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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #280127

Title: Quantitative trait loci analyses and RNA-seq identify genes affecting stress response in rainbow trout

item Rexroad, Caird
item Liu, Sixin
item Gao, Guangtu
item Palti, Yniv
item Weber, Gregory - Greg
item Vallejo, Roger

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/23/2012
Publication Date: 6/17/2012
Citation: Rexroad III, C.E., Liu, S., Gao, G., Palti, Y., Weber, G.M., Vallejo, R.L. 2012. Quantitative trait loci analyses and RNA-seq identify genes affecting stress response in rainbow trout [abstract]. p. 185.

Interpretive Summary:

Technical Abstract: Genomic analyses have the potential to impact aquaculture production traits by identifying markers as proxies for traits which are expensive or difficult to measure and characterizing genetic variation and biochemical mechanisms underlying phenotypic variation. One such trait is the response of rainbow trout to the stressors of the aquaculture environment. Typical stressors can be categorized under handling and overcrowding, sub-optimal water quality parameters, and social interactions. These stressors may negatively impact growth, feed intake, feed efficiency, disease resistance, flesh quality, and reproductive performance. We employed genetic mapping and RNA-seq based approaches towards identifying genes affecting stress response with the eventual goal of improving animal welfare and aquaculture production efficiency. In general, fish respond to stress by activating the neuro-endocrine system leading to elevated blood concentrations of cortisol, the principle corticosteroid in salmonids. Plasma cortisol concentrations following a 3 hour confinement have been used as a measure for stress responsiveness in rainbow trout. We conducted a genome scan with over 400 microsatellite loci on a three generation pedigree to identify QTL affecting stress response. Analyses of F1 and F2 families detected QTL on 16 chromosomes. RNA-seq data analysis in species for which a reference genome sequence is not available is difficult; therefore we initiated a two-step strategy that included generation of a reference stress transcriptome. Roche 454 pyrosequencing technology was used to sequence multiple tissues from fish challenged with a variety of individual stressors including high temperature (25C), low temperature (2C), high salinity (32‰), re-use water, handling/crowding and unchallenged control fish. Over 3 million reads were obtained from a pooled normalized library constructed from gill, brain, liver, spleen, kidney and muscle transcripts. These 454 sequences were assembled and annotated with Gene Ontology (GO) terms and used as a reference transcriptome. Equal amounts of total RNA from the liver crowding challenge were pooled by tank (3 treatments, 2 controls) to create 5 libraries (one per tank) which were sequenced in three runs on an Illumina HiSeq 2000. Analyses of over 200 million reads have identified over 300 differentially expressed genes with a FDR =0.05 that can be annotated through the GO terms associated with the reference transcriptome.