P.E.I. research team digs into potato wart

Dr. Xander Wang, Associate Professor, School of Climate Change and Adaptation, U.P.E.I., reveals how gene-sequencing data is being collected to identify spud varieties on the island that are both potato wart-resistant and climate change-resilient.

For more information check out UPEI’s article https://www.upei.ca/communications/news/2022/04/upei-researchers-seek-identify-climate-resilient-and-wart-resistant

N.L. prepares to raise the bar in bench-to-bedside genomics

The new multimillion dollar Centre for Translational Genomics is operated by Eastern Health and housed, here, on the third floor of the new medical building of the Faculty of Medicine, Memorial University, St. John’s. Photo credit: MUN

The pieces are coming together that could soon make Newfoundland and Labrador a leader in bench-to- bedside genomics, with the capacity to attract significant research and to change the lives of many Canadians and others with genetic-based disorders.

Central to this vision, doggedly pursued for a decade by molecular geneticists, Drs. Darren O’Rielly, at Eastern Health, and Terry-Lynn Young, at Memorial University, is the new multimillion-dollar Centre for Translational Genomics in St. John’s. A joint initiative by Eastern Health and Memorial University, the CTG will be operated by Eastern Health.

The CTG’s suite of gene sequencing equipment, housed in the university’s medical school, is now undergoing validation. The star of the impressive collection is an Illumina NovaSeq 6000, the highest throughput second-generation sequencer on the market. 

Dr. O’Rielly, now the centre’s director, expects all systems will be firing by fall, or early next year, for a phase-one focus on hereditary diseases.

When it comes to capability, he said, “We have a full gamut for a comprehensive array of services to both researchers as well as clinicians,” he said.

For two molecular geneticists, Dr. Terry-Lynn Young, Memorial University and Dr. Darren O’Rielly, Eastern Health, the new Centre for Translational Genomics is a dream come true for their home province, Newfoundland and Labrador.

When fully operational, the CTG, will offer clinical germline and somatic testing, in addition to a range of different sequencing options. Germline mutations are inherited while somatic ones are not. Somatic testing is usually done on tumors, often to provide personalized care.

No longer will the majority of samples have to be shipped outside the region for sequencing and analysis. This change alone, once the CTG is fully functioning, promises faster turnaround times for researchers, clinicians and patients.

Primarily conceived as a Newfoundland and Labrador enterprise, the centre has a close secondary aim to serve Atlantic Canada. To help realize the project, Genome Atlantic supplied a letter of support to tap the Atlantic Canada Opportunities Agency’s (ACOA’s) Atlantic Innovation Fund.

In addition, Genome Atlantic accessed its Genomics Opportunity Review Program to fund a business case assessment to support the ACOA submission. “That was really helpful,” said Project Co-Lead, Dr. Young. “It gave both us and our funders, and the institutions involved, confidence that what we were building would actually have clients at the end of the day, besides just Eastern Health – just the health care providers.”  

Funding for the CTG came from the Atlantic Canada Opportunities Agency, via its Regional Economic Growth Through Innovation program; from the Government of Newfoundland and Labrador, through the Department of Industry, Energy and Technology; and from the Health Care Foundation of Newfoundland and Labrador, as  well as the Janeway Children’s Hospital Foundation, the Dr. H. Bliss Murphy Cancer Care Foundation, Eastern Health and Memorial University.

“In phase two, which is focused on sporadic diseases that includes most cancers,” Dr. Rielly explained, “there is an opportunity to partner with several of the different big pharma companies. And there’s also other companies in this realm, within Atlantic Canada, that have expressed an interest and willingness to use our centre as well.”

Generating researcher interest in the new centre should pose few difficulties, given the province’s extensive population of genomic isolates – that is, inhabitants separated into distinct groups that have historically avoided genetic mixing through intermarriage for various reasons, including geography. Sometimes referred to as Newfoundland and Labrador’s founder population, it includes the province’s indigenous residents and those whose trace their ancestry to the European settlers. For anyone in genetic research, this is a dream population begging for study.

