Drs. Matthew Rise (L) and Chris Parrish. Photo credit: Chris Hammond, Memorial University
Aquaculture is an important and emerging industry in Canada, generating approximately $1.35 billion in revenue and employing 25,000 people*. With regard to farmed salmon in particular, one of the biggest threats is infectious diseases caused by sea lice, pathogenic viruses and bacteria. High-quality, therapeutic feeds can play a big role in helping salmon to resist infectious diseases and stay healthy.
Using genomics, East coast scientists are partnering with international aqua food giant, Cargill Aqua Nutrition, to revolutionize its feed formulas to shield farmed salmon and their investors from the costly scourges of sea lice, and microbial pathogens. The Canadian division of Cargill Aqua Nutrition sources approximately 80 percent of their feed ingredients from Canada and sells feeds to aquaculture operators in Canada, the U.S., Mexico and Asia.
For insight into this pioneering endeavour, Genome Atlantic contacted two of the leading scientists involved: Dr. Matt Rise, a functional genomics specialist who investigates fish immunology and aquaculture nutrigenomics, and Dr. Chris Parrish, a lipids researcher who probes nutritional and biomarker lipids in marine food webs. Both of these scientists are faculty members with the Department of Ocean Sciences at Memorial University, where Rise also heads a sustainable aquaculture module at the Ocean Frontier Institute. He was also recently appointed to a federal government Independent Expert Panel on Aquaculture Science led by Dr. Mona Nemer, Canada’s Chief Scientific Advisor.
Drs. Rise and Parrish, along with colleagues Dr. Mark Fast at the University of Prince Edward Island and Dr. Javier Santander of Memorial University, have been working with Cargill Aqua Nutrition on applying genomics to nutritional science.
The pair’s large-scale collaboration with Cargill actually consists of two large-scale research projects sponsored by Genome Atlantic and Genome Canada, funded in part under Genome Canada’s Genomic Applications Partnership Program (GAPP): a completed $3.8 million investigation into single pathogen infections to produce a Biomarker Platform for Commercial Aquaculture Feed Development; and an ongoing second project, worth $4.5 million, dealing with the development of diets to combat co-infections from multiple pathogens and tagged as Integrated Pathogen Management of Co-infection in Atlantic Salmon.
The first project produced a new method to evaluate how diet affects farmed salmon’s growth and immune response at the gene and cellular levels. While it remains important to measure fish weight and growth, the new biomarker gene expression platforms developed by the scientists and their collaborators provide more detailed information on the impact of diets and feed ingredients on fish metabolism and immune response. This is needed in order to gain a more complete picture of the impact of novel diets on fish health and growth performance.
From individual salmon, the researchers use “gene chips” (also DNA microarrays) representing 44,000 different genes, as well as lipid biochemistry, to screen for diet-responsive biomarkers of fish health. The research team, including graduate students, post-doctoral fellows and technicians, use the genomic data to develop and use smaller panels of biomarker genes in a technique called “multiplex qPCR”. These panels of about 30 genes allow the researchers to rapidly collect detailed information on how novel diets and feed ingredients affect growth, metabolism and immune responses.
It is estimated that the use of therapeutic feeds could save the Canadian aquaculture industry approximately $60 million annually, while decreasing the use of chemical treatments and minimizing the risk of disease in aquaculture salmon.
Drs. Rise and Parrish also worked together on a highly successful project with fellow researchers at Memorial and Dalhousie universities that validated Camelina sativa, a plant commonly known as camelina or false flax, as a cost-effective, sustainable substitute for wild-sourced fish meal and especially fish oil.
The harvest of foraged fish used for animal feed has been stable during the past 30 years (FAO), but the animal feed industry increases at about three percent annually so the percentage use of fish products in feed must decrease. Plant oils and plant protein concentrates are viable alternatives to animal ingredients, and camelina has potential health benefits for fish in addition to growth support.
The $6.1 million camelina research project managed by Genome Atlantic, was done with principal support from the Atlantic Canada Opportunities Agency’s Atlantic Innovation Fund. The results enabled the Canadian Food Inspection Agency to approve a Genome Atlantic application to allow mechanically extracted camelina oil as a feed ingredient for farmed salmon and trout.
