About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

BackgroundThe comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we have compared the transcriptomic and eQTL profiles of two porcine tissues (skeletal muscle and liver) with highly divergent expression profiles by using a data set of 103 Duroc pigs genotyped with the Porcine SNP60 BeadChip (Illumina) and with available microarray measurements of hepatic and muscle mRNA levels. Since structural variation could have effects on gene expression, we have also investigated the co-localization of cis-eQTL with copy number variant regions (CNVR) segregating in the Duroc population under study. ResultsThe analysis of differential expresssion revealed the existence of 1,204 and 1,490 probes that were overexpressed and underexpressed in the gluteus medius muscle when compared to liver, respectively (|fold-change| > 1.5, q-value ConclusionDespite the fact that there are considerable differences in the gene expression patterns of the porcine liver and skeletal muscle, we have identified a substantial proportion of common cis-eQTL regulating gene expression in both tissues. Several of these cis-eQTL influence the mRNA levels of genes with important roles in meat (CTSF) and carcass quality (TAPT1), lipid metabolism (TMEM97) and obesity (MARC2), thus evidencing the practical importance of dissecting the genetic mechanisms involved in their expression.