Differences in muscle transcriptome among pigs phenotypically extreme for fatty acid composition.
Identifieur interne : 003620 ( PubMed/Curation ); précédent : 003619; suivant : 003621Differences in muscle transcriptome among pigs phenotypically extreme for fatty acid composition.
Auteurs : Anna Puig-Oliveras [Espagne] ; Yuliaxis Ramayo-Caldas [France] ; Jordi Corominas [Espagne] ; Jordi Estellé [France] ; Dafne Pérez-Montarelo [Espagne] ; Nicholas J. Hudson [Australie] ; Joaquim Casellas [Espagne] ; Josep M. Folch [Espagne] ; Maria BallesterSource :
- PloS one [ 1932-6203 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Transcriptome.
- métabolisme : Acides gras, Muscles squelettiques.
- Analyse de profil d'expression de gènes, Animaux, Femelle, Suidae, Sus scrofa.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Fatty Acids.
- genetics : Transcriptome.
- metabolism : Muscle, Skeletal.
- Animals, Female, Gene Expression Profiling, Sus scrofa, Swine.
Abstract
Besides having an impact on human health, the porcine muscle fatty acid profile determines meat quality and taste. The RNA-Seq technologies allowed us to explore the pig muscle transcriptome with an unprecedented detail. The aim of this study was to identify differentially-expressed genes between two groups of 6 sows belonging to an Iberian × Landrace backcross with extreme phenotypes according to FA profile.
DOI: 10.1371/journal.pone.0099720
PubMed: 24926690
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Folch</name><affiliation wicri:level="1"><nlm:affiliation>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra</wicri:regionArea></affiliation></author><author><name sortKey="Ballester, Maria" sort="Ballester, Maria" uniqKey="Ballester M" first="Maria" last="Ballester">Maria Ballester</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24926690</idno><idno type="pmid">24926690</idno><idno type="doi">10.1371/journal.pone.0099720</idno><idno type="wicri:Area/PubMed/Corpus">003734</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">003734</idno><idno type="wicri:Area/PubMed/Curation">003620</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">003620</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Differences in muscle transcriptome among pigs phenotypically extreme for fatty acid composition.</title><author><name sortKey="Puig Oliveras, Anna" sort="Puig Oliveras, Anna" uniqKey="Puig Oliveras A" first="Anna" last="Puig-Oliveras">Anna Puig-Oliveras</name><affiliation wicri:level="1"><nlm:affiliation>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra</wicri:regionArea></affiliation></author><author><name sortKey="Ramayo Caldas, Yuliaxis" sort="Ramayo Caldas, Yuliaxis" uniqKey="Ramayo Caldas Y" first="Yuliaxis" last="Ramayo-Caldas">Yuliaxis Ramayo-Caldas</name><affiliation wicri:level="1"><nlm:affiliation>Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas</wicri:regionArea></affiliation></author><author><name sortKey="Corominas, Jordi" sort="Corominas, Jordi" uniqKey="Corominas J" first="Jordi" last="Corominas">Jordi Corominas</name><affiliation wicri:level="1"><nlm:affiliation>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra</wicri:regionArea></affiliation></author><author><name sortKey="Estelle, Jordi" sort="Estelle, Jordi" uniqKey="Estelle J" first="Jordi" last="Estellé">Jordi Estellé</name><affiliation wicri:level="1"><nlm:affiliation>Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France; Génétique Animale et Biologie Intégrative UMR1313 (GABI), AgroParisTech, Jouy-en-Josas, France; Laboratoire de Radiobiologie et Etude du Génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Jouy-en-Josas, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France; Génétique Animale et Biologie Intégrative UMR1313 (GABI), AgroParisTech, Jouy-en-Josas, France; Laboratoire de Radiobiologie et Etude du Génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Jouy-en-Josas</wicri:regionArea></affiliation></author><author><name sortKey="Perez Montarelo, Dafne" sort="Perez Montarelo, Dafne" uniqKey="Perez Montarelo D" first="Dafne" last="Pérez-Montarelo">Dafne Pérez-Montarelo</name><affiliation wicri:level="1"><nlm:affiliation>Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid</wicri:regionArea></affiliation></author><author><name sortKey="Hudson, Nicholas J" sort="Hudson, Nicholas J" uniqKey="Hudson N" first="Nicholas J" last="Hudson">Nicholas J. Hudson</name><affiliation wicri:level="1"><nlm:affiliation>Computational and Systems Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Animal, Food and Health SciencesQLD, Brisbane, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Computational and Systems Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Animal, Food and Health SciencesQLD, Brisbane</wicri:regionArea></affiliation></author><author><name sortKey="Casellas, Joaquim" sort="Casellas, Joaquim" uniqKey="Casellas J" first="Joaquim" last="Casellas">Joaquim Casellas</name><affiliation wicri:level="1"><nlm:affiliation>Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain; Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologies Agroalimentàries (IRTA), Lleida, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain; Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologies Agroalimentàries (IRTA), Lleida</wicri:regionArea></affiliation></author><author><name sortKey="Folch, Josep M" sort="Folch, Josep M" uniqKey="Folch J" first="Josep M" last="Folch">Josep M. Folch</name><affiliation wicri:level="1"><nlm:affiliation>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra</wicri:regionArea></affiliation></author><author><name sortKey="Ballester, Maria" sort="Ballester, Maria" uniqKey="Ballester M" first="Maria" last="Ballester">Maria Ballester</name></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Fatty Acids (metabolism)</term><term>Female</term><term>Gene Expression Profiling</term><term>Muscle, Skeletal (metabolism)</term><term>Sus scrofa</term><term>Swine</term><term>Transcriptome (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Acides gras (métabolisme)</term><term>Analyse de profil d'expression de