Lab Canada

$93M supports genomics projects in agriculture and fisheries

Saskatoon, SK – Genome Canada and Western Grains Research Foundation have announced a total of $93-million in funding for 11 new genomics research projects that address challenges and opportunities for Canadian agriculture, fisheries and aquaculture.

The projects chosen for funding under Genome Canada’s 2014 Large-Scale Applied Research Project Competition called Genomics and Feeding the Future – each valued at between $5 million to $10 million – will be led by leading academic institutions based in British Columbia, Alberta, Saskatchewan, Ontario and Quebec, and involve researchers from across Canada.

“With its privileged supply of fresh water, unpolluted oceans and productive farm lands, Canada is ideally suited to play a leadership role in presenting solutions to major global challenges in the agri-food and fisheries & aquaculture sectors, said Lorne Hepworth, chair of Genome Canada. “Genome Canada is pleased to make these strategic investments that allow our genomics research community to innovate in these sectors for the benefit of all Canadians and people worldwide.”

Projects receiving funding are as follows, separated by province:


Enhancing production in Coho: Culture, Community, Catch (EPIC4). Project leaders: William S. Davidson, Simon Fraser University; Louis Bernatchez, Université Laval. Lead Genome Centres: Genome British Columbia, Génome Québec. Total funding: $9.9 million. The project will develop and use new genomics tools to address challenges facing the safe, secure and sustainable production of Coho Salmon. The interdisciplinary team of natural and social scientists will sequence the Coho Salmon genome, document the genetic diversity of thousands of individuals and determine how Coho Salmon from different geographic regions vary genetically. They will apply their knowledge to revive and sustain the wild Coho Salmon fisheries.

Sustaining and securing Canada’s honey bees using ‘omic tools. Project leaders: Leonard Foster, University of British Columbia; Amro Zayed, York University. Lead Genome Centre: Genome British Columbia. Total funding: $7.2 million. The team will develop genomics and proteomics tools that will provide markers to selectively breed 12 economically valuable traits. This will enable beekeepers to quickly and cost-effectively breed healthy, disease-resistant, productive bee colonies that are better able to survive harsh Canadian winters. While this will lessen, it will not eliminate, the need to import bees from other regions, so the team will also develop an accurate and cost-effective test to detect bees with Africanized genetics (“killer” bees). The team will work with beekeepers and other stakeholders and end users to ensure its tools are implemented and accessible to beekeepers by the end of the project.

Genomics of abiotic stress resistance in wild and cultivated sunflowers. Project leaders: Loren H. Rieseberg, University of British Columbia; John M. Burke, University of Georgia. Lead Genome Centre: Genome British Columbia. Total funding: $7.9 million. This international team is investigating why wild plants are more resistant to environmental stresses such as drought, flooding, salt and low nutrient levels. The team is focusing on the sunflower, a $20 billion crop that is the only oilseed in the Global Crop Diversity Trust’s list of 25 priority food security crops because it is grown widely in developing countries. The project will identify and fully characterize the genetic basis of stress resistance in sunflowers and create resources that will enable partners from the public and private sectors to efficiently breed stress-resistant, high-yield cultivars. The team will also develop models to predict likely yields of the new cultivars in different soil and climate conditions across Canada and develop strategies to overcome barriers to R&D caused by international treaties on the use of plant genetic resources thus ensuring the maximum use of new plant materials developed from this project for growers in Canada and around the World.


Application of genomics to improve disease resilience and sustainability in pork production. Project leaders: Michael Dyck, University of Alberta; John Harding, University of Saskatchewan; Bob Kemp, PigGen Canada Inc. Lead Genome Centres: Genome Alberta, Genome Prairie. Total funding: $9.8 million. The team is developing genomics tools that Canadian genetic companies and breeders can use to select pigs that are more genetically resilient due to increased tolerance of and/or resistance to multiple diseases (as opposed to simply resistant to one particular disease). The tools will also permit producers to manage the nutritional content of pig feed to optimize pig health so pigs stay healthier, grow more efficiently and have more successful litters and reduce the need for antibiotic use in pig production.

Increasing feed efficiency and reducing methane emissions through genomics: A new promising goal for the Canadian dairy industry. Project leaders: Filippo Miglior, University of Guelph; Paul Stothard, University of Alberta. Lead Genome Centres: Genome Alberta, Ontario Genomics Institute. Total funding: $10.3 million. The team will use genomics-based approaches to select for cattle with the genetic traits needed for more efficient feed conversion and lower methane emissions. To date, it has been both difficult and expensive to collect the data required for such selection. The latest genomic approaches offer an opportunity to address these problems and collect and assess the required data to carry out the selection. The results of this project will assist dairy farmers and the industry more broadly to develop cattle that will carry these two important traits.


Application of genomics to innovation in the lentil economy (AGILE). Project leaders: Kirstin Bett and Albert Vandenberg, University of Saskatchewan. Lead Genome Centre: Genome Prairie. Total funding: $7.9 million (includes funding from Western Grains Research Foundation). The AGILE team will characterize the genetic variability found in an expansive collection of lentils to determine the genetics underlying the ability for lentils to grow well in different global environments. The team, led by Drs. Kirstin Bett and Albert Vandenberg of the University of Saskatchewan, will then develop breeder-friendly genetic markers that can be used to reduce the impact of genes that cause poor adaptation to Canadian conditions while retaining advantageous genes from these strains. The team will also investigate the factors that influence farmer’s decisions to adopt lentil or not in their crop rotation, and develop a strategy to increase Canadian lentil production in a sustainable way.

