Skip to main content

Alternative feeds in aquaculture: Transcriptome and Proteome Analyses in Salmon

Final Activity Report Summary - TAPAS (Alternative feeds in aquaculture: transcriptome and proteome analyses in salmon)

Fish are the only major dietary source for humans of omega-3 highly unsaturated fatty acids (HUFA) including eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids that are essential for protecting humans against cardiovascular diseases. With declining fisheries, farmed fish such as Atlantic salmon (Salmo salar) constitute an increasing proportion of the fish in the human diet. Flesh n-3 HUFA content is a trait of considerable importance in farmed fish, particularly now that the fishmeal and fish oil (FO) components of traditional aquaculture diets have to be replaced by more sustainable alternatives including plant meals and vegetable oils (VO). However, selection strategies towards high flesh n-3 HUFA contents require a phenotypic and quantitative genetic basis.

In a dietary trial A. salmon smolts were fed diets containing either FO or VO for 3 months. Samples of flesh were taken for fatty acid analyses and samples of liver and blood taken for transcriptome (gene expression) and proteome (protein expression) analyses. Total lipid and fatty acid composition of all flesh samples were determined and the inter-individual variation of flesh n-3 HUFA content analysed. The results show clear differences between individual fish and give a first indication of how large inter-family differences may have to be in order for families with particular phenotypes in the trait to be identified. A general regression model based on flesh lipid content, morphometric and blood fatty acid measurements was developed which allows to determine the flesh n-3 HUFA contents of Atlantic salmon smolts in a non-fatal way. This would give the opportunity to choose from a range of selection methods, including mass selection or within family selection, if this important flesh quality trait would be included in future breeding programmes for A. salmon. However, the most important prerequisite for genetic improvement through selection is the additive genetic variation between individuals for the trait of interest. The identification of the genes and pathways underlying the physiological adjustments, that are inherent in the phenotypic variation of flesh n-3 HUFA content, is required to select a set of genes which could serve as indicators of "performance" in terms of the trait.

Cutting edge molecular techniques for the analysis of fish transcriptomes (microarrays) and proteomes (modern proteomics; DIGE) were applied to determine differential expression patterns in liver tissues of A. salmon smolts fed the FO and VO based diets. The study gave clear indications for changes in liver gene and protein expression, associated with phenotype. However, further studies are required to define a fingerprint characteristic of good performance (high flesh n-3 HUFA).