Changes in the liver transcriptome of farmed Atlantic salmon (Salmo salar) fed experimental diets based on terrestrial alternatives to fish meal and fish oil

Abstract

BackgroundDependence on marine natural resources threatens the sustainability of Atlantic salmon aquaculture. In the present study, Atlantic salmon fed for 14 weeks with an experimental diet based on animal by-products and vegetable oil (ABP) exhibited reduced growth performance compared with others fed a fish meal/fish oil based experimental diet (MAR) and a plant protein/vegetable oil-based experimental diet (VEG). To characterize the molecular changes underlying the differences in growth performance, we conducted a 44 K microarray study of the liver transcriptome of the three dietary groups.ResultsThe microarray experiment identified 122 differentially expressed features (Rank Products, PFP < 10%). Based on their associated Gene Ontology terms, 46 probes were classified as metabolic and growth-relevant genes, 25 as immune-related, and 12 as related to oxidation-reduction processes. The microarray results were validated by qPCR analysis of 29 microarray-identified transcripts. Diets significantly modulated the transcription of genes involved in carbohydrate metabolism (gck and pfkfb4), cell growth and proliferation (sgk2 and htra1), apoptosis (gadd45b), lipid metabolism (fabp3, idi1, sqs), and immunity (igd, mx, ifit5, and mhcI). Hierarchical clustering and linear correlation analyses were performed to find gene expression patterns among the qPCR-analyzed transcripts, and connections between them and muscle and liver lipid composition. Overall, our results indicate that changes in the liver transcriptome and tissue lipid composition were driven by cholesterol synthesis up-regulation by ABP and VEG diets, and the lower carbohydrate intake in the ABP group. Two of the microarray-identified genes (sgk2 and htra1) might be key to explaining glucose metabolism regulation and the dietary-modulation of the immune system in fish. To evaluate the potential of these genes as predictive biomarkers, we subjected the qPCR data to a stepwise discriminant analysis. Three sets of no more than four genes were found to be able to predict, with high accuracy (67–94%), salmon growth and fatty acid composition.ConclusionsThis study provides new findings on the impact of terrestrial animal and plant products on the nutrition and health of farmed Atlantic salmon, and a new method based on gene biomarkers for potentially predicting desired phenotypes, which could help formulate superior feeds for the Atlantic salmon aquaculture industry.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5188-6) contains supplementary material, which is available to authorized users.

Minimizing marine ingredients in diets of farmed Atlantic salmon (Salmo salar): Effects on growth performance and muscle lipid and fatty acid composition

“…It was shown in [ 32 ] that 7% inclusion of porcine blood meal had no negative effects on salmon performance compared with fish meal based control diets. The animal by-product diet also resulted in the lowest concentrations of muscle triacylglycerols which is consistent with the down-regulation of fatty acid synthesis in the livers of these fish [ 33 ].…”

Hepatopancreas Transcriptome Profiling Analysis Reveals Physiological Responses to Acute Hypoxia and Reoxygenation in Juvenile Qingtian Paddy Field Carp Cyprinus carpio var qingtianensis

“…RNA-seq had been successfully applied to the study of environmental toxicology, nutritional intervention and growth and development of fish (Wang et al, 2016;Caballero-Solares et al, 2018;Qi et al, 2018). RNA-seq analysis is an appropriate analysis for this study, because it can effectively differentiate differentially expressed genes (DEGs) between different test groups.…”

The Transcriptomic Responses of Atlantic Salmon (Salmo salar) to High Temperature Stress Alone, and in Combination with Moderate Hypoxia

“…To identify any existing paralogs, and to verify the identity of each GOI, we performed BLASTn searches against the non-redundant nucleotide (nr/nt) and the expressed sequence tag (EST) databases of NCBI (year: 2018) (Additional le 3). For nine GOIs (camp-a, cat, cyp1a1, epx, gck, hif1α, hsp70, il8, and mmp9) the paralog-speci c primer sequences were obtained from previous studies [67,68] or the Genomic Applications Partnership Program (GAPP # 6604) database, given that they were targeting the identical probe sequences (Additional les 2 and 3). Table 1 Functional annotation and fold change (FC) transcript expression for 41 qPCR genes.…”