the VO diet. Other genes which were significantly and consistently regulated were FAS and EL, while GST, HOX and AGPAT only showed signifi cant regulation in Fat fish. Finally, comparison between the two family groups showed a significantly lower expression of 5 fad, 6 fad, PPARa, PPARb, SREBP 1 and GST in the Lean group but only when fish were fed FO, in the case of fads, or when fed the VO diet, in the case of PPARs, SREBP 1 and GST. In addition, FAS was also significantly down regulated in the Lean group, inde pendent of diet. Liver fatty acid composition Fatty acid analysis of liver showed significant differences in all fatty acid classes related mostly to diet but also to genotype. The percentage of total n 6 PUFA was significantly increased when VO replaced FO in the diet.
Levels of total n 3 PUFA were, on the other hand, significantly higher in the FO treat ments independent of genotype. For EPA and DHA there was a significant diet �� genotype interaction, GSK-3 resulting from the fact that, when comparing Fat and Lean fish, higher levels of these LC PUFA were found in the Fat family group when fed the FO diet but the inverse was observed when the same fish were fed the VO diet. In the present study we analysed the effects of diets containing high levels of plant proteins and with com plete replacement of FO by VO on the liver transcrip tome of Atlantic salmon, which is the primary metabolic organ of fish, as well as the influence of genotype on these responses.
Here we focus on the separate effects of diet and genotype given that interactions, indicating pathways that were differentially affected by diet depending on the genetic background of the fish, were discussed in detail previously. A common methodological difficulty in this type of nutritional experiment is that effects are typically quite subtle although physiological and metabolic pathways can be impacted by even small fold changes in gene expres sion. This has been demonstrated by several studies and by previously reported data from the present study showing that low fold changes in gene expression were associated with biochemical differences in tissue lipid class and apolipoprotein composition. Furthermore, low fold changes observed in this study were generally cor roborated by RT qPCR, even if the low expression ratios meant that differences were not always significant.
It should also be noted that a total match between the microarray and the RT qPCR results is not expected due to the approach taken to design RT qPCR primers on bet ter annotated reference sequences rather than on less well characterized microarray clones. In view of the whole gen ome duplication event that occurred in salmonid fishes, transcriptomic and gene expression studies are often more challenging due to the presence of duplicated and highly similar genes whose transcripts might be differen tially regulated, as observed previously for lipoprotein lipase. Therefore, collectively, and in conjunction with previou