Global GO enrichment analysis performed with DAVID software on the list of eQTL-regulated genes.

<p>(A) List of most significant GO terms represented in the biological process category (<i>P<</i>0.01). (B) List of most significant GO terms represented in the molecular function category (<i>P<</i>0.01).</p

Correlation coefficients (r) between muscle mRNA expression of several <i>cis-</i> and <i>trans-</i> regulated genes and intramuscular fat content, fatty acid profile and cholesterol content of the <i>gluteus medius</i> muscle.

1<p>IMF – intramuscular fat content; FA – Fatty Acid content (%).</p>2<p>Significant correlation coefficients are indicated in bold.</p

Porcine genomic regions with eQTL regulating more than four genes (eQTL hotspots).

<p>Porcine genomic regions with eQTL regulating more than four genes (eQTL hotspots).</p

List of genes regulated by each one of the 11 <i>trans-</i>regulatory hotspots regions.

<p>List of genes regulated by each one of the 11 <i>trans-</i>regulatory hotspots regions.</p

DAVID analysis of pathways significantly enriched in the list of <i>cis-</i> and <i>trans-</i>regulated genes.

<p>In bold, pathways related to lipid and muscle metabolism and fat deposition.</p

Genome-wide significant <i>trans-</i>eQTL for <i>gluteus medius</i> expression traits whose target genes are functionally related to lipid metabolism and fat deposition.

1<p>Positional genes fitting in the confidence interval of the eQTL are indicated.</p>2<p>IMF – intramuscular fat content; FA – Fatty Acid content (%); SFA – % saturated fatty acids.</p

Distribution of genome-wide expression QTL amongst pig chromosomes.

<p>(A) Total number of eQTL and (B) <i>cis-</i>acting (▪) and <i>trans-</i>acting (▴) eQTL.</p

Distribution of high and low quality porcine <i>Affymetrix</i> probes (and corresponding number of genes) regulated by either <i>cis-</i> or <i>trans-</i>acting eQTL.

<p>Distribution of high and low quality porcine <i>Affymetrix</i> probes (and corresponding number of genes) regulated by either <i>cis-</i> or <i>trans-</i>acting eQTL.</p

Genome-wide significant <i>cis-</i>eQTL for <i>gluteus medius</i> expression traits whose target genes are functionally related to lipid metabolism and fat deposition.

1<p>IMF – intramuscular fat content; FA – Fatty Acid content (%); SFA – % saturated fatty acids; MUFA – % monounsaturated fatty acids; PUFA – % polyunsaturated fatty acids.</p

Summary of single marker analyses in relation to atherosclerotic plaque presence.

<p>*maf: minor allele frequency/Aff: Affected/Unaff: Unaffected</p><p>**Adjusted by clinical variables: Age, Abdominal Obesity, Metabolic Syndrome, Hypertension, Diabetes, Dyslipidemia and Antiretroviral Therapy</p><p>Summary of single marker analyses in relation to atherosclerotic plaque presence.</p