Abstract
BackgroundNearly 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 FindingsWe utilized a whole genome expression microarray and an F2 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/SignificanceResults of this analysis provide novel candidate genes for important complex pig phenotypes.
Highlights
Integration of transcriptional profiling with genotyping data in segregating populations allows linkage mapping of expression quantitative trait loci [1,2]
Genetical genomics studies in livestock have concentrated on experimental design and modeling issues [5,6,7,8], on the analysis of selected transcripts [9] or on the comparative transcriptional profiling of genetically diverging lines [6,10], and only recently has a global analysis been published for pigs [11]
This group has recently performed an expression QTL (eQTL) analysis for longissimus dorsi transcripts and their association with meat quality traits [11], and they have identified over 9,000 eQTL at a suggestive significance threshold of LOD
Summary
Integration of transcriptional profiling with genotyping data in segregating populations allows linkage mapping of expression quantitative trait loci (eQTL) [1,2]. Results were derived from a series of pre-selected transcripts based on phenotypic correlations with a trait of interest. This group has recently performed an eQTL analysis for longissimus dorsi transcripts and their association with meat quality traits [11], and they have identified over 9,000 eQTL at a suggestive significance threshold of LOD .2. 6,000 QTL have been reported for 588 different traits in pigs, more than in any other livestock species 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
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