Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio)

Abstract

Background: 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.

Results: 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).

Conclusions: 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.

Figure 1

Box plots of behavioral variation among two wild and two domesticated zebrafish strains. (a) Domesticated zebrafish [Scientific Hatcheries (SH) and TM1] had lower Vertical Depth, spending more time close to the water surface than wild zebrafish [Nadia and Gaighatta] (P < 0.0001). (b) Domesticated zebrafish also had higher levels of Horizontal Position, spending a larger portion of time within one body length of the front of the aquarium nearest the human observer (P < 0.0001). Boxes represent the 25^th and 75^th percentiles, while the median is indicated by the interior horizontal line. The 5^th and 95^th percentiles are represented by the whiskers. Significant differences among strains are represented by lower case letters within each figure.

Figure 2

qRT-PCR was used to validate microarray results for six genes. Microarray and qRT-PCR showed similar patterns for five of the six genes: glial fibrillary acidic protein (gfap), proopiomelanocortin a (pomca), selenoprotein P1a (sepp1a), synaptoporin (synpr), and deiodinase, iodothyronine, type II (dio2). Validation failed for glutamate decarboxylase 2 (gad2), suggesting that additional factors may be affecting hybridization to the microarray. Abbreviations: G = Gaighatta, N = Nadia, S = Scientific Hatcheries, T = TM1.