Characterization of the <i>UCP1</i> Locus in Pigs

<div><p>(A) Wild boar sow with striped piglets in their nest.</p><p>(B) Dotpath alignments of genomic <i>UCP1</i> sequences from pigs, humans, and cattle. The approximate positions of the six exons in human <i>UCP1</i> are indicated. Gap1 and Gap2 indicate two gaps in the alignment between the pig and human sequences.</p><p>(C) Rate of <i>nonsynonymous</i> and <i>synonymous</i> substitutions in pairwise comparisons of <i>UCP1</i> sequences from humans, mice, cattle, and pigs. The data are based on sequences from exon 1, 2, and 6. B, <i>Bos taurus;</i> H, <i>Homo sapiens;</i> M, <i>Mus musculus;</i> and S, Sus scrofa.</p><p>(Photo: Anneli Andersson, Linköping University, Sweden)</p></div

ZBED evolution.

<p>Phylogenetic tree for <i>ZBED</i> genes and related sequences from the <i>Ac</i> family. Two separate ZBED domestications are indicated. Numbers of included taxa are provided next to schematic clades. Active DNA transposons are marked with asterisks, and bold branches indicate posterior probabilities ≥95%.</p

Chromosomal locations of human <i>ZBED</i> genes, frog <i>ZBEDX</i> and human Buster1 (<i>ZBED5</i>).

a<p>Positions in the human genome (hg19 assembly), and the frog genome (<i>Xenopus tropicalis</i>, xenTro3 assembly).</p>b<p>Also referred to in the literature as hDREF, Tramp, and Human-<i>Ac</i>.</p>c<p>The frog <i>ZBEDX</i> gene.</p>d<p>This gene is also referred to as Buster1 of the <i>Buster</i> DNA transposon family in the literature, and is distinct from other ZBEDs.</p>e<p>Sequence conversion is not currently available for these genomes in the UCSC Genome Browser (<a href="http://genome.ucsc.edu" target="_blank">http://genome.ucsc.edu</a>).</p

Phylogenetic relationships of Buster1 (ZBED5).

<p>ZBED5 is identical to Buster1 and groups within the <i>Buster</i> family with strong support. Buster sequences are separate from collapsed clades representing the <i>Ac</i> family. Active DNA transposons are marked with asterisks, and bold branches indicate posterior probabilities ≥95%. Proposed nomenclature updates for ZBEDs 7, 8 and 9 are indicated next to branches ancestral to the respective ZBED (Buster) clade.</p

Phylogenetic relationships of separate BED domains.

<p>Roman numerals refer to BED domain position within ZBED genes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059940#pone-0059940-g001" target="_blank">Fig. 1</a>). Grey boxes on branches indicate hypothesized BED domain duplication events for the various <i>ZBED</i> genes. Posterior probabilities are provided next to tree nodes.</p

Table of high-confidence candidate eQTL with location of the gene, LOD score, and p-value for association between gene expression and bone trait.

<p>Table of high-confidence candidate eQTL with location of the gene, LOD score, and p-value for association between gene expression and bone trait.</p

Candidate quantitative trait genes (A) <i>DNB1</i> for female medullary and (B) <i>HSF5</i> for female cortical traits: LOD curves and confidence intervals of bone QTL and associated eQTL, and scatterplots of residual phenotypes against gene expression values.

<p>Candidate quantitative trait genes (A) <i>DNB1</i> for female medullary and (B) <i>HSF5</i> for female cortical traits: LOD curves and confidence intervals of bone QTL and associated eQTL, and scatterplots of residual phenotypes against gene expression values.</p

Candidate quantitative trait genes osteonectin and <i>B4GALT7</i> for total bone content: LOD curves and confidence intervals of bone QTL and associated eQTL, and scatterplots of residual phenotypes against gene expression values.

<p>Candidate quantitative trait genes osteonectin and <i>B4GALT7</i> for total bone content: LOD curves and confidence intervals of bone QTL and associated eQTL, and scatterplots of residual phenotypes against gene expression values.</p

Results from the ANOVA tests investigating the effects of age (days post hatching), salinity (16 vs. 35) and genetics (purebred vs. hybrid) on otolith width and length.

<p>Results from the ANOVA tests investigating the effects of age (days post hatching), salinity (16 vs. 35) and genetics (purebred vs. hybrid) on otolith width and length.</p

Comparison of phenotypic traits among the four herring groups.

<p>(A) length-at-age and von Bertalanffy growth models, (B) number of vertebrae, and (C) otolith aspect ratio were compared among H16 = hybrids at salinity 16, P16 = purebreds at salinity 16, H35 = hybrids at salinity 35, P35 = purebreds at salinity 35. Mean values and 1*SE are shown. Letters indicated posterior Tukey-HSD test results of all pair-wise comparisons. Groups which do not share a letter are significantly different to each other.</p