RNA-Seq Analysis of Stress Response in Rainbow Trout

Fish under intensive rearing conditions experience various stress conditions, which have negative impacts on survival, growth and fillet quality. Understanding the molecular mechanisms underlying stress responses will facilitate improvement of animal welfare and production efficiency. Our objective was to characterize the transcriptome of rainbow trout in response to multiple stressors using RNA-seq. Equal amount of total RNA extracted from the liver of the individual fish was pooled by tank (eight fish per tank). Five RNA-seq libraries were sequenced from the three tanks of fish that underwent confinement stress and two tanks of untreated control fish using Illumina HiSeq 2000. Over 300 differentially expressed transcripts were identified. Twenty one differentially expressed transcripts were selected for quantitative RT-PCR to validate the RNA-seq analysis results. The gene expression fold changes identified by RNA-seq analysis and RT-PCR were highly correlated (r = 0.94). Pathways associated with stress response were implicated by mapping the differentially expressed transcripts to the pathways in KEGG database. Currently, we are using RNA-seq to identify differentially expressed transcripts in gill of rainbow trout exposed to high temperature (25⁰C), low temperature (2⁰C), high salinity, re-used water and handling/confinement stress.