Abstract
BackgroundThe main goal of the present study was to analyse the genetic architecture of mRNA expression in muscle, a tissue with an outmost economic importance for pig breeders. Previous studies have used F2 crosses to detect porcine expression QTL (eQTL), so they contributed with data that mostly represents the between-breed component of eQTL variation. Herewith, we have analysed eQTL segregation in an outbred Duroc population using two groups of animals with divergent fatness profiles. This approach is particularly suitable to analyse the within-breed component of eQTL variation, with a special emphasis on loci involved in lipid metabolism.Methodology/Principal Findings GeneChip Porcine Genome arrays (Affymetrix) were used to determine the mRNA expression levels of gluteus medius samples from 105 Duroc barrows. A whole-genome eQTL scan was carried out with a panel of 116 microsatellites. Results allowed us to detect 613 genome-wide significant eQTL unevenly distributed across the pig genome. A clear predominance of trans- over cis-eQTL, was observed. Moreover, 11 trans-regulatory hotspots affecting the expression levels of four to 16 genes were identified. A Gene Ontology study showed that regulatory polymorphisms affected the expression of muscle development and lipid metabolism genes. A number of positional concordances between eQTL and lipid trait QTL were also found, whereas limited evidence of a linear relationship between muscle fat deposition and mRNA levels of eQTL regulated genes was obtained.Conclusions/SignificanceOur data provide substantial evidence that there is a remarkable amount of within-breed genetic variation affecting muscle mRNA expression. Most of this variation acts in trans and influences biological processes related with muscle development, lipid deposition and energy balance. The identification of the underlying causal mutations and the ascertainment of their effects on phenotypes would allow gaining a fundamental perspective about how complex traits are built at the molecular level.
Highlights
Expression quantitative trait loci mapping represents a valuable approach towards identifying regulatory regions and DNA sequence variants affecting the expression levels of genes
Genetical genomics studies performed in human have indicated that: (i) expression QTL (eQTL) maps obtained in different cell types are partially concordant [1,2], i.e. often regulatory polymorphisms exert their effects on multiple tissues, and (ii) these maps might differ amongst populations with different genetic backgrounds [3,4], mainly because of differences in the frequency of regulatory alleles rather than in the specific set of mechanisms involved in the fine-tuning of mRNA levels [5]
More controversy exists about the abundance of regulatory hotspots in the human genome, which have been identified in certain studies but not in others, and the relative impact of cis-eQTL vs trans-eQTL on transcriptome variation [5]
Summary
Expression quantitative trait loci (eQTL) mapping represents a valuable approach towards identifying regulatory regions and DNA sequence variants affecting the expression levels of genes. The few eQTL studies performed in pigs [7,8,9,10] are based on the analysis of samples obtained from crossbred individuals (e.g. Duroc x Pietrain and Large White x Landrace). This experimental design is suited to capture the between-breed component of genetic variation. We have analysed eQTL segregation in an outbred Duroc population using two groups of animals with divergent fatness profiles This approach is suitable to analyse the within-breed component of eQTL variation, with a special emphasis on loci involved in lipid metabolism
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