World Aquaculture Society Meetings

DIFFERENTIAL GENE EXPRESSION IN MUSCLE BETWEEN TROUT MANIFESTING CHRONIC ENTERITIS OR SYMPTOM-FREE WHILE REARING ON PLANT-BASED DIETS  

Jason Abernathy*, Andreas Brezas, Ronald Hardy, and Ken Overturf
 
USDA-ARS
Hagerman Fish Culture Experiment Station
3059F National Fish Hatchery Rd
Hagerman, ID 83332
Jason.Abernathy@ars.usda.gov

As the worldwide demand for aquaculture continues to increase, production of fishmeal and fish-oils for feeds is unsustainable. Plant-based diet substitution remains a viable option; however, production of trout in this manner leads to the development of severe gastrointestinal enteritis. This pathology affects production in several ways including a reduction in growth. Our lab has developed selected lines of rainbow trout that are resistance to developing enteritis when fed plant-based diets, while also showing increased growth compared to other selected strains. We were interested in determining if muscle gene pathways were regulated between commercial and selected trout when given plant-based (PM) diets, which might explain some of these physiological differences.

Muscle tissue (n=20) from wild-type (wt) or selected (sel) trout was extracted and prepped for Illumina RNA-seq. Raw reads (~25M/muscle) were screened for quality and ribosomal sequences. Filtered reads were aligned to the rainbow trout transcriptome (USDA 2015) using Bowtie2 and effective read-counts extracted using eXpress. Differential expression between sel-PM and wt-PM individuals was assessed using the DESeq2 package in R.

We found a total of 46 genes that were differentially expressed (adjusted p-value < 0.1). This included 28 genes that were up-regulated and 18 genes that were down-regulated in the selected fish over the wt. There was not a high-degree of separation between groups by PCA. However, a handful of highly-variable genes contributed to a clear separation by plotting of normalized distances on a heatmap (Fig. 1). They included such genes as tropomyosins and muscle sarcoplasmic reticulum ATPase. Based on the clustering information, more variation is observed between families of selected strains then the wt individuals. While there is some regulation in muscle tissues between and among strains fed a plant-replacement diet, clearly there remain other genetic and physiological factors at work. Current initiatives including the addition of more individuals, additional sequencing analyses, pathway and functional studies of differentially expressed genes that will be presented.




Copyright © 2001-2019 World Aquaculture Society All Rights Reserved.