Differences in Muscle Transcriptome among Pigs Phenotypically Extreme for Fatty Acid Composition
Identifieur interne : 002A16 ( Pmc/Curation ); précédent : 002A15; suivant : 002A17Differences 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 Ballester [Espagne]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
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.
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.
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.
Url:
DOI: 10.1371/journal.pone.0099720
PubMed: 24926690
PubMed Central: 4057286
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<author><name sortKey="Perez Montarelo, Dafne" sort="Perez Montarelo, Dafne" uniqKey="Perez Montarelo D" first="Dafne" last="Pérez-Montarelo">Dafne Pérez-Montarelo</name>
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<author><name sortKey="Casellas, Joaquim" sort="Casellas, Joaquim" uniqKey="Casellas J" first="Joaquim" last="Casellas">Joaquim Casellas</name>
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<country xml:lang="fr">Espagne</country>
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</nlm:aff>
<country xml:lang="fr">Espagne</country>
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<author><name sortKey="Folch, Josep M" sort="Folch, Josep M" uniqKey="Folch J" first="Josep M." last="Folch">Josep M. Folch</name>
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</nlm:aff>
<country xml:lang="fr">Espagne</country>
<wicri:regionArea>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra</wicri:regionArea>
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<country xml:lang="fr">Espagne</country>
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<author><name sortKey="Ballester, Maria" sort="Ballester, Maria" uniqKey="Ballester M" first="Maria" last="Ballester">Maria Ballester</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain</addr-line>
</nlm:aff>
<country xml:lang="fr">Espagne</country>
<wicri:regionArea>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra</wicri:regionArea>
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</nlm:aff>
<country xml:lang="fr">Espagne</country>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>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.</p>
</sec>
<sec><title>Results</title>
<p>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.</p>
</sec>
<sec><title>Conclusions</title>
<p>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.</p>
</sec>
</div>
</front>
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<author><name sortKey="Roberts, A" uniqKey="Roberts A">A Roberts</name>
</author>
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</author>
<author><name sortKey="Pertea, G" uniqKey="Pertea G">G Pertea</name>
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<author><name sortKey="Kofler, R" uniqKey="Kofler R">R Kofler</name>
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<biblStruct><analytic><author><name sortKey="Ramayo Caldas, Y" uniqKey="Ramayo Caldas Y">Y Ramayo-Caldas</name>
</author>
<author><name sortKey="Mach, N" uniqKey="Mach N">N Mach</name>
</author>
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<author><name sortKey="Corominas, J" uniqKey="Corominas J">J Corominas</name>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24926690</article-id>
<article-id pub-id-type="pmc">4057286</article-id>
<article-id pub-id-type="publisher-id">PONE-D-13-54388</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0099720</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Computational Biology</subject>
<subj-group><subject>Genome Analysis</subject>
<subj-group><subject>Transcriptome Analysis</subject>
<subj-group><subject>Genome Expression Analysis</subject>
</subj-group>
</subj-group>
<subj-group><subject>Gene Prediction</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group><subject>Genetics</subject>
<subj-group><subject>Animal Genetics</subject>
<subject>Gene Expression</subject>
<subject>Genomics</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Research and Analysis Methods</subject>
<subj-group><subject>Model Organisms</subject>
<subj-group><subject>Animal Models</subject>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Differences in Muscle Transcriptome among Pigs Phenotypically Extreme for Fatty Acid Composition</article-title>
<alt-title alt-title-type="running-head">Exploring the Porcine Muscle Transcriptome</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Puig-Oliveras</surname>
<given-names>Anna</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ramayo-Caldas</surname>
<given-names>Yuliaxis</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Corominas</surname>
<given-names>Jordi</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Estellé</surname>
<given-names>Jordi</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
<xref ref-type="aff" rid="aff4"><sup>4</sup>
</xref>
<xref ref-type="aff" rid="aff5"><sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pérez-Montarelo</surname>
<given-names>Dafne</given-names>
</name>
<xref ref-type="aff" rid="aff6"><sup>6</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hudson</surname>
<given-names>Nicholas J.</given-names>
</name>
<xref ref-type="aff" rid="aff7"><sup>7</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Casellas</surname>
<given-names>Joaquim</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff8"><sup>8</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Folch</surname>
<given-names>Josep M.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ballester</surname>
<given-names>Maria</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1"><label>1</label>
<addr-line>Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain</addr-line>
</aff>
<aff id="aff2"><label>2</label>
<addr-line>Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain</addr-line>
</aff>
<aff id="aff3"><label>3</label>
<addr-line>Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France</addr-line>
</aff>
<aff id="aff4"><label>4</label>
<addr-line>Génétique Animale et Biologie Intégrative UMR1313 (GABI), AgroParisTech, Jouy-en-Josas, France</addr-line>
</aff>
<aff id="aff5"><label>5</label>
<addr-line>Laboratoire de Radiobiologie et Etude du Génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Jouy-en-Josas, France</addr-line>
</aff>
<aff id="aff6"><label>6</label>
<addr-line>Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain</addr-line>
</aff>
<aff id="aff7"><label>7</label>
<addr-line>Computational and Systems Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Animal, Food and Health SciencesQLD, Brisbane, Australia</addr-line>
</aff>
<aff id="aff8"><label>8</label>
<addr-line>Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologies Agroalimentàries (IRTA), Lleida, Spain</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Guillou</surname>
<given-names>Hervé</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>INRA, France</addr-line>
</aff>
<author-notes><corresp id="cor1">* E-mail: <email>anna.puig@cragenomica.es</email>
</corresp>
<fn fn-type="conflict"><p><bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="con"><p>Conceived and designed the experiments: JMF MB. Performed the experiments: APO JMF MB. Analyzed the data: APO YRC MB JE. Contributed reagents/materials/analysis tools: JMF J. Corominas J. Casellas DPM JE YRC. Wrote the paper: APO JMF MB NH.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>13</day>
<month>6</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="ecorrected"><day>27</day>
<month>6</month>
<year>2014</year>
</pub-date>
<volume>9</volume>
<issue>6</issue>
<elocation-id>e99720</elocation-id>
<history><date date-type="received"><day>23</day>
<month>12</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>19</day>
<month>5</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-year>2014</copyright-year>
<copyright-holder>Puig-Oliveras et al</copyright-holder>
<license><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>
, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p>
</license>
</permissions>
<abstract><sec><title>Background</title>
<p>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.</p>
</sec>
<sec><title>Results</title>
<p>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.</p>
</sec>
<sec><title>Conclusions</title>
<p>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.</p>
</sec>
</abstract>
<funding-group><funding-statement>This work has been funded by MICINN project AGL2011-29821-C02 (Ministerio de Economía y Competitividad) and by the Innovation Consolider-Ingenio 2010 Program (CSD2007-00036). A. Puig-Oliveras was funded by a Personal Investigador en Formación (PIF) PhD grant from the Universitat Autònoma de Barcelona (458-01-1/2011). J. Corominas was funded by a Formación de Personal Investigador (FPI) PhD grant from Spanish Ministerio de Educación (BES-2009-018223), Y. Ramayo by a Formación del Profesorado Universitario (FPU) PhD grant (AP2008-01450). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement>
</funding-group>
<counts><page-count count="11"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>
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