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

Abstract

Background The 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) which typically show highly divergent expression profiles, in 103 Duroc pigs genotyped with the Porcine SNP60 BeadChip (Illumina) and with available microarray-based 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- eQTLs with copy number variant regions (CNVR) segregating in this Duroc population. Results The analysis of differential expresssion revealed the existence of 1204 and 1490 probes that were overexpressed and underexpressed in the gluteus medius muscle when compared to liver, respectively (|fold-change| > 1.5, q-value < 0.05). By performing genome scans in 103 Duroc pigs with available expression and genotypic data, we identified 76 and 28 genome-wide significant cis- eQTLs regulating gene expression in the gluteus medius muscle and liver, respectively. Twelve of these cis -eQTLs were shared by both tissues (i.e. 42.8% of the cis- eQTLs identified in the liver were replicated in the gluteus medius muscle). These results are consistent with previous studies performed in humans, where 50% of eQTLs were shared across tissues. Moreover, we have identified 41 CNVRs in a set of 350 pigs from the same Duroc population, which had been genotyped with the Porcine SNP60 BeadChip by using the PennCNV and GADA softwares, but only a small proportion of these CNVRs co-localized with the cis -eQTL signals. Conclusion Despite 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- eQTLs regulating gene expression in both tissues. Several of these cis -eQTLs 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. Electronic supplementary material The online version of this article (10.1186/s12864-019-5889-5) contains supplementary material, which is available to authorized users.

Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits

“…In humans, significant commonalities of sQTL between tissues and of geQTL between tissues were reported [ 57 , 58 ]. Recent studies have suggested that, in cattle, three types of eQTL (sQTL, eeQTL and geQTL) were shared between tissues [ 12 ] and that, in pig, geQTL were extensively shared between liver and muscle [ 59 ]. Our results support the extensive sharing of all eQTL types between liver and muscle, but disagree with other studies [ 47 , 60 ].…”

Expression Quantitative Trait Loci in Equine Skeletal Muscle Reveals Heritable Variation in Metabolism and the Training Responsive Transcriptome

“…We have for the first time systematically catalogued eQTL in equine skeletal muscle, both at rest and post-exercise. Previous investigations of eQTL in skeletal muscle have focussed primarily on human T2D (Sharma et al, 2011; Keildson et al, 2014a; Sajuthi et al, 2016; Langefeld et al, 2018) and meat quality traits in production animals (Ponsuksili et al, 2015; Gonzalez-Prendes et al, 2017; Pampouille et al, 2018; Gonzalez-Prendes et al, 2019; Velez-Irizarry et al, 2019). Our investigation of eQTL in the context of skeletal muscle and exercise present some of the only work to-date in this area (Kelly et al, 2014).…”

Identification of expression quantitative trait loci in the skeletal muscle of Thoroughbreds reveals heritable variation in expression of genes relevant to cofactor metabolism

“…We have for the first time systematically catalogued eQTL in equine skeletal muscle, both at rest and post-exercise. Previous investigations of eQTL in skeletal muscle have focussed primarily on human T2D (Sharma et al, 2011; Keildson et al, 2014a; Sajuthi et al, 2016a; Langefeld et al, 2018)and meat quality traits in production animals (Ponsuksili et al, 2015; Gonzalez-Prendes et al, 2017; Pampouille et al, 2018; Gonzalez-Prendes et al, 2019; Velez-Irizarry et al, 2019). Our investigation of eQTL in the context of skeletal muscle and exercise present some of the only work to-date in this area (Kelly et al, 2014).…”