Microarray analysis of differential utilization of plant-based diets by rainbow trout

Abstract

Microarray analysis was conducted using liver samples from two families of rainbow trout that differed in their growth responses when compared between individuals fed a fishmeal or plant protein-based diet. Differential expression relating to dietary utilization between the two families found significant changes in expression of 33 expressed sequence tags (ESTs). Eight of the differentially expressed ESTs had identified mammalian homologs that had been previously researched with identified cellular interactions and functions. Utilizing pathway analysis software to analyze sequences annotated with known mammalian genes, we were able to map gene pathways and process interactions. From this information, we were able to infer that the metabolic changes associated with utilization of plant protein versus fishmeal were associated with differential regulation of genes related to cell oxidative stress, proliferation, growth and survival. Furthermore, we inferred from the changes we observed in immune response gene expression that ingestion of this plantbased diet upregulated the expression of genes involved in immunoregulatory processes.

Why Do Some Rainbow Trout Genotypes Grow Better With a Complete Plant-Based Diet? Transcriptomic and Physiological Analyses on Three Isogenic Lines

“…The transcriptomic analysis also revealed a genetic variability in the expression of genes involved in different immunity pathways, linked to their capacity to grow with a diet devoid of FO and FM. Previous studies found similar results in sea bass and RBT (Geay et al, 2011 ; Overturf et al, 2012 ). Although no differences in immune parameters were detected among lines, analyses of gene expression may be more sensitive with respect to detecting differences among the fish.…”

“…One of the potential ways to further reduce the use of fish oil and fishmeal is to thus take advantage of the genetic variability which exists in the salmonid population. With this objective, we sought to identify the mechanisms implemented by some trout genotypes to grow more efficiently with a complete plant-based diet, as until now, this question has been little studied (Geay et al, 2011 ; Overturf et al, 2012 ; Callet et al, 2018 ).…”

“…Some genotypes are thus better able to survive and grow than others, when fed such diets (Le Boucher et al, 2012 ; Callet et al, 2017 ). For salmonids, a study which focused on RBT analyzed two families with different growth capacities when fed a diet devoid of fishmeal, but only revealed a few markers, which were all linked to the immune response (Overturf et al, 2012 ). Finally, a recent study found several potential markers linked to feed intake and sensory perception among three different RBT isogenic lines (Callet et al, 2018 ).…”

Detection of new pathways involved in the acceptance and the utilisation of a plant-based diet in isogenic lines of rainbow trout fry

“…Effects of plant-based diets have been largely studied, but only few transcriptomic studies have analysed the effect of fish genetic background. Overall, these studies indicated only a limited number of genes to be differentially expressed according to the genotype in RBT [ 20 , 21 ], in salmon [ 11 ] or in sea bass [ 14 ]. In the present experiment, we found a high number of genes differentially expressed between genotypes, with a cut-off p-value corrected for multiple testing, controlling thus the number of false positives.…”

“…A study on European sea bass revealed differences between two families characterized by their different abilities to use a plant-based diet [ 14 ]. And only two studies focused on RBT, and analysed two families with different ability to grow with a diet devoid of fishmeal [ 20 , 21 ].…”