Segregation of Regulatory Polymorphisms with Effects on the Gluteus Medius Transcriptome in a Purebred Pig Population

Background: The 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...

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Autores: Cánovas, Angela, Pena, Romi, Gallardo, David, Ramırez, Oscar, Amills, Marcel, Quintanilla, Raquel
Tipo de recurso: artículo
Fecha de publicación:2012
País:España
Institución:Institut de Recerca i Tecnologia Agroalimentàries (IRTA)
Repositorio:IRTA Pubpro. Open Digital Archive
OAI Identifier:oai:repositori.irta.cat:20.500.12327/2910
Acceso en línea:http://hdl.handle.net/20.500.12327/2910
https://doi.org/10.1371/journal.pone.0035583
Access Level:acceso abierto
Palabra clave:575
636
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spelling Segregation of Regulatory Polymorphisms with Effects on the Gluteus Medius Transcriptome in a Purebred Pig PopulationCánovas, AngelaPena, RomiGallardo, DavidRamırez, OscarAmills, MarcelQuintanilla, Raquel575636Background: The 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/Significance: Our 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.This project has been funded by the Spanish Ministry of Science (projects GEN2003-20658-C05-05, AGL2007-66707-C02-01 and AGL2010-22208-C02- 01). AC received a predoctoral scholarship from INIA (Instituto Nacional de Investigacio ´ n y Tecnologı ´a Agraria y Alimentaria). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.info:eu-repo/semantics/publishedVersionPublic Library of ScienceProducció AnimalGenètica i Millora Animal202420242012info:eu-repo/semantics/article12application/pdfhttp://hdl.handle.net/20.500.12327/2910https://doi.org/10.1371/journal.pone.0035583reponame:IRTA Pubpro. Open Digital Archiveinstname:Institut de Recerca i Tecnologia Agroalimentàries (IRTA)InglésPLoS ONEMICYT//GEN2003-20658-C05-05/ES/Análisis genómico mediante microarrays de la arquitectura genética de fenotipos complejos en porcino/MEC/ /AGL2007-66707-C02-01/ES/Mapeo e identificación de genes implicados en el metabolismo lipídico en porcino, la calidad de la carne y la calidad del jamón curado/MICINN/Programa Nacional de Proyectos de Investigación Fundamental/AGL2010-22208-C02-01/ES/Utilización de aceites ácidos esterificados en la alimentación de animales monogástricos. Nutrición comparada y repercusiones sobre la calidad lipídica de la carne/ESTERIFATSAttribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.irta.cat:20.500.12327/29102026-06-16T08:51:17Z
dc.title.none.fl_str_mv Segregation of Regulatory Polymorphisms with Effects on the Gluteus Medius Transcriptome in a Purebred Pig Population
title Segregation of Regulatory Polymorphisms with Effects on the Gluteus Medius Transcriptome in a Purebred Pig Population
spellingShingle Segregation of Regulatory Polymorphisms with Effects on the Gluteus Medius Transcriptome in a Purebred Pig Population
Cánovas, Angela
575
636
title_short Segregation of Regulatory Polymorphisms with Effects on the Gluteus Medius Transcriptome in a Purebred Pig Population
title_full Segregation of Regulatory Polymorphisms with Effects on the Gluteus Medius Transcriptome in a Purebred Pig Population
title_fullStr Segregation of Regulatory Polymorphisms with Effects on the Gluteus Medius Transcriptome in a Purebred Pig Population
title_full_unstemmed Segregation of Regulatory Polymorphisms with Effects on the Gluteus Medius Transcriptome in a Purebred Pig Population
title_sort Segregation of Regulatory Polymorphisms with Effects on the Gluteus Medius Transcriptome in a Purebred Pig Population
dc.creator.none.fl_str_mv Cánovas, Angela
Pena, Romi
Gallardo, David
Ramırez, Oscar
Amills, Marcel
Quintanilla, Raquel
author Cánovas, Angela
author_facet Cánovas, Angela
Pena, Romi
Gallardo, David
Ramırez, Oscar
Amills, Marcel
Quintanilla, Raquel
author_role author
author2 Pena, Romi
Gallardo, David
Ramırez, Oscar
Amills, Marcel
Quintanilla, Raquel
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Producció Animal
Genètica i Millora Animal
dc.subject.none.fl_str_mv 575
636
topic 575
636
description Background: The 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/Significance: Our 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.
publishDate 2012
dc.date.none.fl_str_mv 2012
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12327/2910
https://doi.org/10.1371/journal.pone.0035583
url http://hdl.handle.net/20.500.12327/2910
https://doi.org/10.1371/journal.pone.0035583
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv PLoS ONE
MICYT//GEN2003-20658-C05-05/ES/Análisis genómico mediante microarrays de la arquitectura genética de fenotipos complejos en porcino/
MEC/ /AGL2007-66707-C02-01/ES/Mapeo e identificación de genes implicados en el metabolismo lipídico en porcino, la calidad de la carne y la calidad del jamón curado/
MICINN/Programa Nacional de Proyectos de Investigación Fundamental/AGL2010-22208-C02-01/ES/Utilización de aceites ácidos esterificados en la alimentación de animales monogástricos. Nutrición comparada y repercusiones sobre la calidad lipídica de la carne/ESTERIFATS
dc.rights.none.fl_str_mv Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 12
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
dc.source.none.fl_str_mv reponame:IRTA Pubpro. Open Digital Archive
instname:Institut de Recerca i Tecnologia Agroalimentàries (IRTA)
instname_str Institut de Recerca i Tecnologia Agroalimentàries (IRTA)
reponame_str IRTA Pubpro. Open Digital Archive
collection IRTA Pubpro. Open Digital Archive
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.301629

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