RNA-Sequencing in Trout Selected for Growth and Tolerance to Plant-Based Diets Reveals Differential Liver Gene Expression Compared to Control Fish Under Enteritic Conditions

Rainbow trout (Oncorhynchus mykiss) and other salmonids are piscivorous fish. In aquaculture, fish-based feed ingredients are rapidly becoming unsustainable due to increased demand and diminishing supply. Total replacement of fishmeal with plant proteins 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 a high soy plant protein-based feed and also shows increased growth compared to other strains. Since central metabolism plays a role in dietary alterations, we set out to determine globally which liver gene pathways were differentially regulated between commercial and selected trout strains when fed plant-based diets. After 7.5 months of rearing on a high soy plant protein-based feed (PM), liver tissue (n=20) from a domestic non-selected strain (NS; enteritis) and a selected strain (ARS; no enteritis) was extracted and prepped for Illumina RNA-seq. Raw reads (~25M/liver) were screened for quality then aligned to the rainbow trout transcriptome (USDA 2015). Read-counts were used to assess differential expression between ARS-PM and NS-PM individuals. We identified a total of 533 transcripts that were differentially expressed (adjusted p-value ≤ 0.01), including 279 transcripts that were up-regulated and 254 transcripts that were down-regulated in the ARS-PM fish compared to NS-PM fish. There was clear separation between strains by PCA. In addition, several hundred highly-variable genes contributed to a clear strain separation when clustering normalized distances and plotting on a heatmap. They included such genes encoding NODs, EGRs and transmembrane proteins of tight junctions – potential indicators of gastrointestinal disturbances and autoimmune responses. Ongoing work includes testing more individuals and tissues, additional sequencing analyses, and functional studies of differentially expressed genes.