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United States Department of Agriculture

Agricultural Research Service

Research Project: UTILIZATION OF GENOMICS FOR IMPROVING PRODUCTION TRAITS IN COOL AND COLD WATER AQUACULTURE

Location: Cool and Cold Water Aquaculture Research

Title: Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors

Authors
item Sanchez, Cecilia -
item WEBER, GREGORY
item GAO, GUANGTU
item CLEVELAND, BETH
item Yao, Jianbo -
item REXROAD, CAIRD

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 9, 2011
Publication Date: December 21, 2011
Citation: Sanchez, C., Weber, G.M., Gao, G., Cleveland, B.M., Yao, J., Rexroad III, C.E. 2011. Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors. Biomed Central (BMC) Genomics. 12:626.

Interpretive Summary: Fish under intensive culture conditions are exposed to a variety of acute and chronic stressors, including high rearing densities, sub-optimal water quality, and severe thermal fluctuations. Such stressors are inherent in aquaculture production and can induce physiological responses with adverse effects on traits important to producers and consumers, including those associated with growth, nutrition, reproduction, immune response, fillet quality, and environmental impacts. Although gene expression can provide indicators of how organisms respond to stress, most contemporary approaches to characterizing gene expression require a genome sequence. In the absence of a genome sequence for rainbow trout, we created a resource of gene DNA sequences to serve as a proxy when conducting genome analyses on response to stress in this species. We subjected rainbow trout to various stressors (high and low temperature, high salinity, crowding, or re-use water low in dissolved oxygen and high in carbon dioxide) to initiate physiological stress responses which were verified by measuring known physiological parameters associated with stress. Tissue samples were collected and DNA sequencing was used to identify a unique set of genes which is inclusive of all responses to stress. Results of analyzing 3,160,306 sequences indicate that the fish had significant stressor-specific changes in their physiological conditions, much of these data were previously unrecognized in rainbow trout. Understanding and monitoring the biological mechanisms underlying stress responses will facilitate alleviating their negative effects through selective breeding and changes in management practices, resulting in improved animal welfare and production efficiency.

Technical Abstract: Fish under intensive culture conditions are exposed to a variety of acute and chronic stressors, including high rearing densities, sub-optimal water quality, and severe thermal fluctuations. Such stressors are inherent in aquaculture production and can induce physiological responses with adverse effects on traits important to producers and consumers, including those associated with growth, nutrition, reproduction, immune response, fillet quality, and environmental impacts. Understanding and monitoring the biological mechanisms underlying stress responses will facilitate alleviating their negative effects through selective breeding and changes in management practices, resulting in improved animal welfare and production efficiency. Physiological responses to five treatments associated with stress were characterized by measuring plasma lysozyme activity, glucose, lactate, chloride, and cortisol concentrations, in addition to stress-associated transcripts by quantitative PCR. Results indicate that the fish had significant stressor-specific changes in their physiological conditions. Sequencing of a pooled normalized transcriptome library created from gill, brain, liver, spleen, kidney and muscle RNA of control and stressed fish produced 3,160,306 expressed sequence tags which were assembled and annotated. SNP discovery resulted in identification of ~58,000 putative single nucleotide polymorphisms including 24,479 which were predicted to fall within exons. Of these, 4907 were predicted to occupy the first position of a codon and 4110 the second, increasing the probability to impact amino acid sequence variation and potentially gene function. We have generated and characterized a reference transcriptome for rainbow trout that represents multiple tissues responding to multiple stressors common to aquaculture production environments. This resource compliments existing public transcriptome data and will facilitate approaches aiming to evaluate gene expression associated with stress in this species.

Last Modified: 9/10/2014
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