are utilized by our industrial partners, but their domestication has not been completed.”

Pursuit of that objective suggests plenty of scope for further cleaner fish research at Memorial and lots of added commercial potential to come.

A new balsam fir on the path to Christmas stardom

🎶🎤O Christmas tree O Christmas tree How lovely are thy branches!

That German carol could be singing the praises of SMART balsam fir, a new balsam fir variety inching up in 12 Nova Scotia test sites and destined for stardom in Christmases to come.

The SMART seedlings, developed in the Faculty of Agriculture at Dalhousie University, are expected to be a game changer for the region’s Christmas tree industry and put a lot more money in growers’ pockets. The industry in Nova Scotia is now worth an estimated $55 million annually, factoring in the complete supply chain.

Jim DeLong, president of the SMART Christmas Tree Research Cooperative Ltd., set up to help finance the research and commercialization effort, says, “with naturally occurring Christmas trees, you have 10 percent premium grade trees, and we’re looking at 80-90 per cent premium grade trees with the SMART tree seedlings.” Last year, on average, premium trees sold for $72 USD each.

Although SMART seedlings are not yet commercially available, they are attracting plenty of grower interest.

For now, the SMART seedlings remain in the field trial research phase, while cloning, through somatic embryogenesis, a particularly complicated process with balsam fir, proceeds apace at Phytocultures Ltd., Clyde River, P.E.I. to get the numbers up to meet anticipated grower demand. Somatic embryogenesis reproduces exact copies or clones of plants through an asexual process that relies on a single somatic cell.

These newly developed trees are following a path to commercialization set out by Greg Adams of GWA and Applied Biosciences Consulting, of Sussex, N.B., a forestry consultant hired with funding from Genome Atlantic’s Genomics Opportunity Review Program (GORP) to take SMART balsam fir to the next level.

Executive Director of the Christmas Tree Council of Nova Scotia Angus Bonnyman said, “thanks to the work that the consultant did, through the money from Genome Atlantic, along with money from the Christmas Tree Council of Nova Scotia, we think we have the right clones.”

SMART is an acronym for senescence modulated abscission regulating technology, developed by Dr. Rajasekaran Lada, founding director of the former Christmas Tree Research Centre, Truro, and Professor Emeritus, Department of Plant Food and Environmental Sciences, Dalhousie University.

Dr. Lada and his team developed 90 original genetic lines, or varieties, of SMART balsam, by selectively breeding for desired characteristics that are naturally occurring. Some of the resulting genetic lines were planted in Dalhousie’s Plumdale Orchard at the Agriculture Campus in Bible Hill and in three other sites in Nova Scotia. Not all of the lines made it to the cloning stage and for those that did, advanced testing was needed to determine which ones perform best in which soils and conditions, and the most promising lines had to be cloned in sufficient numbers for growers to buy. Those gaps are now being filled.

Jay Woodworth, Perennia Food and Agriculture Inc.’s Christmas Tree specialist, who oversees the Christmas Tree Council of Nova Scotia’s (CTCNS’S) research program, says for Phytocultures to produce clones via somatic embryogenesis, “selected genetic lines slated for cloning have to be removed from cryo-storage, and are encouraged to form an embryo, so that a germinate, or tiny tree, is produced within a petri dish.”

However, this procedure hasn’t been all smooth sailing. She said, “each individual line takes a little bit of tweaking to get it to grow up to the best of its ability in the lab setting.” As a result, she indicated, “only some of the lines have gone through the process to become trees, and even less of those have been planted out in the field setting to be tested in external conditions.” Before they reach the field, clones from Phytocultures spend about a year in the nursery at Scott & Stewart Forestry Consultants Ltd., Antigonish.

“We’re trying to focus now on which lines are the easiest to grow and which ones perform the best, once planted out in their intended environments,” explained Ms. Woodworth. So far, clones from more than 30 lines have been selected for field trials and have been performing well across Nova Scotia.

The first of 360 seedlings from the selected clone lines were planted in the fall of 2020 as part of a SMART tree three-year field evaluation, funded through the Canadian Agriculture Partnerships’ Crop & Livestock Management Trials program.

Phytocultures Laboratory supplied most of the seedlings with the remainder coming from Dalhousie University’s inventory. Nine evaluation sites were established, three in each of Nova Scotia’s active Christmas tree regions: Southwestern, Northeastern and Cobequid.

Each site has 44 trees planted across four rows in six-foot by six-foot spacing. Four control seedlings, conventionally produced and provided by Scott & Stewart Forestry Consultants were also included at each site for comparison purposes. The seedlings were tagged, pinpointed with GPS accuracy, and are seasonally evaluated.

Pre-dating that effort, and while SMART trees were in development at Dalhousie, select lines were field planted in more informal trials in 2015, and some of them are now four to five feet in height. These initial seedlings were incorporated nto the new rigorous evaluation process implemented in 2020 and they too are now tagged and GPS mapped. A total of 446 of these initial seedlings are growing in three Nova Scotia sites: St. Andrews, Onslow Mountain, and New Germany.

The latter site is on Mr. DeLong’s property where he devotes 1,200 acres of his mixed farming operation to Christmas trees. A third-generation Christmas tree grower with one of the bigger operations in Nova Scotia, he said his 115 SMART seedlings were interplanted with his other trees. Roughly 12 clone lines are believed to be represented in the mix.

All the SMART trees are being monitored for quality characteristics such as growth, flush date, colour, budding, needle length etc. Additional test sites are planned as more seedlings become available and more trials are required.

Early results are encouraging. Ms. Woodworth said, “one thing we’re really excited about is that all of these trees, regardless of what line they are from, are late flushers.” That means their buds break late in spring, making them less susceptible to late frosts, an important consideration in an era of climate change.

Memorable for Mr. Bonnyman is the spring of 2018, “when we had an unseasonably late frost and a freeze in Nova Scotia. A lot of the new growth in our Christmas trees were impacted by cold.” He anticipates SMART balsam fir will insulate the industry against incidents like that, which could become more frequent as climate change takes hold.

Describing the distinctive qualities of SMART trees, Mr. DeLong said “I would just say it’s superior characteristics.”

For consumers, that means SMART trees will offer superior shape, longer needle retention, and great balsam fir colour and aroma. Their improved insect and disease resistance bring added attractions for growers, as does the tree’s architecture which promises far less manual shearing. Still, the biggest bonus all round may be longer needle retention.

As Ms. Woodworth explained, “we’ve been cutting trees for export since the last week of September, so if you think of it, those trees need to last for Christmas. They have to be good at holding onto their needles.” Ninety per cent of Nova Scotia’s Christmas trees are sold outside the province. Half of them are shipped to other parts of Canada and the rest are exported, mainly to the United States, but also to countries as far away as Saudi Arabia and Panama.

SMART trees’ profit potential may also help rejuvenate the Nova Scotia industry with new recruits, who so far have failed to replace the number of producers, mainly an older demographic, who have left or are leaving to retire. According to Mr. Bonnyman, the province now has 350 active growers.

Most importantly, SMART trees represent a potential boost for the Maritimes’ hard-hit rural economy. “It’s quite a privilege to still make a living in rural Nova Scotia and to be part of the Christmas celebration,” acknowledged Mr. DeLong. “So, if you can plant some seedlings that can return you 80-90 per cent premium trees instead of 10 per cent premium trees,” he said, “that’s a big return on investment.”