Understanding molecular mechanisms drive feed efficiency in Chinook salmon farmed in freshwater and seawater using proteomics and metabolomics

Feed efficiency (FE), the relative ability to convert feed nutrients into growth, is an important phenotype in aquaculture. Understanding the molecular mechanisms using omics technologies that underlie differences in FE is an important step towards optimising growth and achieving sustainable salmonid aquaculture. Proteomics, as one the closest omics level to phenotype, provides approaches to discover biochemical mechanisms driving FE. This thesis aims to discover functional terms and pathways that drive FE in Chinook salmon using proteomics (Chapters 2, 3 and 4) and metabolic approaches (Chapter 5). Further, integration of multiple ‘omics’ datasets is required to reconstruct complex physiological networks of less-known phenotypes like FE. Therefore, integrating proteomics and metabolomics (Chapter 5) was another aim of this thesis to possibly discover a higher level of molecular information that drives FE. The research in the theses was based around two large experimental trials. For trial 1 (Chapters 2 and 3), chinook salmon of an average initial weight of 150 g grew to 800 g after six months in freshwater. For trial 2 (Chapters 4 and 5), the approximate weight of farmed chinook salmon in seawater for six months at the start and end of the trial were 400 and 2140 g, respectively. In both trials, efficient (EFF) and inefficient (INEFF) fish were selected based on the consistency of having high or low (top or bottom 33 percentile) FE during assessments. The EFF group was more efficient than INEFF fish due to having a higher weight gain and lower daily feed intake.
A considerable knowledge gap exists regarding the molecular physiology of FE in salmonids such as Chinook salmon. After selecting 14 EFF and 12 INEFF individuals in trial 1, 2,433 liver and 635 white muscle proteins were quantified across all samples. Bioinformatics showed enrichment of gene ontology (GO) terms related to lipid metabolism in the liver of EFF fish. Protein metabolism was the top enriched pathway in the white muscle of EFF fish. In INEFF fish, protein processing in endoplasmic reticulum and proteolysis were the highest enriched GO terms in the liver.
In groups of fish, there is often interindividual and intraindividual variation in feed intake. To better understand mechanisms that underpin feed intake (which play a key role in FE), the proteomic profiles of brain, liver, and intestine in high feed intake (HFI) and low feed intake (LFI) Chinook salmon from trial 1 were investigated. 2520 liver, 2783 intestine, and 4052 brain proteins in twenty-seven fish (12 HFI and 15 LFI individuals) were quantified. The growth rate and feed conversion ratio were not significantly different between HFI and LFI fish. Protein synthesis in both the intestine and liver of HFI was enriched, indicating increased cellular production in these tissues. In HFI fish, lipid metabolism was the most enriched pathway in the brain. The distribution of % share of the meal may suggest that individuals in the HFI and LFI groups were dominant and subordinate, respectively. The LFI group may have suffered from internal or external stressors and accordingly, proteolysis and stress response were activated relating to a lower feed intake.
Shifts in physiology and metabolism occur at various stages of salmonids life, in particular around successful smoltification and the response to increased salinity. Physiological and proteomic differences between EFF and INEFF groups observed in freshwater were assessed post transfer to seawater. In total, 2,746 liver and 702 white muscle proteins were quantified and compared between 21 EFF and 22 INEFF fish reared in seawater. Protein synthesis was enriched in the liver and white muscle of the EFF group, while conversely, pathways related to protein degradation (amino acid catabolism and proteolysis, respectively) were the most affected processes in the liver and white muscle of INEFF fish. Estimates of individual daily feed intake and share of the meal within the tank were significantly higher in the INEFF than the EFF fish showing INEFF fish were likely more dominant during feeding and overfed. This overeating by the INEFF fish was associated with an increase in protein catabolism.
Metabolite-protein interactions control a variety of cellular processes, therefore, playing a key role in maintaining cellular homeostasis. The integration of proteomics and metabolomics help us to possibly discover new involved pathways and biomarkers that were not accessible to be identified by analysing each omics level separately. In total, 2,748 liver and 703 white muscle proteins and 140, 127, and 70 metabolites in the liver, plasma, and muscle, respectively, were quantified and compared between 21 EFF and 19 INEFF fish from the seawater trial. Protein synthesis was enriched in the liver and white muscle of the EFF fish, while conversely, pathways related to protein degradation (amino acid catabolism and proteolysis, respectively) were the most affected processes in the liver and white muscle of INEFF fish. The metabolic data showed that pyruvate metabolism in the liver and phenylalanine, tyrosine and tryptophan metabolism in the plasma of EFF group was enriched. Glutathione metabolism and valine, leucine and isoleucine metabolism were the top enriched pathways in plasma and muscle of the INEFF group. The integrated multi-omics analysis provided evidence to connect lipids and amino acids with catabolism proteins in the INEFF group.
In conclusion, this thesis indicates protein metabolism and energy production (lipid in freshwater and protein in seawater) in both freshwater and seawater play a key role in FE. Multiple factors (such as stress, overfeeding, and being dominant) that can stimulate protein degradation and decrease protein synthesis eventually cause a fish to be less efficient. This thesis, as the first proteomic and metabolomics investigation of FE and feed intake in an aquaculture species, advances our molecular understanding of FE phenotypes that can play a key role in aquaculture sustainability. Identification of molecular mechanisms, pathways, and potential biomarkers highlight the potential of proteomics, metabolomics, and integrated analytical approaches to get insight into different complex phenotypes like FE in aquaculture. These omics technologies can provide the capacity to design targeted experiments toward the development of specific nutritional and husbandry strategies to improve fish production sustainably.