Linking genomic prediction of fillet fat content in Atlantic salmon to underlying changes in lipid metabolism regulation

Fillet fat content is an important production trait in Atlantic salmon (Salmo salar) because it influences the flavor, texture, and nutritional properties of the product. Selection can be applied to alter muscle fat content, however how such selection changes the underlying molecular physiology of these animals is unknown. Here, we examine the link between genomic predicted breeding value for fillet fat of 184 fish and gene expression in the liver with an emphasis on lipid metabolism genes. We found that salmon with higher genomic breeding values for fillet fat had higher expression of genes in lipid metabolism pathways. This included key lipid metabolism genes hmgcrab, fasn-b, fads2d5, and fads2d6, and lipid transporters fatp2f, fabp7b, and apobc. We also found several regulators of lipid metabolism with negative correlation to genomic breeding values, including pparg-b, fxr-a, and fxr-b. A quantitative trait loci analysis for variation in gene expression levels (eQTLs) for 167 fillet fat associated genes found that 71 genes had at least one eQTL, and that most were trans eQTLs. Closer examination revealed distinct eQTL clustering on chromosomes 3 and 6, indicating the presence of putative common regulator in these regions. Taken together, these results suggest that salmon with high genomic breeding value for fillet fat have elevated lipid synthesis, elevated lipid transport, and reduced glycerolipid breakdown; and that this is at least partly due to genetic variants that impact the function of top-level transcription factors involved in liver metabolism. Our study sheds light on how genomic selection for reduced or increased fillet fat content in Atlantic salmon alters gene regulation in the liver of the fish. These results could be used to prioritize SNPs with an association to phenotype related gene expression to improve the efficiency and reduce the cost of genomic selection in the future.