Multiplex PCR platforms to evaluate diet-induced gene expression changes in the liver of Atlantic salmon (Salmo salar)

Authors: CABALLERO-SOLARES, ALBERT - Memorial University Of Newfounland; XUE, XI - Memorial University Of Newfounland; Cleveland, Beth; BEHESHTI FOROUTANI, MARYAM - Memorial University Of Newfounland; PARRISH, CHRISTOPHER - Memorial University Of Newfounland; TAYLOR, RICHARD - Cargill Feed Applications; RISE, MATTHEW - Memorial University Of Newfounland

Submitted to: Marine Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/25/2020
Publication Date: 6/4/2020
Citation: Caballero-Solares, A., Xue, X., Cleveland, B.M., Beheshti Foroutani, M., Parrish, C., Taylor, R., Rise, M. 2020. Multiplex PCR platforms to evaluate diet-induced gene expression changes in the liver of Atlantic salmon (Salmo salar). Marine Biotechnology.
DOI: https://doi.org/10.1007/s10126-020-09972-5

Interpretive Summary: The future of the aquaculture of carnivorous fish like Atlantic salmon and rainbow trout lies in the utilization of aquafeeds with a minimum contribution from ingredients sourced in wild fish stocks. The replacement of these marine products – namely fish meal (FM) and fish oil (FO) – by different terrestrial alternatives has been investigated, with a particular focus on their impact on fish performance and chemical composition. However, the fish must make metabolic adjustments while consuming novel aquafeeds since the nutrient profile varies from traditional marine-based diets. In this study a panel of gene biomarkers was evaluated to determine whether Atlantic salmon consuming aquafeeds with terrestrial ingredients regulate physiological mechanisms affecting fish health, nutrient utilization, and growth performance. Although growth performance was not affected by diet, genes associated with fat and glucose metabolism, oxidative stress, and inflammation were regulated in salmon consuming alternative feeds. These findings indicate that the fish exhibits metabolic and physiological adaptations to terrestrial-based diets. Understanding how nutrient-gene interactions are affected by novel feed ingredients will aid in development of novel growth- and health-promoting aquafeeds with lower levels of marine-sourced nutrients.

Technical Abstract: The simultaneous quantification of several transcripts via multiplex PCR could accelerate the development of superior aquafeeds for farmed fish, with minimum content in marine ingredients, as well as the research in fish nutrition and physiology. We designed two multiplex PCR panels based on transcriptome profiling studies in Atlantic salmon liver and hepatocytes. Together, the panels included assays for 40 biomarker genes representing key aspects of fish physiology (i.e., growth, metabolism, oxidative stress, and inflammation), and 3 normalizer genes. We used both panels to assess the physiological effects of replacing fish meal and fish oil by terrestrial alternatives on Atlantic salmon smolts. Three experimental treatments consisted of diets based on 1) marine ingredients (MAR), 2) animal by-products and vegetable oil (ABP), and 3) plant protein and vegetable oil (VEG). There were diet effects on expression of genes involved in hepatic glucose and lipid metabolism (e.g., elovl2, srebp1), cell redox status (e.g., txna, prdx1b), and inflammation (e.g., pgds, 5loxa). At the multivariate level, gene expression profiles were more divergent between fish fed the marine and terrestrial diets (MAR vs ABP/VEG), than between the two terrestrial (ABP vs VEG). Linear regression analysis showed correlations between ARA, EPA, and DHA and the abundance of numerous gene transcripts. Liver ARA was inversely related to glucose metabolism- (gck) and growth- (igfbp5a, htra1b) related biomarkers and HSI. Liver DHA and EPA levels correlated negatively with elovl2, whereas liver ARA levels correlated positively with fadsd5. Lower hepatic EPA/ARA in ABP-fed fish related with the increased expression of molecular biomarkers related to mitochondrial function (i.e., fabp3a), oxidative stress (i.e., txna, prdx1b), and inflammation (i.e., pgds, 5loxa). Application of multiplex PCR enabled investigation of a suite of gene biomarkers that indicated differential regulation of physiological mechanisms regulating fish health, nutrient utilization, and growth performance by feed ingredients of marine versus terrestial origin. Understanding how nutrient-gene interactions are affected by novel feed ingredients will aid in development of novel growth- and health-promoting aquafeeds with lower levels of marine-sourced nutrients.