Equally attractive will be integrated research and clinical services, a key objective that Drs. O’Rielly and Young are working hard to facilitate.

They are hoping to significantly cut the time between the discovery of a gene-caused medical condition and the clinical response, by periodically re-analyzing sequencing data on patients. This would be done as new knowledge is translated from peer-reviewed research in the literature and in-house data confirm a genetic variant to be the source of a specific medical disorder. The move would end the need for multiple retests and shave years off the current gap between gene discovery and clinical action.

Dr. Young traces the impetus for the CTG to her experience with Arrhythmogenic Right Ventricular Cardiomyopathy or ARVC, a genetic heart disease that can trigger sudden death. It affects a great many Newfoundlanders and Labradorians, and in 2008 Dr. Young and her colleagues chased the cause to a single mutation on a single gene, TMEM43.

The potential hit home, she said, “once we realized if we could connect both the research side and the diagnostic side…we could really make a huge impact.”  They connected those dots and today, a simple blood test can diagnose ARVC, and an implanted defibrillator can protect sufferers from cardiac death.

With the centre established, work is now focused on generating projects, building networks of researchers and bioinformaticians as well as partnerships and collaborations to actualize their vision of a centre for Canadian excellence in translational genomics. Work is proceeding apace on all fronts.

“We’ve got a huge project now with the Terry Fox Institute Marathon of Hope Initiative, where they’re looking at all the different types of mutations that happen to single genes and to many genes within tumors, cells and tissues,” said Dr. Young. “All the Atlantic provinces are working together as one node,” Dr. O’Rielly said. The massive project is being divided up among different institutions in the region to keep the work in Atlantic Canada, he added.  The Atlantic node of the initiative is Dr. Sherri Christian, Department of Biochemistry, Memorial University.

Collaborations and partnerships have already been established with colleagues at the IWK Health Centre in Halifax, N.S. Dr. O’Rielly said they are looking at common challenges, sharing resources and datasets, as well as working to establish common practices, so that the CGT can eventually process samples from the IWK seamlessly and the two organizations can provide backup for each other.

Undoubtedly, the centre will be a regional asset, but the major beneficiaries are expected to be Newfoundlanders and Labradorians, due to their close proximity to the CTG and their ease of access to the new services provided through Eastern Health. Research on the province’s genetic isolates, which includes most of its residents, is also expected to grow exponentially now because of the CTG.

 

Genomic Evaluations On the Way for Milking Shorthorns

After many years in the background of Canada’s Holstein-dominated dairy industry, Milking Shorthorns have begun to attract the attention of a growing number of dairy producers.

Breeders, represented by the P.E.I.-based Canadian Milking Shorthorn Society, are seizing the moment to elevate their dairy breed with genomic evaluations. The move will level the playing field for Milking Shorthorns with Canada’s five other established breeds of dairy cattle. These animals, all registered, have genomic evaluations accessible through Lactanet, a farmer-run organization. 

Ryan Barrett, the society’s secretary-manager and an enthusiastic booster of Milking Shorthorns, explained: “we want to build a reference population in order to hopefully start offering genomic evaluations for our breed very soon.”

To get started, the society landed a grant through the Small-Scale Climate Change Fund set up by Genome Atlantic and supported by Research Nova Scotia. The money has allowed the society to begin work with Milking Shorthorn breeders in the Maritimes to genotype their animals  – that is, to do a complete genetic workup on each animal by way of DNA analysis.

Milking Shorthorn dairy cattle on pasture at Oceanbrae Farms near Miscouche, Eastern Prince County, P.E.I. Photo credit: Ryan Barrett.

This groundwork will supply 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 aim is to help breeders improve the quality of their Milking Shorthorn herds through genomic selection, a faster, more precise and reliable way to improve dairy herds with desired attributes that generally revolve around milk production, reproduction, longevity and health.

