Segregation of regulatory polymorphisms with effects on the gluteus medius transcriptome in a purebred pig population.

<h4>Background</h4>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 F(2) crosses to detect porcine expression QTL (eQTL), so they contributed...

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Autores principales:	Angela Cánovas, Ramona N Pena, David Gallardo, Oscar Ramírez, Marcel Amills, Raquel Quintanilla
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Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e5fb5eea83bb4ef1bf5bb49c317f6d48
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spelling	oai:doaj.org-article:e5fb5eea83bb4ef1bf5bb49c317f6d482021-11-18T07:21:08ZSegregation of regulatory polymorphisms with effects on the gluteus medius transcriptome in a purebred pig population.1932-620310.1371/journal.pone.0035583https://doaj.org/article/e5fb5eea83bb4ef1bf5bb49c317f6d482012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22545120/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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 F(2) 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.<h4>Methodology/principal findings</h4>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.<h4>Conclusions/significance</h4>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.Angela CánovasRamona N PenaDavid GallardoOscar RamírezMarcel AmillsRaquel QuintanillaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 4, p e35583 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Angela Cánovas Ramona N Pena David Gallardo Oscar Ramírez Marcel Amills Raquel Quintanilla Segregation of regulatory polymorphisms with effects on the gluteus medius transcriptome in a purebred pig population.
description	<h4>Background</h4>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 F(2) 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.<h4>Methodology/principal findings</h4>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.<h4>Conclusions/significance</h4>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.
format	article
author	Angela Cánovas Ramona N Pena David Gallardo Oscar Ramírez Marcel Amills Raquel Quintanilla
author_facet	Angela Cánovas Ramona N Pena David Gallardo Oscar Ramírez Marcel Amills Raquel Quintanilla
author_sort	Angela Cánovas
title	Segregation of regulatory polymorphisms with effects on the gluteus medius transcriptome in a purebred pig population.
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.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/e5fb5eea83bb4ef1bf5bb49c317f6d48
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Segregation of regulatory polymorphisms with effects on the gluteus medius transcriptome in a purebred pig population.

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