Number of probe sets showing a significantly altered abundance in muscle tissue.

<p>The number of altered probe sets between adjacent developmental stages in AP or HP offspring are indicated at horizontal arrows; the number of commonly altered probe sets between stages in AP and HP offspring are indicated at intersections; the number of probe sets showing a different abundance between HP and AP offspring at the same developmental stage are indicated at vertical arrows; small arrows at the numbers indicate a higher or lower probe set abundance, respectively.</p

Genotype-phenotype correlations.

<p>The animals were grouped according to genotype at the best associated SNPs of each of the four detected QTL. Animal numbers are indicated at the bottom. The call rates for these SNPs were >98.9%. For each of the four QTL the homozygous alternative genotype classes have different phenotypic distributions (p<0.05, Welch's t-test). (A) EBV pH1 distributions with respect to genotype at SNP ASGA0061594 on SSC 14. (B) EBV carcass length in boars with respect to genotype at SNP ASGA0010032 on SSC 2. (C) EBV rear view hind legs distributions in Swiss Large White boars with respect to genotype at SNP ALGA0058443 on SSC 10. (D) EBV rear view hind legs distributions in Swiss Large White boars with respect to genotype at SNP H3GA0045902 on SSC 16.</p

Top allelic association hits in the GWAS for QTL affecting commercially important traits.

a<p>p-values were calculated using χ2 tests in an allelic association study.</p>b<p>The positions of the associated SNPs on the latest version of the pig reference genome were determined by BLAST searches with the flanking sequences of the SNPs as provided by illumina with respect to the Sscrofa 10.2 assembly. Some of the flanking sequences did not give a significant BLAST hit with respect to this genome reference sequence.</p

Association of the three identified missense SNPs in porcine <i>NR3C1</i> with weight of the left adrenal gland (g) in three different commercial populations.

1<p>LR-German Landrace, PiF1-(Pietrain × (German Large White × German Landrace), LW-German Large White.</p>2<p>Least-squares means (LSM) with different superscripts ^A,B,C differ significantly at p≤0.01.</p>3<p>Allele substitution effect in fractions of phenotypic standard deviation.</p>4<p>Phenotypic variance in percent explained by the SNP.</p

Manhattan plots of genome-wide association studies for EBVs of commercially important traits in pigs.

<p>The red lines indicate the significance threshold for moderately significant associations (p = 5×10⁻⁵). “Chromosome 0” harbors SNP markers that have not yet been mapped to the pig reference genome. The inserted quantile-quantile (QQ) plots show the observed versus expected log p-values. The straight line in the QQ plots indicates the distribution of SNP markers under the null hypothesis and the skew at the right edge indicate that these markers are stronger associated with the traits than it would be expected by chance. Please note that in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055951#pone-0055951-g001" target="_blank">Figure 1A</a> there are appear to be associated SNPs on SSC 3, 11, and 14. The two associated SNPs on SSC 3 and 11 mapped to these chromosomes in the Sscrofa 9.2 assembly, but are no longer placed on any chromosome in the Sscrofa 10.2 assembly.</p

Manhattan plot of the genome-wide association analysis of plasma cortisol levels (A) and adrenal weight (B).

<p>The red line indicates the significance threshold corresponding to a genome-wide false discovery rate q-value ≤0.05.</p

Top 20 canonical pathways within the first 24 h of immune response after the first vaccination.

<p>1 Cellular Immune Response.</p><p>2 Cytokine Signaling.</p><p>3 Pathogen-Influenced Signaling.</p><p>4 Cellular Growth, Proliferation and Development.</p><p>5 Intracellular and Second Messenger Signaling.</p><p>6 Nuclear Receptor Signaling.</p><p>7 Cell Cycle Regulation.</p><p>8 Cellular Stress and Injury.</p><p>9 Organismal Growth and Development.</p><p>10 Growth Factor Signaling.</p><p>11 Neurotransmitters and Other Nervous System Signaling.</p><p>12 Cardiovascular Signaling.</p><p>13 Ingenuity Toxicity List Pathways.</p><p>n.s. not significant.</p

The p.Ala610Val substitution increases sensitivity of porcine GR to glucocorticoids <i>in vitro</i>.

<p>Transcriptional activity of the two GR-alpha variants was investigated in COS-7 cells cotransfected with the pGL4.36 reporter construct expressing firefly luciferase under the control of the glucocorticoid-inducible mouse mammary tumor virus promoter after induction with dexamethasone at the indicated concentrations. (A) Fold induction of normalized luciferase expression in dexamethasone- vs. vehicle-treated cells. Significant differences (p<0.05) are indicated by an asterisk; (B) Estimated dose-response curve and EC50. Data are means ± SEM of four separate experiments performed in triplicate.</p

Experimental Design.

<p>Animals were vaccinated twice with TT. Directly before (0), as well as 2, 4, 8, 24 and 75 hours after each vaccination blood samples were collected. A final blood sample was taken at day 28. Pairwise comparisons of the reference time 0 hours against each following sampling time point were set up for the identification of DE-genes. * reference time point.</p

Primer sequences used for quantitative real-time PCR.

*<p>reference genes used for normalization.</p