Changes in the liver transcriptome of farmed Atlantic salmon (Salmo salar) fed diets based on terrestrial alternatives to fish meal and fish oil

After a 14-week feeding trial, Atlantic salmon fed a diet based on animal by-product meal and vegetable oil (ABP) showed lower growth rates compared to others fed an FM/FO-based diet (MAR). Interestingly, feeding a vegetable meal/oil-based diet (VEG) resulted in growth rates similar to the FM/FO-based diet. A 44K microarray experiment conducted on liver total RNA samples from these three dietary groups identified 46 genes related to metabolic and growth-relevant pathways, 25 immune-related, and 12 related to oxidation-reduction processes. Atlantic salmon were fed the three experimental diets (MAR, ABP, and VEG) for 14 weeks. Four tanks were dedicated to each experimental diet. At the end of the feeding trial, liver samples were collected from five individuals per tank. Each dietary group contributed liver RNA samples of eight individual fish (two from each tank) to the microarray experiment (i.e., 24 fish in total). Differences among dietary groups in the liver transcriptome of fish were assessed by contrasting individual RNA samples against a common reference pool of equal quantities of RNA from all 24 fish. Test samples were labeled with Cy5, whereas the reference pool was labeled with Cy3. Please note that sample titles represent 'tissue_diet_tank number_individual fish number' for each sample.