Submitted to: National Center for Biotechnology Information (NCBI)
Publication Type: Other
Publication Acceptance Date: 3/23/2016
Publication Date: N/A
Technical Abstract: In aquaculture, fish-based feed ingredients are rapidly becoming unsustainable due to increased demand and diminishing supply. However, total replacement of fishmeal with plant proteins in diets causes severe intestinal enteritis, leading to reduced growth and lower feed efficiency. Through selective breeding, we have developed a strain of rainbow trout that does not develop distal intestine enteritis when reared on plant protein-based feed and also shows increased growth compared to other strains. Since central metabolism plays a major role in dietary alterations, and as growth was a major factor in the selection program, liver and muscle gene expression were examined for differential regulation between commercial and selected trout strains when fed alternative diets. After three months of rearing on either a fishmeal or plant protein-based diet, muscle and liver tissues from a domestic non-selected strain (House Creek; develops enteritis) and the selected strain (ARS-KO; no enteritis) were extracted and prepped for high-throughput Illumina RNA-sequencing. Raw sequence reads were screened for quality then aligned to the rainbow trout transcriptome. Read-counts were compiled from sequence alignments and used to assess differential gene expression between strains given different diets. Raw sequencing data, read-count information and a complete description of computational methods have been made available to the public at the NCBI GEO database under the accession number GSE79531.