Proteomic investigation of liver and white muscle in efficient and inefficient Chinook salmon (Oncorhynchus tshawytscha): fatty acid metabolism and protein turnover drive feed efficiency

Feed efficiency, the relative ability to convert feed nutrients into growth, is an important factor in the primary production of animals. Farming fish with improved feed efficiency is necessary to reduce production costs and achieve sustainability for the aquaculture industry. Proteomics provides an approach to discover biochemical mechanisms driving feed efficiency. To do this, we have evaluated the proteomic profile of liver and white muscle in efficient (EFF) and inefficient (INEFF) Chinook salmon (Oncorhynchus tshawytscha). Twenty-six fish, 14 EFF and 12 INEFF individuals, were assessed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and a data-independent acquisition method. In total, 2433 liver and 635 white muscle proteins were quantified across all samples. Bioinformatics showed enrichment of gene ontology (GO) terms related to lipid metabolism in liver of EFF fish (~30% of total GO terms). Protein metabolism (~30% of total GO terms) were the top enriched pathways in white muscle of EFF fish. In INEFF fish, protein processing in endoplasmic reticulum and proteolysis (~40% of total GO terms) were the highest enriched GO terms in the liver. This is the first study to compare feed efficient and inefficient individuals at the proteomic level in an aquatic species and the results provide a preliminary insight into the fundamental molecular landscape of feed efficiency in Chinook salmon.