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 tiss...
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BMC
2019-06-01
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Series: | BMC Genomics |
Online Access: | http://link.springer.com/article/10.1186/s12864-019-5889-5 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Rayner González-Prendes Emilio Mármol-Sánchez Raquel Quintanilla Anna Castelló Ali Zidi Yuliaxis Ramayo-Caldas Tainã Figueiredo Cardoso Arianna Manunza Ángela Cánovas Marcel Amills |
spellingShingle |
Rayner González-Prendes Emilio Mármol-Sánchez Raquel Quintanilla Anna Castelló Ali Zidi Yuliaxis Ramayo-Caldas Tainã Figueiredo Cardoso Arianna Manunza Ángela Cánovas Marcel Amills About the existence of common determinants of gene expression in the porcine liver and skeletal muscle BMC Genomics |
author_facet |
Rayner González-Prendes Emilio Mármol-Sánchez Raquel Quintanilla Anna Castelló Ali Zidi Yuliaxis Ramayo-Caldas Tainã Figueiredo Cardoso Arianna Manunza Ángela Cánovas Marcel Amills |
author_sort |
Rayner González-Prendes |
title |
About the existence of common determinants of gene expression in the porcine liver and skeletal muscle |
title_short |
About the existence of common determinants of gene expression in the porcine liver and skeletal muscle |
title_full |
About the existence of common determinants of gene expression in the porcine liver and skeletal muscle |
title_fullStr |
About the existence of common determinants of gene expression in the porcine liver and skeletal muscle |
title_full_unstemmed |
About the existence of common determinants of gene expression in the porcine liver and skeletal muscle |
title_sort |
about the existence of common determinants of gene expression in the porcine liver and skeletal muscle |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2019-06-01 |
description |
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. |
url |
http://link.springer.com/article/10.1186/s12864-019-5889-5 |
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doaj-11eb7c628ea64395aa7d928c231b550a2020-11-25T03:47:20ZengBMCBMC Genomics1471-21642019-06-0120111510.1186/s12864-019-5889-5About the existence of common determinants of gene expression in the porcine liver and skeletal muscleRayner González-Prendes0Emilio Mármol-Sánchez1Raquel Quintanilla2Anna Castelló3Ali Zidi4Yuliaxis Ramayo-Caldas5Tainã Figueiredo Cardoso6Arianna Manunza7Ángela Cánovas8Marcel Amills9Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaAnimal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre MarimonDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaAbstract 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.http://link.springer.com/article/10.1186/s12864-019-5889-5 |