Candidate <i>cis</i>-acting eQTLs for gene-based selection.

<p>Candidate <i>cis</i>-acting eQTLs for gene-based selection.</p

Candidate eQTLs for selection.

<p>The left Y-axis indicates summarised estimated breeding values (EBVs) for skatole and human nose score. The right Y-axis indicates the mean normalised expression levels where liver is symbolised with a square and testis is symbolised by a triangle. Due to filtering of low gene counts, some eQTLs only have expression levels from one tissue presented. The X-axis indicates the three possible genotypes of each eQTL. The title indicates the rs code of SNP and gene name associated with the eQTL. Red box indicates upregulation and blue box indicates downregulation of the eQTL at each genotype. A green barplot indicates candidate genotypes for gene-based selection, defined as genotypes with a median of summarised EBV equal or lower than the maximum summarised EBV of the low boar taint pigs.</p

Functional characterisation and pathway analysis of the filtered <i>cis</i>-acting eQTLs.

<p>Filtered <i>cis</i>-acting eQTLs with expression data (a) liver and (b) testis were subjected to functional characterisation and pathway analysis. Functional characterisation is represented by gene ontology (GO) terms and pathways are represented by their Kyoto Encyclopedia Genes and Genomes (KEGG) pathways. Each function/pathway is visualised by a uniquely coloured symbol. Each gene is represented by a circle where the colour in the centre indicates the function of the gene from the corresponding GO term. The diameter of the circle is negatively correlated with the adjusted <i>P</i> value (FDR) of the GO term from the functional enrichment test made by ClueGO software. Each node represents a gene where the expression levels are indicated in the circle where the green group (left side) represents the expression level in low boar taint pigs and the red group (right side) represents the expression level in high boar taint pigs. <i>Ellipse symbol</i>: Biological process; <i>hexagon symbol</i>: cellular component; <i>octagon symbol</i>: molecular function; <i>parallelogram</i>: KEGG pathway.</p

Top 30 enriched QTL traits from the filtered <i>cis</i>-acting eQTLs of liver and testis.

<p>Top 30 enriched QTL traits from the filtered <i>cis</i>-acting eQTLs of liver and testis.</p

Correlations analysis between expression levels of multi-tissue eQTLs.

<p>To identify co-expression patterns between multi-tissue eQTLs, correlations of expression levels of genes associated with multi-tissue eQTLs was analysed by Spearman rank correlation analysis. Correlations were calculated from expression data from both liver and testis. Edges indicating correlation are shown for both liver and testis expression data. Green circles indicate filtered multi-tissue eQTLs with significant association to summarised EBVs for skatole and HNS. The two types of correlations are discerned by both colour and shape. Positive correlations between expression levels are indicated with dashed red line. Negative correlations between expression levels are indicated by a dashed green line. Boldness of lines indicates the degree of correlation. Only edges representing Spearman rank correlations above R² > 0.5 or below R² < -0.5 are shown.</p