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 Tienda, Angela, Pena i Subirà, Ramona Natacha, Gallardo García, David, Ramírez Bellido, Óscar, Amills i Eras, Marcel, Quintanilla Aguado, Raquel
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2012
País:España
Institución:Universitat de Lleida (UdL)
Repositorio:Repositori Obert UdL
OAI Identifier:oai:repositori.udl.cat:10459.1/46374
Acceso en línea:https://doi.org/10.1371/journal.pone.0035583
http://hdl.handle.net/10459.1/46374
Access Level:acceso abierto
Palabra clave:Porcs -- Genètica
RNA
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spelling Segregation of regulatory polymorphisms with effects on the gluteus medius transcriptome in a purebred pig populationCánovas Tienda, AngelaPena i Subirà, Ramona NatachaGallardo García, DavidRamírez Bellido, ÓscarAmills i Eras, MarcelQuintanilla Aguado, RaquelPorcs -- GenèticaRNABackground: 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.Public Library of Science (PLoS)2012info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://doi.org/10.1371/journal.pone.0035583http://hdl.handle.net/10459.1/46374reponame:Repositori Obert UdL instname:Universitat de Lleida (UdL)InglésReproducció del document publicat a: https://doi.org/10.1371/journal.pone.0035583PLoS ONE, 2012, vol. 7, núm. 4, e35583cc-by, (c) Cánovas et al., 2012info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by/2.5/es/deed.caoai:repositori.udl.cat:10459.1/463742026-06-24T12:42:17Z
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 Tienda, Angela
Porcs -- Genètica
RNA
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 Tienda, Angela
Pena i Subirà, Ramona Natacha
Gallardo García, David
Ramírez Bellido, Óscar
Amills i Eras, Marcel
Quintanilla Aguado, Raquel
author Cánovas Tienda, Angela
author_facet Cánovas Tienda, Angela
Pena i Subirà, Ramona Natacha
Gallardo García, David
Ramírez Bellido, Óscar
Amills i Eras, Marcel
Quintanilla Aguado, Raquel
author_role author
author2 Pena i Subirà, Ramona Natacha
Gallardo García, David
Ramírez Bellido, Óscar
Amills i Eras, Marcel
Quintanilla Aguado, Raquel
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Porcs -- Genètica
RNA
topic Porcs -- Genètica
RNA
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
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://doi.org/10.1371/journal.pone.0035583
http://hdl.handle.net/10459.1/46374
url https://doi.org/10.1371/journal.pone.0035583
http://hdl.handle.net/10459.1/46374
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.1371/journal.pone.0035583
PLoS ONE, 2012, vol. 7, núm. 4, e35583
dc.rights.none.fl_str_mv cc-by, (c) Cánovas et al., 2012
info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by/2.5/es/deed.ca
rights_invalid_str_mv cc-by, (c) Cánovas et al., 2012
http://creativecommons.org/licenses/by/2.5/es/deed.ca
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Public Library of Science (PLoS)
publisher.none.fl_str_mv Public Library of Science (PLoS)
dc.source.none.fl_str_mv reponame:Repositori Obert UdL
instname:Universitat de Lleida (UdL)
instname_str Universitat de Lleida (UdL)
reponame_str Repositori Obert UdL
collection Repositori Obert UdL
repository.name.fl_str_mv
repository.mail.fl_str_mv
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