Silver_fox_dataset_DRYAD

mtDNA sequences for 3 breeding lines of russian silver foxe

Estimation of population structure using STRUCTURE.

<p>Cluster analysis of fox genotypes was performed at four values of K (2, 3, 4, and 5) without population information. The numbers of assumed clusters are indicated on the y-axis. The population origin of individuals is indicated on x-axis. On each graph the individuals are listed in the order obtained at K = 3. Each individual is represented by a bar that is segmented into colors based on the assignment into inferred clusters given the assumption of K populations. The length of the colored segment is the estimated proportion of the individual’s genome belonging to that cluster. The analysis was run in 8 replicates for each K, the replicate with the highest likelihood is shown. The genetic structure analysis clearly differentiated the tame population from the aggressive one and did not reveal significant population stratification within the tame population at every K tested. In contrast, the population stratification within the aggressive population became apparent at K = 3.</p

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

SNPs with significant allele frequency differences between tame and aggressive populations.

<p>SNPs with differences in allele frequency between two populations at p <10^-7 (Bonferroni correction of PLINK2 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127013#pone.0127013.ref032" target="_blank">32</a>] association test). The absolute differences of SNP minor allele frequencies between the tame and aggressive populations are listed. These SNPs are presented as dots above the significance line (–log10 >6) on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127013#pone.0127013.g004" target="_blank">Fig 4</a>. SNPs are listed in the order of the fox map. Multi SNP clusters are in bold and numbered in the rightmost column. Multi SNP clusters are regions where SNPs that met the threshold are within 2 Mb to the next significant SNP. Genes that are in or near (50,000 bp) the multi SNP clusters are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127013#pone.0127013.t003" target="_blank">Table 3</a>. Dog chromosome—CFA; Fox chromosome—VVU.</p><p>SNPs with significant allele frequency differences between tame and aggressive populations.</p

Genotyping-By-Sequencing (GBS) Detects Genetic Structure and Confirms Behavioral QTL in Tame and Aggressive Foxes (<i>Vulpes vulpes</i>)

<div><p>The silver fox (<i>Vulpes vulpes</i>) offers a novel model for studying the genetics of social behavior and animal domestication. Selection of foxes, separately, for tame and for aggressive behavior has yielded two strains with markedly different, genetically determined, behavioral phenotypes. Tame strain foxes are eager to establish human contact while foxes from the aggressive strain are aggressive and difficult to handle. These strains have been maintained as separate outbred lines for over 40 generations but their genetic structure has not been previously investigated. We applied a genotyping-by-sequencing (GBS) approach to provide insights into the genetic composition of these fox populations. Sequence analysis of <i>Eco</i>T22I genomic libraries of tame and aggressive foxes identified 48,294 high quality SNPs. Population structure analysis revealed genetic divergence between the two strains and more diversity in the aggressive strain than in the tame one. Significant differences in allele frequency between the strains were identified for 68 SNPs. Three of these SNPs were located on fox chromosome 14 within an interval of a previously identified behavioral QTL, further supporting the importance of this region for behavior. The GBS SNP data confirmed that significant genetic diversity has been preserved in both fox populations despite many years of selective breeding. Analysis of SNP allele frequencies in the two populations identified several regions of genetic divergence between the tame and aggressive foxes, some of which may represent targets of selection for behavior. The GBS protocol used in this study significantly expanded genomic resources for the fox, and can be adapted for SNP discovery and genotyping in other canid species.</p></div