Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs

Abstract

Background: Nearly 6,000 QTL have been reported for 588 different traits in pigs, more than in any other livestock species. However, this effort has translated into only a few confirmed causative variants. A powerful strategy for revealing candidate genes involves expression QTL (eQTL) mapping, where the mRNA abundance of a set of transcripts is used as the response variable for a QTL scan.

Methodology/principal findings: We utilized a whole genome expression microarray and an F(2) pig resource population to conduct a global eQTL analysis in loin muscle tissue, and compared results to previously inferred phenotypic QTL (pQTL) from the same experimental cross. We found 62 unique eQTL (FDR <10%) and identified 3 gene networks enriched with genes subject to genetic control involved in lipid metabolism, DNA replication, and cell cycle regulation. We observed strong evidence of local regulation (40 out of 59 eQTL with known genomic position) and compared these eQTL to pQTL to help identify potential candidate genes. Among the interesting associations, we found aldo-keto reductase 7A2 (AKR7A2) and thioredoxin domain containing 12 (TXNDC12) eQTL that are part of a network associated with lipid metabolism and in turn overlap with pQTL regions for marbling, % intramuscular fat (% fat) and loin muscle area on Sus scrofa (SSC) chromosome 6. Additionally, we report 13 genomic regions with overlapping eQTL and pQTL involving 14 local eQTL.

Conclusions/significance: Results of this analysis provide novel candidate genes for important complex pig phenotypes.

Figure 1. Histogram of oligonucleotide and gene densities across chromosomes.

Green bars pointing up represent the distribution of oligonucleotides on the microarray. Blue bars pointing down represent the distribution of genes in the pig genome assembly (Build 9, www.ensembl.org). The bar width is proportional to chromosome length in base pairs, the height of the bar is proportional to the feature density, and the area of the bar is proportional to the feature count. Counts next to each bar represent oligonucleotide (green bars) and gene counts (blue bars).

Figure 2. Quantile-quantile plot of p-values.

Each point represents the p-value (log-scale) from a test. Expected values are plotted on the horizontal axis and observed values are plotted on the vertical axis. The expected distribution under the null hypothesis is represented by the diagonal red line. An excess of small p-values is observed compared to the null model represented by the red line.

Figure 3. Global plot of physical position of oligonucleotide probe versus linkage position of eQTL across the pig genome.

Points along the gray curve represent local eQTL (most likely cis-acting), while points off the line represent trans-acting eQTL. Colors represent increasing significance from yellow to green to blue to indigo.

Figure 4. Number of putative eQTL per genomic position (p<0.0001).

Vertical dotted lines represent the chromosome limits in the linkage map. The horizontal line indicates the expected number of significant eQTL under the null hypothesis (of no linkage). The number of putative eQTL rises above the threshold in only two hotspots. This indicates that despite finding strong evidence of eQTL, our study does not show evidence of the presence of hotspots.