*Sources:Canadian Aquaculture Association and Statistics Canada (2016)
Genome Atlantic: How did you come up with the idea of applying genomics and nutrition to prevent disease in farmed salmon?
Drs. Matt Rise and Chris Parrish: It has become self-evident for humans that eating healthily can help prevent disease. We know that dietary ingredients such as the types of fats we eat have important health implications. So extending work on salmon nutrition from a focus on uniform weight gain to reducing dependence on antibiotics and other interventions was a natural next step. Not only did we want to look at disease prevention through the use of safe and sustainable dietary ingredients, but also to understand the mechanisms that underlie these processes.
Nutrigenomics, the use of genomics tools and techniques to study how nutrients influence gene expression, is a rapidly growing area of both human and animal (including fish) health related research. At the Ocean Sciences Centre of Memorial University, we are fortunate to have excellent research infrastructure and collaborations (e.g., with Cargill) for aquaculture nutrigenomics research.
GA: Can you briefly describe how genomics has been used in your two recent research projects: first with single pathogen infections and now with co-infections from multiple pathogens in farmed salmon.
MR &CP: Both of our GAPP (Genomic Applications Partnership Program) projects involve close collaboration between our lab groups (with the Rise lab focusing on genomics and the Parrish lab focusing on lipidomics), Dr. Richard Taylor (Cargill Aqua Nutrition) and many other collaborators with the goal of using functional genomics tools and techniques to accelerate development of novel grower and clinical diets for farmed salmon.
The first GAPP project (which was recently completed) focused on diets to combat salmon diseases such as infectious salmon anemia (ISA, caused by a virus) and salmonid rickettsial septicemia (SRS, caused by a bacterium). The current GAPP project uses similar genomics tools (such as DNA microarrays, also called ‘gene chips’, used to screen the expression of thousands of genes simultaneously) with the goal of developing diets to combat co-infections of salmon (for example, a primary sea lice infection with a secondary viral or bacterial infection).
We have been able to correlate gene expression with the ingredients in the diets as well as with diet-induced changes in chemical composition in tissues.
GA: Do you see other areas of aquaculture where genomics could play an important role in solving pressing problems?
MR & CP: Doing lipid nutrition and biochemistry research alongside genomics work has greatly helped us understand mechanisms involved in responses to diet and implications of dietary alterations. In turn this has helped us define minimal levels of key components of fish oil and fish meal and of maximal levels of alternatives. We have been working very hard on effects of diet ingredients on salmon generally, but a great next step would be to reverse the approach and to look at matching individual strains of salmon to make the best of available diets. This would be akin to eating based on your genetics.
In addition to the area of nutrition, genomics research will contribute to many other areas of aquaculture such as breeding (for example, the selection of broodstock with rapid growth rate, resistance to stress and disease, and other traits of interest) and the development of effective diagnosis and vaccines to combat infectious diseases.
GA: Does this line of inquiry that marries genomics and nutrition have potential applications beyond marine life?
MR & CP: Certainly. The field of nutrigenomics is an emerging science which is gaining a lot of attention in the field of human nutrition. Our work at the interface of nutrigenomics and lipidomics is showing that salmon immune responses can be manipulated by varying dietary raw materials such as plant products and functional ingredients. The research on salmon may provide hints regarding how immune system function in other vertebrates (such as humans) may be influenced by nutrition.
GA: In your experience, how important are academic-industry partnerships in advancing research in your fields?
MR & CP: For us this is a key component as we are completely up to date with the latest advances and challenges associated with the feed industry. We also get very quick feedback on our scientific results.
Our GAPP projects involve large research teams including graduate and undergraduate students, post-doctoral fellows, and technicians in our labs, as well as other academic collaborators (such as Dr. Mark Fast at the University of Prince Edward Island and Dr. Javier Santander at Memorial University) and industry collaborators. These academic-industry partnerships provide excellent opportunities for personnel in our labs to work closely with industry scientists to solve real-world problems. The knowledge generated in our research translates directly to gains for the industry partner, in this case, Cargill Aqua Nutrition. By accelerating the development of health-promoting diets for farmed salmon, our research also directly benefits aquaculture production.