Recently, we have shown that much of the variation in n-3 LC-PUFA levels in salmon is due to genetics, and therefore there is clear potential to breed fish with improved ability to produce and/or retain omega-3 LC-PUFA as a long-term and practical solution to this problem. The major goal of this research is to understand the genetic and physiological factors that underlie the variation in salmon’s ability to produce and/or retain n-3 LC-PUFA when fed diets containing only low levels of these fatty acids. This can be achieved by combining the expertise in the Institute of Aquaculture in both fatty acid metabolism and salmon genetics. Thus, fatty acid compositions will be measured for a large sample of fish harvested from a commercial salmon population and, by using recent advances in DNA sequencing, markers (SNPs) can be developed to identify genetic mutations that are linked to flesh lipid composition. This would enable the mapping and characterization of the regions of the salmon genome that control the observed variation in omega-3 content, and to employ this knowledge to selectively breed salmon with improved fatty acid compositions. Furthermore, a range of approaches will be applied simultaneously to elucidate the biological mechanisms that underlie the observed differences in n-3 levels and, by combining these approaches and interpreting the findings in relation to the Atlantic salmon genome sequence, we aim to uncover the actual genes that underlie n-3 LC-PUFA levels in salmon. In addition to gaining fundamental knowledge concerning the control of lipid levels in salmon, the outcomes of this type of research will provide salmon farmers with the tools they need to selectively breed salmon with a superior ability to make and retain n-3 LC-PUFA. The work would ensure that the salmon farming industry is better equipped to deal with the substantial challenge of retaining the beneficial content of n-3 LC-PUFA in the fish, as marine feed ingredients are replaced with sustainable vegetable alternatives.