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Series GSE38729 Query DataSets for GSE38729
Status Public on Jun 15, 2012
Title Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio)
Organism Danio rerio
Experiment type Expression profiling by array
Summary Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals. Experiments conducted in common environments indicate that these behavioral differences have a genetic basis. In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation.
Compared to wild zebrafish, domesticated zebrafish spent more time near the water surface and were more likely to occupy the front of the aquarium nearest a human observer. Microarray analysis of the brain transcriptome identified high levels of population variation in gene expression, with 1,749 genes significantly differentially expressed among populations. Genes that varied among populations belonged to functional categories that included DNA repair, DNA photolyase activity, response to light stimulus, neuron development and axon guidance, cell death, iron-binding, chromatin reorganization, and homeobox genes. Comparatively fewer genes (112) differed between domesticated and wild strains with notable genes including gpr177 (wntless), selenoprotein P1a, synaptophysin and synaptoporin, and acyl-CoA binding domain containing proteins (acbd3 and acbd4).
Microarray analysis identified a large number of genes that differed among zebrafish populations and may underlie behavioral domestication. Comparisons with similar microarray studies of domestication in rainbow trout and canids identified sixteen evolutionarily or functionally related genes that may represent components of shared molecular mechanisms underlying convergent behavioral evolution during vertebrate domestication. However, this conclusion must be tempered by limitations associated with comparisons among microarray studies and the low level of population-level replication inherent to these studies.
 
Overall design RNA was extracted from the brains of fish from four behaviorally distinct strains of zebrafish and hybridized on Affymetrix microarrays. Brains from 2-5 individual fish of the same sex were pooled and homogenized together, for a total of two biological replicate pools per sex per strain (16 microarrays total).
 
Contributor(s) Drew RE, Settles ML, Churchill EJ, Williams SM, Balli S, Robison BD
Citation(s) 22817472
Submission date Jun 14, 2012
Last update date Jan 25, 2018
Contact name Robert Drew
E-mail(s) rdrew@umassd.edu
Phone 508-990-8950
Organization name University of Massachusetts Dartmouth
Department Biology
Street address 285 Old Westport Road
City N. Dartmouth
State/province MA
ZIP/Postal code 02747
Country USA
 
Platforms (1)
GPL1319 [Zebrafish] Affymetrix Zebrafish Genome Array
Samples (16)
GSM948754 Brain from TM1 Female rep 1
GSM948755 Brain from TM1 Female rep 2
GSM948756 Brain from TM1 Male rep 1
Relations
BioProject PRJNA168578

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Supplementary file Size Download File type/resource
GSE38729_RAW.tar 31.9 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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