Reverse vaccinology approach for the prevention of mycobacterial disease in cattle. Project leaders: Andrew Potter, VIDO-InterVac, University of Saskatchewan; Robert Hancock, University of British Columbia. Lead Genome Centres: Genome Prairie, Genome British Columbia. Total funding: $7.4 million. This team will take a “reverse vaccinology” approach to preventing infectious diseases in cattle. This approach uses genomic technology to screen large numbers of bacterial proteins simultaneously to identify those with proper
ties that can stimulate a protective immune response in cattle. These proteins then form the basis for developing novel vaccines and immunization strategies. The team will focus on two common cattle diseases, bovine tuberculosis, a debilitating disease that can spread to man and other domestic and wild animals, and Johne’s Disease, a gastrointestinal disease, developing and bringing to market vaccines for these costly diseases within two years’ of the project’s end. The team will also develop companion diagnostics that will differentiate vaccinated from infected animals.

Canadian Triticum Applied Genomics (CTAG2). Project leaders: Curtis Pozniak, University of Saskatchewan; Andrew Sharpe, National Research Council Canada. Lead Genome Centre: Genome Prairie. Total funding: $8.5 million (includes funding from Western Grains Research Foundation). Dr. Curtis Pozniak is leading the CTAG2 team, with scientists participating from four Canadian research institutions: The National Research Council of Canada, Agriculture and Agri-Food Canada, University of Guelph, and the University of Regina. The emphasis of CTAG2 is to conduct research to better understand the wheat genome and to apply this research to develop genetic markers and predictive genetic tests to improve selection efficiency in Canadian wheat breeding programs. The CTAG2 team will work with the International Wheat Genome Sequencing Consortium to generate a high quality reference of chromosome 2B of wheat and drive innovation in wheat breeding by developing genomic strategies to improve utilization of untapped genetic variation from related species. The end result will be the development of tools and strategies for wheat breeders to develop improved cultivars that are more productive and resistant to disease and pests, and resilient to heat and drought stresses.


Towards a Sustainable Fishery for Nunavummiut. Project leaders: Virginia K. Walker, Queen’s University; Stephen C. Lougheed, Queen’s University; Peter Van Coeverden de Groot, Queen’s University; Stephan Schott, Carleton University. Lead Genome Centre: Ontario Genomics Institute. Total funding: $5.6 million. Affordable access to safe, nutritious and culturally relevant food is one of the biggest challenges facing the Nunavummiut, the people of Nunavut. Accelerated melting of Arctic sea ice due to climate change is increasing access to arguably the last remaining under-exploited fishery in the Northern Hemisphere. This increased accessibility, primarily to Arctic char, but also to Arctic cod and Northern shrimp, coupled with a developed, sustainable, science-based fishing plan will offer opportunities for employment and economic benefits for Nunavut communities as well as greater food security. It is the Nunavummiut that should be the beneficiaries of these resources, rather than foreign fishing fleets. Understanding the genetic differences among these fish populations is key to developing that plan. Dr. Virginia K. Walker of Queen’s University and colleagues together with the Nunavut communities will integrate traditional and local knowledge with leading-edge genomic science and bioinformatics to gain an understanding of the genomes of these fish populations. This will allow monitoring of their migration, characteristics and adaptation and inform strategies to maintain genetically diverse and healthy stocks.


SoyaGen: Improving yield and disease resistance in short-season soybean. Project leaders: François Belzile, Université Laval; Richard Bélanger, Université Laval. Lead Genome Centre: Genome Québec. Total funding: $8.3 million (includes funding from Western Grains Research Foundation). This team will probe deeply into the genetic code of soybeans to identify DNA markers that control key aspects of plant growth such as time to maturity and resistance to diseases and pests. Breeders will be able to use these markers to develop improved soybean varieties best suited to Canadian conditions. The team will also breed soybean varieties resistant to certain prevailing pests and diseases. As well, they will conduct research focused on maximizing the growth potential of the soybean industry in Canada to accelerate producer adoption of soybeans in western Canada.

A Syst-OMICS approach to ensuring food safety and reducing the economic burden of salmonellosis. Project Leaders: Lawrence Goodridge, McGill University; Roger C. Levesque, Institute for Integrative Systems Biology (IBIS), Université Laval. Lead Genome Centre: Génome Québec. Total Funding: $9.8 million. Today most outbreaks of Salmonella poisoning come from fruit and vegetables, which become infected from the soil they grow in when that soil is polluted by animal waste or non-potable water. There currently is no method of reducing the growth of Salmonella on such produce. The team is using whole genome sequencing to identify the specific Salmonella strains that cause human disease. With this knowledge, the team will develop natural biosolutions to control the presence of Salmonella in fruit and vegetables as they are growing in the field. The team will also develop new tests to rapidly and efficiently detect the presence of Salmonella on fresh produce before it is sold to consumers, as well as tools to allow public health officials to determine the source of Salmonella outbreaks when they occur, so that contaminated food can be quickly removed from grocery stores and restaurants.