Abstract
BackgroundThe genetics of transcript-level variation is an exciting field that has recently given rise to many studies. Genetical genomics studies have mainly focused on cell lines, blood cells or adipose tissues, from human clinical samples or mice inbred lines. Few eQTL studies have focused on animal tissues sampled from outbred populations to reflect natural genetic variation of gene expression levels in animals. In this work, we analyzed gene expression in a whole tissue, pig skeletal muscle sampled from individuals from a half sib F2 family shortly after slaughtering.ResultsQTL detection on transcriptome measurements was performed on a family structured population. The analysis identified 335 eQTLs affecting the expression of 272 transcripts. The ontologic annotation of these eQTLs revealed an over-representation of genes encoding proteins involved in processes that are expected to be induced during muscle development and metabolism, cell morphology, assembly and organization and also in stress response and apoptosis. A gene functional network approach was used to evidence existing biological relationships between all the genes whose expression levels are influenced by eQTLs. eQTLs localization revealed a significant clustered organization of about half the genes located on segments of chromosome 1, 2, 10, 13, 16, and 18. Finally, the combined expression and genetic approaches pointed to putative cis-drivers of gene expression programs in skeletal muscle as COQ4 (SSC1), LOC100513192 (SSC18) where both the gene transcription unit and the eQTL affecting its expression level were shown to be localized in the same genomic region. This suggests cis-causing genetic polymorphims affecting gene expression levels, with (e.g. COQ4) or without (e.g. LOC100513192) potential pleiotropic effects that affect the expression of other genes (cluster of trans-eQTLs).ConclusionGenetic analysis of transcription levels revealed dependence among molecular phenotypes as being affected by variation at the same loci. We observed the genetic variation of molecular phenotypes in a specific situation of cellular stress thus contributing to a better description of muscle physiologic response. In turn, this suggests that large amounts of genetic variation, mediated through transcriptional networks, can drive transient cell response phenotypes and contribute to organismal adaptative potential.
Highlights
The genetics of transcript-level variation is an exciting field that has recently given rise to many studies
We observed the genetic variation of molecular phenotypes in a specific situation of cellular stress contributing to a better description of muscle physiologic response
The expression levels of 272 genes are genetically regulated by one to four expression QTLs (eQTLs) Using a cDNA microarray, we measured the expression levels for 2,454 transcripts in 57 Longissimus lumborum samples collected on pig carcasses 20 minutes after stuning and exsanguination
Summary
The genetics of transcript-level variation is an exciting field that has recently given rise to many studies. Few eQTL studies have focused on animal tissues sampled from outbred populations to reflect natural genetic variation of gene expression levels in animals. The identification of expression QTLs (eQTLs) should help to characterize the primary effects of genetic variation and provide opportunities to understand the molecular processes that are affected by this variation. Changes in gene regulation have been found to underlie adaptative phenotypes in different species [3,4] For all these reasons, eQTL mapping studies is a new powerful tool to identify genetic variants that regulate gene expression [5,6,7,8,9]. Transcriptome analysis using microarrays measures the expression level, the phenotype in eQTL analysis, of many genes, and segregation of genetic markers within families allows mapping of the loci affecting those phenotypes to specific genomic regions. Global eQTL analyses have enabled detection of cis genetic variation controlling individual genes and significant clustered trans eQTLs that regulate group of genes [10]
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