Genome Canada Annual Report 2016-17 13 I n the past 20 years, aquaculture production in Canada has more than doubled to close to $3.1 bil- lion in economic activity a year. The industry now employs about 15,000 Canadians and exports 101,000 tonnes of food products. However, the health of farmed salmon in Canada is perpetually threatened by infectious diseases, including those caused by sea lice, pathogenic viruses and bacteria. The quality of feed can affect salmon health. Better feed can enhance fish health, reduce the need for antibiotics and improve the rate at which fish grow. But until now, there has been no practical way for aquafeed companies to measure how well novel feeds work beyond weighing the fish and judging feed effectiveness using growth rates. In the Genome Canada-funded Biomarker Platform for Commercial Aquaculture Feed Development proj- ect, launched in 2014, Dr. Matthew Rise of Memorial University, Dr. Rich- ard Taylor of Cargill Aqua Nutrition (a division of Cargill, which purchased salmon nutrition company EWOS in 2015) and other collaborators are identifying and validating salmon genes related to growth, for inclusion in a biomarker panel. From individual fish, the researchers analyze the expression of approximately 30 genes associated with disease response and growth to determine the effects of various feeds and ingredients at the genomic level. One example of this is the impact of diet on lipid metabo- lism or antiviral immune response. The process of translating that information into better-quality feed is about more than just boosting immunity. The genetic biomarkers enable researchers to track what each pathogen or other immune stimulus does to salmon and what a potential treatment does when added to salmon feed. For bacterial infection, for example, it is important to control chronic inflammation. For viral infection, controlling digestible energy and adding immune stimu- lants may be necessary. The genomic tools developed through this project allow Cargill Aqua Nutrition, one of the world’s largest producers of aquafeeds, to determine right down to the cellular level how fish are impacted by the feed. Further- more, the company is able to quickly and accurately assess the impact of new feed ingredients on fish rather than waiting months for a fish to show a noticeable change in size. This technology is helping Cargill Aqua Nutrition to improve their feed formulas and develop new, high-quality feeds. The company is commercializing new feeds within the life of the project, with more new products likely to follow in the coming years. Cargill Aqua Nutrition sources approximately 80 per cent of feed ingredients from Canada, and sells feed to Canada, the U.S.A., Mexico and Asia. Dr. Rise, Dr. Taylor, Dr. Mark Fast of the University of Prince Edward Island and their collaborators sub- sequently received funding for a second GAPP project in 2016 – Integrated Pathogen Management of Co-infection in Atlantic Salmon. This project uses the tools and knowledge developed in the Bio- marker Platform project to better understand salmon response to a very complicated situation that can occur at salmon farms: the exposure of fish to more than one pathogen at a time (co-infection). This academic–industry partner- ship will result in the increased sus- tainability of the Canadian salmon industry, the improvement of animal welfare in the aquaculture indus- try and the application of these same biomarkers to studies of wild salmon stocks. “These collaborative projects, with funding from Genome Canada, have enabled us to bring an entirely new realm of information to bear on scientific problems that, otherwise, would have taken many more years to solve. This has allowed us to better serve our shareholders, our clients, and Canadian and international consumers.” — Dr. Richard Taylor, senior research scientist, Cargill Aqua Nutrition Both Genomic Applications Partnership Program projects – the $3.8-million Biomarker Platform for Commercial Aquaculture Feed Development project and the $4.5-million Integrated Pathogen Manage- ment of Coinfection in Atlantic Salmon project – in- volve partnerships with Genome Atlantic and others.