Integrating genomics and system biology to improve the capacity for synthesis, transport, and filet deposition of EPA/DHA in salmon

Salmon farmed on modern feeds contains less of the healthy, long-chain fatty acids (EPA and DHA) than before. Until about 15 years ago, farmed salmon were fed fish oil as a replacement for their omega-3 rich natural prey. However, fish oil is now a scarce resource, and more than half of the fat in modern feeds comes from plant oils that are inexpensive, but devoid of long-chain omega-3 fatty acids. How can we increase the omega-3 content of salmon on sustainable feeds? One option is to breed salmon that are well adapted to the feeds of the future. There is heritable variation in salmon's ability to build EPA and DHA from shorter omega-3 fatty acids. The DNA sequence of salmon is now well known, allowing rapid characterization of heritable differences in nutrient utilization. A salmon family that appears promising on one feed, may not be the best on another. Therefore, we need to understand the salmon's body as a system: a functional whole made up of parts that mutually affect, but also depend on, each other. A systems understanding of the interplay between feed and genetic factors will allow a tailoring of fish to feed and vice versa, which is robust to fluctuations in feedstuff availability and pricing. As a first step towards such a systems understanding, the GenoSysFat project involves two biological experiments. 1) A traditional feeding experiment using high- vs low-omega-3 diets and salmon families that differ in feed utilization. 2) A novel study with pieces of liver kept alive and "fed" in laboratory dishes, studying for each fish how different feeds affect metabolism and gene activity. This allows faster and more detailed exploration of the interplay between genetics and feeds. Results will be interpreted with the help of novel mathematical models for the biochemical reaction networks, which are well established for other species and will be adapted to salmon based on the newly sequenced salmon genome.

Genosysfat has generated a large resource of gene expression data from salmon liver and gut, which serve as an important resource for researchers. Our analyses reveal that future experiments on lipid metabolism in salmon should carefully consider life-stage as a critical factor before designing experiments. We have successfully developed a method to conduct experiments on live liver tissue on the lab bench. This method will help researchers conduct better, more controlled experiments on lipid metabolism in salmon, and minimize the number of fish that needs to be sacrificed in future experiments. Our collaboration with Aquagen has provided new information about the functional molecular consequences of selective breeding based on estimated breeding values for lipid contents. Hence, the Genosysfat project has provided Norwegian salmon breeders with important knowledge and improved tools to "create" a next-generation salmon with altered lipid levels and composition.

A major challenge for Norwegian aquaculture is to maintain a healthy and high content of very long omega-3 (i.e. EPA/DHA) when the salmon is fed diets containing limited fish oil. This challenge can be met both by optimizing diet and feeding regimes and by breeding for higher capability to synthesize, transport and deposit EPA/DHA in the muscle. In this application we propose to combine these two strategies in a integrative approach that utilize detailed knowledge of the salmon genome together with detailed understanding of the salmon body as a metabolic system that transforms feed into filet. Using the novel salmon genomic sequence and modern systems biological methods, we will clarify the genotype-by-diet interaction through a combination of feeding experiments, laboratory culture of thin slices of liver (which synthesizes fatty acids), and mathematical analysis and modeling. In particular, gene expression data from experiments can be interpreted in light of the detailed map of the duplicated salmon genome, a detailed map of the biochemical reaction pathways, and mathematical descriptions of how the salmon body functions as a system. In the long term, the project will enable the rapid design of salmon feeds as new feedstuffs become available or prices shift, and targeted selection and breeding of salmon that are healthy to eat and grow well on modern feeds.