Open Access Highly Accessed Research article

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

Cecilia C Sánchez123, Gregory M Weber2, Guangtu Gao2, Beth M Cleveland2, Jianbo Yao3 and Caird E Rexroad2*

Author affiliations

1 Shepherd University, Institute of Environmental and Physical Sciences, Robert C. Byrd Science and Technology Center, Shepherdstown, WV, 25443, USA

2 USDA/ARS/NCCCWA, 11861 Leetown, Kearneysville, WV, 25430, USA

3 West Virginia University, Animal and Nutritional Sciences, Morgantown, WV, 26506, USA

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Citation and License

BMC Genomics 2011, 12:626  doi:10.1186/1471-2164-12-626

Published: 21 December 2011

Abstract

Background

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, and fillet quality. 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.

Results

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.

Conclusion

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.