Feeding the future starts with ingenuity

Canadian Triticum Applied Genomics (CTAG²)

Wheat accounts for a staggering 20 per cent of all calories consumed throughout the world. As global population grows, so too does its dependence on wheat. To meet future demands, productivity for wheat needs to increase by 1.6 per cent each year – at the same time as climate change is causing temperature and precipitation changes that challenge established patterns. There is, in addition, a need to ensure that productivity increases are achieved sustainably to ensure the long-term stability of the wheat-growing industry.

In Canada, wheat accounts for more than $4.5 billion in annual sales and, when value added processing is factored in, adds more than $11 billion each year to the Canadian economy. Dr. Curtis Pozniak of the University of Saskatchewan is leading the CTAG2 team, with scientists participating from five 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 is working 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. These cultivars will enable wheat farmers to ensure that their product is more productive, profitable and environmentally sustainable.

The project is part of an international collaboration to sequence the entire wheat genome and to characterize genetic variation influencing critical traits targeted by wheat breeders in Canada.

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Using genomics to manage and protect caribou populations.

Genomics is a common tool to study the DNA of model organisms and livestock, but it can also be used to protect wildlife, offering great potential for monitoring genetic diversity, identifying populations at risk and managing these populations.

The conservation of caribou is a particular concern in Québec, where some populations are declining rapidly. For example, the George-River herd has declined from more than 800,000 animals in the early 1990s to just 8,900 in 2016, a drop of around 99 percent! The ministère des Forêts, de la Faune et des Parcs (MFFP, Québec’s Ministry of Forests, Wildlife and Parks) has put together several action plans to protect caribou populations, and is looking forward to integrate genomics. The inclusion of genome-wide descriptive metrics will allow better herd management decisions and more efficient protection actions. To do so, MFFP is working with the research team, directed by Claude Robert and Steeve Côté from Université Laval, to develop a much-needed genomic tool.

The tool will consist of a SNP (single-nucleotide polymorphism) chip that will allow identifying specific herds based on a simple tissue sample, together with a Web portal to host a registry of caribou genotypes and a data analysis pipeline to support caribou management in Québec. The tool will assist MFFP’s wildlife protection officers and biologists in carrying out their mandate to protect and manage the endangered populations of that species and its habitat in a manner consistent with sustainable development and supported by up-to-date knowledge. Caribou is an iconic species not only in Québec, but also in Canada where its sustainability is essential for the stability of the tundra ecosystems and for the food security and economy of Northern communities.

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Using microbial genomics to de risk offshore oil and gas exploration in Nova Scotia.

Atlantic Canada’s petroleum industry has a significant impact on the region’s economy. Since 1995, it has generated investments of $37 billion and more than 12,000 direct jobs. But offshore drilling is expensive. A critical component to Nova Scotia’s ongoing ability to attract interest is a comprehensive set of tools to help de-risk the exploration process. This project offers microbial genomics as one of those tools.

To put it simply, some bacteria thrive on hydrocarbons and can be found around seeps—areas where petroleum naturally bubbles up out of the seabed. These bacteria can provide an indication of petroleum trapped beneath the surface.

Dr. Hubert’s team will develop new genomics-based tools to identify aerobic, anaerobic and thermophilic bacteria associated with seeps. Adam MacDonald will lead the core sample collection, geochemical analysis, and integration of the results to deliver a deeper understanding of the characteristics and origins of the petroleum. This adds a valuable layer of information to more conventional geological data to de-risk offshore exploration.

The project will initially focus on the southwestern to central Scotian Slope and then extend to other areas off the coast of Nova Scotia. Results will expand the understanding of offshore petroleum resources developed through the original Play Fairway Analysis conducted by the Department of Energy in 2011. That initiative helped to attract over $2 billion in new exploration commitments.

This project is intended to develop new analytical techniques and data that will provide additional insights to heighten industry interest, enhance exploration activity and increase the dollar value of work commitments arising from future licensing rounds. This could lead to job creation, royalties and taxes that benefit both Nova Scotia and Canada as a whole.