gènes</term><term>Animaux</term><term>Femelle</term><term>Muscles squelettiques (métabolisme)</term><term>Suidae</term><term>Sus scrofa</term><term>Transcriptome (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Fatty Acids</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Transcriptome</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Transcriptome</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Muscle, Skeletal</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Acides gras</term><term>Muscles squelettiques</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Female</term><term>Gene Expression Profiling</term><term>Sus scrofa</term><term>Swine</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Animaux</term><term>Femelle</term><term>Suidae</term><term>Sus scrofa</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Besides having an impact on human health, the porcine muscle fatty acid profile determines meat quality and taste. The RNA-Seq technologies allowed us to explore the pig muscle transcriptome with an unprecedented detail. The aim of this study was to identify differentially-expressed genes between two groups of 6 sows belonging to an Iberian × Landrace backcross with extreme phenotypes according to FA profile.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24926690</PMID><DateCreated><Year>2014</Year><Month>06</Month><Day>14</Day></DateCreated><DateCompleted><Year>2015</Year><Month>05</Month><Day>11</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>6</Issue><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS ONE</ISOAbbreviation></Journal><ArticleTitle>Differences in muscle transcriptome among pigs phenotypically extreme for fatty acid composition.</ArticleTitle><Pagination><MedlinePgn>e99720</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0099720</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Besides having an impact on human health, the porcine muscle fatty acid profile determines meat quality and taste. The RNA-Seq technologies allowed us to explore the pig muscle transcriptome with an unprecedented detail. The aim of this study was to identify differentially-expressed genes between two groups of 6 sows belonging to an Iberian × Landrace backcross with extreme phenotypes according to FA profile.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We sequenced the muscle transcriptome acquiring 787.5 M of 75 bp paired-end reads. About 85.1% of reads were mapped to the reference genome. Of the total reads, 79.1% were located in exons, 6.0% in introns and 14.9% in intergenic regions, indicating expressed regions not annotated in the reference genome. We identified a 34.5% of the intergenic regions as interspersed repetitive regions. We predicted a total of 2,372 putative proteins. Pathway analysis with 131 differentially-expressed genes revealed that the most statistically-significant metabolic pathways were related with lipid metabolism. Moreover, 18 of the differentially-expressed genes were located in genomic regions associated with IMF composition in an independent GWAS study in the same genetic background. Thus, our results indicate that the lipid metabolism of FAs is differently modulated when the FA composition in muscle differs. For instance, a high content of PUFA may reduce FA and glucose uptake resulting in an inhibition of the lipogenesis. These results are consistent with previous studies of our group analysing the liver and the adipose tissue transcriptomes providing a view of each of the main organs involved in lipid metabolism.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The results obtained in the muscle transcriptome analysis increase the knowledge of the gene regulation of IMF deposition, FA profile and meat quality, in terms of taste and nutritional value. Besides, our results may be important in terms of human health.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Puig-Oliveras</LastName><ForeName>Anna</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ramayo-Caldas</LastName><ForeName>Yuliaxis</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Corominas</LastName><ForeName>Jordi</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Estellé</LastName><ForeName>Jordi</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France; Génétique Animale et Biologie Intégrative UMR1313 (GABI), AgroParisTech, Jouy-en-Josas, France; Laboratoire de Radiobiologie et Etude du Génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Jouy-en-Josas, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pérez-Montarelo</LastName><ForeName>Dafne</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hudson</LastName><ForeName>Nicholas J</ForeName><Initials>NJ</Initials><AffiliationInfo><Affiliation>Computational and Systems Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Animal, Food and Health SciencesQLD, Brisbane, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Casellas</LastName><ForeName>Joaquim</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain; Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologies Agroalimentàries (IRTA), Lleida, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Folch</LastName><ForeName>Josep M</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ballester</LastName><ForeName>Maria</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>SRA</DataBankName><AccessionNumberList><AccessionNumber>SRP039424</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>06</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005227">Fatty Acids</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>PLoS One. 2014 Jul;9(7):e103668</RefSource></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Genomics. 2013;14:453</RefSource><PMID Version="1">23829541</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Comp Biochem Physiol Part D Genomics Proteomics. 2007 Sep;2(3):200-6</RefSource><PMID Version="1">20483293</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Biochim Biophys Acta. 2007 Feb;1771(2):210-27</RefSource><PMID Version="1">17234449</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2008 Mar 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