Why the revived interest in the Milking Shorthorn? The breed, once known as Durhams or Dual-Purpose Shorthorns and considered one of the oldest recognized cattle breeds in the world, are gaining new recognition for their climate-friendly qualities in an era of climate change. With greater efficiency they turn forage into milk with higher percentages of fat and protein than the industry standard Holstein breed.

Rated ideal for farms using rotational grazing, Mr. Barrett said the Milking Shorthorn “generally last longer, have fewer health and breeding problems and have a quiet temperament.” He added, “While Milking Shorthorns rarely produce as much milk as Holsteins, they make up for it with lower input costs.”  

Even by 2022 standards, Milking Shorthorns are high achievers, which is perhaps all the more surprising for a breed developed in the late 1700s in Northwest England in the Valley of the Tees River, bordering the counties of Durham, Northumberland and York. 

“In recent years, we have seen more Canadian dairy producers who have started to reconsider the Milking Shorthorn, either as part of a mixed herd or as a dominant breed in their herd,” said Mr. Barrett.

Without the benefit of genomics, he explained, genetic evaluations must rely solely on information about an animal’s lineage and its progeny’s performance.

“Depending on how much data has gone into that animal’s genetic evaluation, the reliability of an individual animal’s evaluation will vary,” he said. “For example: a proven sire with thousands of daughters across the country will have a reliability over 95 per cent. On the other hand, a newborn calf only has the average performance of its parents, so it starts with a reliability of 30-40 per cent. “

With this method, the reliability of the rating depends on the time it takes to establish the data.

By comparison, genomics substantially improves the reliability factor while dramatically reducing the time involved to supply results with greater precision. “By doing a genomic test of an individual animal from a hair or other tissue sample and identifying how that animal will code for more than 65,000 markers (SNPs) that are commonly used in dairy cattle,” he said, “we can compare that animal’s genetic profile against other genetic profiles, identify individual SNP’s or groups of SNPs with favourable or unfavourable performance for a number of traits and improve the reliability of genetic evaluation without that animal having to be calved, and having a milk record etc. This provides the dairy producer with more reliable information to chose how to breed his cattle, which cattle to keep for replacements, which to sell, etc.”

The Canadian Milking Shorthorn Society is betting that genomic evaluations for the Milking Shorthorn will ensure the moderate-sized cows with the climate friendly advantage will gain even greater traction on Canadian dairy farms.

Certainly, the Milking Shorthorn is a firm favourite with Mr. Barrett and his family. His grandfather, Keith, purchased his first one in 1950 and since then the breed has remained at the heart of Oceanbrae Farms, now run part-time by Mr. Barrett and full-time by his brother, Matt, and their father, Fred, on the southern shore of Malpeque Bay, near Miscouche, in Eastern Prince County.

Oceanbrae Farms was recognized for having a Master Breeder herd in 2008 and the operation is said to be in the running to claim the title again this year, a significant year for Milking Shorthorn advocates everywhere.

This year marks the 200th anniversary of the Coates Herd Book, the first cattle herd book ever produced, “Containing the pedigrees of Short-Horned Bulls and Cows Etc. of the Improved Durham Breed.” It is a reminder of how important genetic improvement has been for the Shorthorn breed and the potential that lies ahead with genomic evaluation.

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 https://genomecanada.ca/news-and-events/news/ 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 (ktweel@genomeatlantic.ca) and/or Andrew Yoshioka (ayoshioka@genomeatlantic.ca).  


*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

FOR IMMEDIATE RELEASE MARCH 23, 2022

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.

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For more information contact:

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

Stephanie Reid MA, Director, Marketing & Communications, Research Nova Scotia,
Stephanie.Reid@researchns.ca | 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

FOR IMMEDIATE RELEASE – March 09, 2022

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: https://bit.ly/3tCIBkJ


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Quotes:

“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
CGaudet@genomeatlantic.ca | 902-488-7837 (Halifax, N.S.)

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

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

Antoine Gascon, Communications and Public Affairs Specialist, Génome Québec
agascon@genomequebec.com | 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 (ktweel@genomeatlantic.ca)

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.