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The Centre for Applied Genomics

The Centre for Applied Genomics (TCAG), founded in 1998, has been a Genome Canada Technology Platform since 2001. TCAG provides genomics support and analysis to more than 800 Principal Investigator labs per year, a total of more than 2,000 over its lifetime, spanning 45 countries, 317 academic institutions, 150 companies and 46 government agencies and non-governmental organizations. Through its work, TCAG has catalyzed many significant scientific advances. TCAG developed and hosts the Database of Genomic Variants and the Ontario Population Genomics Platform repository, leads the “MSSNG” autism genome sequencing project and the Canadian Personal Genome Project, and is the Toronto node of Canada’s Genomics Enterprise (CGEn), a national network of whole genome sequencing centres.

With additional funding from Genome Canada, TCAG will continue to actively develop novel methodologies for whole genome sequencing, genome assembly and statistical analysis of genome-wide data. These activities will complement the development and implementation of additional pipelines and methods for generating and analyzing genomic data. TCAG will continue to work with national and international partners to advance the utilization of genomics to address many facets of multidisciplinary science, including a strong focus on human diseases and neurodevelopmental disorders.

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Delivering innovative diagnostic care for rare genetic diseases in Canada.

There are more than 7,000 rare genetic diseases in Canada, which have a devastating impact on some one million Canadians and their families: two-thirds of these diseases cause significant disability; three-quarters affect children; more than half lead to early death; and, almost none has any targeted treatment.

Further, more than one-third of these diseases remain unsolved (their genetic cause is unknown). Building on the work of the Care4Rare Canada Consortium, the C4R-SOLVE project is working to identify the genetic cause of unsolved rare diseases and make genomic sequencing available to Canadians for rare disease diagnosis. Genomic sequencing will speed up the diagnostic process, thereby ending or even preventing years of diagnostic testing and visits to multiple specialists. Providing a timely diagnosis improves the care and wellbeing of patients and their families and reduces unnecessary healthcare spending.

Key to C4R-SOLVE’s success will be new sequencing technologies and improved worldwide data sharing. In addition, the group will work with provincial ministries of health to determine how best to include genomic sequencing as a clinical test to diagnose rare diseases, beginning with Alberta and Ontario. In doing so, C4R-SOLVE will more than double our ability to diagnose unsolved rare disease, while building the infrastructure and tools needed to improve rare disease diagnosis worldwide. Accurate and early diagnosis will optimize care, improve the wellbeing of patients and their families and provide new insights into these devastating diseases.

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Silent Genomes: Reducing health-care disparities and improving diagnostic success for Indigenous children with genetic disease.

First Nations, Inuit and Métis’ populations, collectively known as the Indigenous Peoples’ of Canada, face strikingly similar health challenges with global Indigenous Peoples’. Inequities include barriers to healthcare access that produce poorer health outcomes compared to non-Indigenous groups.

Whereas genomic technologies are advancing health care by allowing medical treatments to be tailored to the specific needs of individual patients (‘precision medicine’), this ‘genomics revolution’ is widening the health inequities gap. In particular, compared to what is becoming routinely available to other Canadians, Indigenous populations often have little or no access to genomic technologies and the research that drives them, hence intensifying the ‘genomic divide’.

A key concern in the growing genomic divide is the lack of background genetic variation data for Indigenous populations living in Canada and globally. This prevents accurate diagnosis because the reference data are needed for precise genetic diagnosis. Notably, standard genomics resources are silent with respect to First Nations (FN), Inuit and Métis’. Silent Genomes will address the genomic divide by reducing access barriers to diagnosis of genetic disease in Indigenous children.

Silent Genomes is a game changing partnership with First Nations, Inuit and Métis Peoples that is working to:

• Establish processes for Indigenous governance of biological samples and genome data,
• Lead to policy guidelines and best practice models, bringing equitable genomic testing to Indigenous children in Canada with suspected genetic diagnosis, and
• Develop an Indigenous Background Variant Library (IBVL) of genetic variation from a diverse group of First Nations in Canada.

Silent Genomes will improve health outcomes by enhancing equitable access to diagnosis, treatment, and care while assessing cost effectiveness of precision medicine.

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