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Agropur's Michel Pouliot, left, and Manon Duquenne, right, work at their R&D centre in St-Hubert, Que., with Laval University's Steve Labrie. (Benoit Desjardin/Genome)
Agropur's Michel Pouliot, left, and Manon Duquenne, right, work at their R&D centre in St-Hubert, Que., with Laval University's Steve Labrie. (Benoit Desjardin/Genome)

Canadian companies look to genomics to drive innovation Add to ...

For Michel Pouliot, a fine cheese is not just something to be savoured, it’s a microcosmic universe to be explored.

“There’s a lot of biochemistry in cheese and a lot of it is not very obvious,” said Mr. Pouliot, who is vice-president of research and development for Agropur Cooperative Agro-Alimentaire, a Quebec-based dairy co-operative that processes more than 3.4 billion litres of milk annually.

Now, spurred by growing consumer demand for artisanal-style cheese, Mr. Pouliot’s company will be among the first to access funds from a $37.8-million federal competition that seeks to leverage the tools of genomics – the analysis and comparison of the DNA of various organisms – to channel private-sector investment into Canadian labs.

Agropur is one of 12 companies expected to be named on Wednesday when Ed Holder, the Minister of State for Science and Technology unveils projects that will receive federal dollars under the new Genomic Applications Partnership Program (GAPP).

While government programs aimed at boosting industrial R&D are not new, GAPP is noteworthy, officials say, because it requires companies to spend $2 for every federal dollar they receive as they team up with university-based researchers to solve problems that are directly relevant to their businesses.

“It’s at a level where there is a real potential that things will become commercializable,” said Pierre Meulien, president and CEO of Genome Canada, the federally-funded agency behind the program.

In some cases, the winning proposals will involve research that may lead to new products. In others, it will be aimed at improvements in process or quality control that may improve a company’s competitiveness.

Either way, the partnerships that GAPP funds are meant to help address the long-standing gap in Canadian business investment in research and development – a metric where Canada falls well short of most western economies, including the United States, when it is calculated as a percentage of GDP.

“I do think, in our own way, that we’re demonstrating a part of the solution to the Canadian problem,” Dr. Meulien said.

In Agropur’s case, the commercial driver that led the company to compete for a share of the GAPP pot is simply the need for a better way of knowing what’s happening as cheese ripens.

Scaling the production of an aged cheese up to mass-market levels is an inherent risk, because it may be years before the product is ready to sell, and in the meantime, there’s no way to be sure if the aging process is proceeding on course.

This is because each variety of cheese is the handiwork of a complex community of microorganisms that interact with each other and their environment during ripening. Therein lies the magic that determines flavour and texture. But until recently, there has been no practical way to know if the process is proceeding on course for any given batch of cheese.

That would entail somehow identifying all the microbes present, and working out if a cheese has the correct microbial population profile.

Enter metagenomics. It’s a method for capturing a genetic snapshot of an entire community of organisms based on a mass reading of all the fragments of DNA that turn up in a particular sample.

While the process has been in use for a decade to sample the diversity of microscopic life in different settings, it has only recently become inexpensive enough for many industrial applications.

“We can profile what kind of microbial species are present in the cheese and find out what their contribution is to the cheese ripening,” said Steve Labrie, a microbiologist at Laval University who is partnering with Agropur on the project.

Seven of the 12 winning projects are in the food and agriculture sector, including a project to use genomic analysis to improve salmon breeding, another to build disease resistance in greenhouse crops and a third to create enzymes to food digestion of commercial feed by swine and poultry. That last project – a collaboration between researchers at Concordia University and Elanco Animal Health, a division of Eli Lilly – is expected to provide the backdrop for Mr. Holder’s Wednesday unveiling of the GAPP winners.

Dr. Meulien said the diverse list of projects reflects how genomics research is expanding beyond the boundaries of health and medical science, where it has long been focused. In future rounds of the GAPP competition, he said he hopes to engage other sectors such as the mining industry, where genomics can be applied to tailoring microbial communities for environmental cleanup.

Robert Fessenden, a fellow at the University of Alberta’s Institute for Public Economics, said that while the impact of the program was likely to be small on its own, “it is a useful element” toward a national innovation strategy that recognizes the central importance of science and technology for industrial success.

“The degree to which [GAPP] is successful will depend very much on the quality of the projects that are supported,” Dr. Fessenden added.

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Here is a complete list of winning projects that are slated to receive co-funding from Genome Canada under the Genomic Applications Partnership Program (GAPP).

Amounts shown represent full cost of each project (three times the federal government’s investment).

Agropur Cooperative & Laval University

Enhanced Cheesemaking ($0.7 million)

AssureRx Health Inc. & Centre for Addiction and Mental Health

Enhanced genomics tool for matching mental-health patients with effective drug therapies ($6 million)

Canadian Food Inspection Agency & University of British Columbia

Genome based surveillance for invasive forest species ($2.4 million)

Cooke Aquaculture Inc./Kelly Cove Salmon Ltd. & University of Guelph

Improved farmed Atlantic salmon breeding ($3.8 million)

Elanco Animal Health (Eli Lily & Co.) & Concordia University

Development of new enzyme supplements for swine and poultry ($6 million)

EWOS Innovation & Memorial University

Improved farmed salmon growth through better feed ($3.8 million)

MRM Proteomics Inc. & University of Victoria

Development of new techniques to support drug development ($1.2 million)

Roche Diagnostics International Ltd. & University of Ottawa Heart Institute

Development of a bio-marker diagnostic for heart patients ($5.9 million)

Symbiota, LLC. & University of Saskatchewan

Increased crop yield and stress resilience ($16.1 million)

Vasomune Therapeutics & Sunnybrook Research Institute

Develpment of treatment for acute kidney injury ($1.5 million)

Vineland Research and Innovation Centre & University of Toronto

Enhanced disease resistance in greenhouse crops ($2.4 million)

 Xagenic Inc. & University of Toronto

Improved Hepatitis C test ($6 million)

Editor's Note: Genome Canada is a federally funded agency, not a federal agency.

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