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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: Analysis of differential gene expression in response to handling and confinement stress in rainbow trout using whole transcriptome RNA-seq

Authors
item Liu, Sixin
item Gao, Guangtu
item Castano-Sanchez, Cecilia -
item Palti, Yniv
item Rexroad, Caird

Submitted to: International Symposium on Genetics in Aquaculture
Publication Type: Abstract Only
Publication Acceptance Date: February 18, 2012
Publication Date: June 30, 2012
Citation: Liu, S., Gao, G., Castano-Sanchez, C., Palti, Y., Rexroad III, C.E. 2012. Analysis of differential gene expression in response to handling and confinement stress in rainbow trout using whole transcriptome RNA-seq [abstract]. International Symposium on Genetics in Aquaculture. p. 367.

Technical Abstract: 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. Rainbow trout currently lack a reference genome assembly, hence we initiated a two-step strategy that included generation of a reference stress response transcriptome. To this end we challenged fish from four full-sib families in three replicates with high temperature (25 degrees C), low temperature (2 degrees C), high salinity, re-use water and handling/confinement. Over three million Roche-454 reads that were obtained from a pooled and normalized library from gill, brain, liver, spleen, kidney and muscle of stressed and untreated control fish were assembled and annotated. Next, we used this reference transcriptome to characterize the stress response to handling and confinement. 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 stressed fish and two tanks of untreated control fish using Illumina HiSeq 2000. Gene expression levels between control and challenged groups were compared, and the enrichment of Gene Ontology categories was analyzed.

Last Modified: 10/20/2014
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