Research Article: Integrative functional analyses using rainbow trout selected for tolerance to plant diets reveal nutrigenomic signatures for soy utilization without the concurrence of enteritis

Date Published: July 19, 2017

Publisher: Public Library of Science

Author(s): Jason Abernathy, Andreas Brezas, Kevin R. Snekvik, Ronald W. Hardy, Ken Overturf, Hanping Wang.


Finding suitable alternative protein sources for diets of carnivorous fish species remains a major concern for sustainable aquaculture. Through genetic selection, we created a strain of rainbow trout that outperforms parental lines in utilizing an all-plant protein diet and does not develop enteritis in the distal intestine, as is typical with salmonids on long-term plant protein-based feeds. By incorporating this strain into functional analyses, we set out to determine which genes are critical to plant protein utilization in the absence of gut inflammation. After a 12-week feeding trial with our selected strain and a control trout strain fed either a fishmeal-based diet or an all-plant protein diet, high-throughput RNA sequencing was completed on both liver and muscle tissues. Differential gene expression analyses, weighted correlation network analyses and further functional characterization were performed. A strain-by-diet design revealed differential expression ranging from a few dozen to over one thousand genes among the various comparisons and tissues. Major gene ontology groups identified between comparisons included those encompassing central, intermediary and foreign molecule metabolism, associated biosynthetic pathways as well as immunity. A systems approach indicated that genes involved in purine metabolism were highly perturbed. Systems analysis among the tissues tested further suggests the interplay between selection for growth, dietary utilization and protein tolerance may also have implications for nonspecific immunity. By combining data from differential gene expression and co-expression networks using selected trout, along with ontology and pathway analyses, a set of 63 candidate genes for plant diet tolerance was found. Risk loci in human inflammatory bowel diseases were also found in our datasets, indicating rainbow trout selected for plant-diet tolerance may have added utility as a potential biomedical model.

Partial Text

Manufactured from wild-catch marine forage fish and byproducts from fish processing, fishmeal (FM) is a primary source of protein in aquaculture feeds (aquafeeds). Since annual FM production is already fully utilized, mainly in aquafeeds, finding replacements for FM has been a concern for decades. A growing concern in recent years is the rising cost, as global demand for salmonid and other marine foods has increased while, over the same period, global production of FM has been in decline. Costs notwithstanding, the amount of marine-produced protein needed to feed expanding global aquaculture production systems is not available and is a barrier to the long-term growth of the industry. The decrease in availability of FM along with the increase in costs has led to international efforts toward reformulation of aquafeeds with higher percentages of plant-based products, replacing ever-decreasing amounts of marine protein with ever-increasing amounts from plant-protein sources including plant-meal (PM) and plant-protein concentrates. Supply-and-demand along with the push toward more sustainable aquaculture are not the only concerns with such changes however, as biological barriers to the reformulation of aquafeeds also exist in attempts to reduce and replace FM. Main barriers include incomplete information on nutritional requirements of major farmed species, differences in the digestibility and bioavailability of essential nutrients in reformulated feeds, the presence of antinutritional factors in plant feedstuffs, and the potential for a reduction in palatability and ingestion of aquafeeds with lower percentages of fish-derived ingredients [1–7].

The reformulation of aquafeeds along with the advancement of breeding programs with species adaptive to replacement diets is crucial to the success of sustainable aquaculture. After over a decade of genetic selection, we developed a strain of rainbow trout that performs well over long-term rearing when fed a high-soy, all plant-protein feed without developing enteritis. Since growth and feed efficiency along with diet-tolerance were major selection foci, we examined gene expression by RNA sequencing muscle and liver tissues of selected and non-selected trout strains fed either a fishmeal-based control feed or an all plant-protein feed. Genes identified in this study can be added to the growing list of those associated with diet tolerance and utilization. Among the tissues and strains, thiamine and especially purine metabolism is highly perturbed. Systems analysis among the tissues tested reveals that the interplay between selection for growth, dietary utilization and tolerance may have implications in nonspecific immunity as well. Using an integrative nutrigenomic approach of read-count differential expression, co-expression and other functional analyses, candidate genes that may play major roles in plant-diet utilization were found as these genes were identified in fish in the absence of enteritis. In addition, a major risk locus in ulcerative colitis, IL17REL was identified through these efforts and expression of IL-17 has been indicated in ulcerative colitis and celiac disease; as such, rainbow trout selected for plant-diet tolerance may have added utility as a potential biomedical model for human inflammatory bowel diseases.




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