Submitted to: Genbank
Publication Type: Other
Publication Acceptance Date: 2/7/2017
Publication Date: N/A
Technical Abstract: 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 has been shown to cause severe intestinal enteritis, leading to reduced growth and lower feed efficiency. Through selective breeding, we developed a strain of rainbow trout (strain ARS-KO) 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. That strain forms the material basis for this study, in which subsequent generations were selectively bred for increased deposition of Omega-3 fatty acids in the fillets after being fed a diet where fish oil was replaced by flax oil (termed ARS-KO-LIP strain). Since liver plays a major role in dietary alterations and lipid metabolism, and as fatty acid deposition and growth were factors in selection, both muscle and liver gene expression were examined for differential regulation among fish with different levels of muscle fatty acid profiles. After three months (from 10 to 250 grams) of rearing on plant based diet, muscle and liver tissues from the selected strain (ARS-KO-LIP; 3 different levels of fatty acids) were extracted and prepped for Illumina RNA-seq. Raw reads were screened for quality then aligned to the rainbow trout transcriptome. Read-counts were used to assess differential expression among fish with different levels of fatty acids. Significant differentially expressed genes between comparisons were assessed. 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 GSE94248.