Sequence comparison of prefrontal cortical brain transcriptome from a tame and an aggressive silver fox (Vulpes vulpes)

<p>Abstract</p> <p>Background</p> <p>Two strains of the silver fox (<it>Vulpes vulpes</it>), with markedly different behavioral phenotypes, have been developed by long-term selection for behavior. Foxes from the tame strain exhibit friendly behavior towards humans, paralleling the sociability of canine puppies, whereas foxes from the aggressive strain are defensive and exhibit aggression to humans. To understand the genetic differences underlying these behavioral phenotypes fox-specific genomic resources are needed.</p> <p>Results</p> <p>cDNA from mRNA from pre-frontal cortex of a tame and an aggressive fox was sequenced using the Roche 454 FLX Titanium platform (> 2.5 million reads & 0.9 Gbase of tame fox sequence; >3.3 million reads & 1.2 Gbase of aggressive fox sequence). Over 80% of the fox reads were assembled into contigs. Mapping fox reads against the fox transcriptome assembly and the dog genome identified over 30,000 high confidence fox-specific SNPs. Fox transcripts for approximately 14,000 genes were identified using SwissProt and the dog RefSeq databases. An at least 2-fold expression difference between the two samples (p < 0.05) was observed for 335 genes, fewer than 3% of the total number of genes identified in the fox transcriptome.</p> <p>Conclusions</p> <p>Transcriptome sequencing significantly expanded genomic resources available for the fox, a species without a sequenced genome. In a very cost efficient manner this yielded a large number of fox-specific SNP markers for genetic studies and provided significant insights into the gene expression profile of the fox pre-frontal cortex; expression differences between the two fox samples; and a catalogue of potentially important gene-specific sequence variants. This result demonstrates the utility of this approach for developing genomic resources in species with limited genomic information.</p

Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes

Domesticated species exhibit a suite of behavioral, endocrinological, and morphological changes referred to as “domestication syndrome.” These changes may include a reduction in reactivity of the hypothalamic-pituitary-adrenal (HPA) axis and specifically reduced adrenocorticotropic hormone release from the anterior pituitary. To investigate the biological mechanisms targeted during domestication, we investigated gene expression in the pituitaries of experimentally domesticated foxes (Vulpes vulpes). RNA was sequenced from the anterior pituitary of six foxes selectively bred for tameness (“tame foxes”) and six foxes selectively bred for aggression (“aggressive foxes”). Expression, splicing, and network differences identified between the two lines indicated the importance of genes related to regulation of exocytosis, specifically mediated by cAMP, organization of pseudopodia, and cell motility. These findings provide new insights into biological mechanisms that may have been targeted when these lines of foxes were selected for behavior and suggest new directions for research into HPA axis regulation and the biological underpinnings of domestication

Data from: On the origin of a domesticated species: identifying the parent population of Russian silver foxes (Vulpes vulpes)

No description availabl

A meiotic linkage map of the silver fox, aligned and compared to the canine genome

A meiotic linkage map is essential for mapping traits of interest and is often the first step toward understanding a cryptic genome. Specific strains of silver fox (a variant of the red fox, Vulpes vulpes), which segregate behavioral and morphological phenotypes, create a need for such a map. One such strain, selected for docility, exhibits friendly dog-like responses to humans, in contrast to another strain selected for aggression. Development of a fox map is facilitated by the known cytogenetic homologies between the dog and fox, and by the availability of high resolution canine genome maps and sequence data. Furthermore, the high genomic sequence identity between dog and fox allows adaptation of canine microsatellites for genotyping and meiotic mapping in foxes. Using 320 such markers, we have constructed the first meiotic linkage map of the fox genome. The resulting sex-averaged map covers 16 fox autosomes and the X chromosome with an average inter-marker distance of 7.5 cM. The total map length corresponds to 1480.2 cM. From comparison of sex-averaged meiotic linkage maps of the fox and dog genomes, suppression of recombination in pericentromeric regions of the metacentric fox chromosomes was apparent, relative to the corresponding segments of acrocentric dog chromosomes. Alignment of the fox meiotic map against the 7.6x canine genome sequence revealed high conservation of marker order between homologous regions of the two species. The fox meiotic map provides a critical tool for genetic studies in foxes and identification of genetic loci and genes implicated in fox domestication

Genes located inside or within 50,000 bp from start and end of the multi SNP clusters in the dog genome.

<p>Cluster numbers refer to the numbering from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127013#pone.0127013.t002" target="_blank">Table 2</a>.</p><p>Genes located inside or within 50,000 bp from start and end of the multi SNP clusters in the dog genome.</p

SNP minor allele frequency and heterozygosity in tame and aggressive populations.

<p>SNP minor allele frequency and heterozygosity in tame and aggressive populations.</p

Principal component analysis.

<p>Principal component analysis of SNP data for 20 tame and 20 aggressive foxes. 8,437 SNPs with genotypes available for all individuals were used in this analysis. Aggressive individuals are represented by red dots, tame individuals are represented by green triangles. PC1 is plotted on the x-axis, PC2 is plotted on the y-axis.</p

Estimation of linkage disequilibrium (r²) in tame and aggressive fox populations.

<p>Distributions of r^<b>2</b> values between pairs of SNPs separated by different distances are compared between tame (green) and aggressive (red) populations. SNP pairs were divided into 14 sets (bins) using the estimated distances between SNPs in the fox genome (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127013#pone.0127013.s007" target="_blank">S2 Table</a>). Each bin is represented by a doubled bar (green and red) on the graph. The range of distances between SNPs in each bin is indicated on the x-axis. The width of the bar represents the relative number of SNP pairs in that bin for that population after a log transformation (wider bars have more pairs of SNPs). Exact numbers of SNP pairs in each bin are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127013#pone.0127013.s007" target="_blank">S2 Table</a>. The y-axis indicates r^<b>2</b> values for pairs of SNPs. The yellow diamonds correspond to the mean r^<b>2</b> for all SNPs in that bin in the population. The white circles correspond to the median values. The thin black line within each bar represents r^<b>2</b> values in that bin in the population in the interval from the 25th to 75th percentile. The horizontal line corresponds r^<b>2</b> = 0.2.</p