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Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition

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Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition

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dc.contributor.author Ramayo-Caldas, Y. es_ES
dc.contributor.author Mach, N. es_ES
dc.contributor.author Esteve-Codina, A. es_ES
dc.contributor.author Corominas, J. es_ES
dc.contributor.author Castelló, A. es_ES
dc.contributor.author Ballester, M. es_ES
dc.contributor.author Estellé, J. es_ES
dc.contributor.author Ibáñez-Escriche, Noelia es_ES
dc.contributor.author Fernández, A.I. es_ES
dc.contributor.author Pérez-Enciso, M. es_ES
dc.contributor.author Folch, J.M. es_ES
dc.date.accessioned 2020-09-19T03:34:57Z
dc.date.available 2020-09-19T03:34:57Z
dc.date.issued 2012-10-11 es_ES
dc.identifier.issn 1471-2164 es_ES
dc.identifier.uri http://hdl.handle.net/10251/150457
dc.description.abstract [EN] Background: New advances in high-throughput technologies have allowed for the massive analysis of genomic data, providing new opportunities for the characterization of the transcriptome architectures. Recent studies in pigs have employed RNA-Seq to explore the transcriptome of different tissues in a reduced number of animals. The main goal of this study was the identification of differentially-expressed genes in the liver of Iberian x Landrace crossbred pigs showing extreme phenotypes for intramuscular fatty acid composition using RNA-Seq. Results: The liver transcriptomes of two female groups (H and L) with phenotypically extreme intramuscular fatty acid composition were sequenced using RNA-Seq. A total of 146 and 180 unannotated protein-coding genes were identified in intergenic regions for the L and H groups, respectively. In addition, a range of 5.8 to 7.3% of repetitive elements was found, with SINEs being the most abundant elements. The expression in liver of 186 (L) and 270 (H) lncRNAs was also detected. The higher reproducibility of the RNA-Seq data was validated by RT-qPCR and porcine expression microarrays, therefore showing a strong correlation between RT-qPCR and RNA-Seq data (ranking from 0.79 to 0.96), as well as between microarrays and RNA-Seq (r=0.72). A differential expression analysis between H and L animals identified 55 genes differentially-expressed between groups. Pathways analysis revealed that these genes belong to biological functions, canonical pathways and three gene networks related to lipid and fatty acid metabolism. In concordance with the phenotypic classification, the pathways analysis inferred that linolenic and arachidonic acids metabolism was altered between extreme individuals. In addition, a connection was observed among the top three networks, hence suggesting that these genes are interconnected and play an important role in lipid and fatty acid metabolism. Conclusions: In the present study RNA-Seq was used as a tool to explore the liver transcriptome of pigs with extreme phenotypes for intramuscular fatty acid composition. The differential gene expression analysis showed potential gene networks which affect lipid and fatty acid metabolism. These results may help in the design of selection strategies to improve the sensorial and nutritional quality of pork meat. es_ES
dc.description.sponsorship This work was funded by MICINN projects AGL2008-04818-C03/GAN and AGL2011-29821-C02 (Ministerio de Economia y Competitividad), and by the Innovation Consolider-Ingenio 2010 Program (CSD2007-00036, Centre for Research in Agrigenomics). Y. Ramayo-Caldas was funded by a FPU PhD grant from the Spanish Ministerio de Educacion (AP2008-01450), J. Corominas was funded by a FPI PhD grant from the Spanish Ministerio de Educacion (BES-2009-018223), A. Esteve-Codina is recipient of a FPI PhD fellowship from the Ministerio de Educacion (BES-2008-005772), Spain. This manuscript has been proofread by Mrs. Valma Ruth Dunstan, BA, BEdSt, CELTA, MA (TESOL), a native English-speaker and instructor of English at the University of Queensland (Brisbane, Australia). es_ES
dc.language Inglés es_ES
dc.publisher Springer (Biomed Central Ltd.) es_ES
dc.relation.ispartof BMC Genomics es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Rich dietary-fat es_ES
dc.subject Meat quality es_ES
dc.subject RNA-Seq es_ES
dc.subject Peroxisome proliferator es_ES
dc.subject Increasing amounts es_ES
dc.subject Lipid-Metabolism es_ES
dc.subject Gene-Expression es_ES
dc.subject Copy number es_ES
dc.subject PPAR-Alpha es_ES
dc.subject Quantification es_ES
dc.subject.classification PRODUCCION ANIMAL es_ES
dc.title Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/1471-2164-13-547 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//AGL2008-04818-C03-03/ES/GENES CANDIDATOS E IDENTIFICACION GENOMICA DE LOCI Y RUTAS GENICAS QUE AFECTAN A LA CALIDAD DE LA CARNE EN CERDOS/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//AGL2008-04818-C03-02/ES/GENES CANDIDATOS E IDENTIFICACION GENOMICA DE LOCI Y RUTAS GENETICAS QUE AFECTAN A LA CALIDAD DE LA CARNE EN CERDOS/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MECD//AP2008-01450/ES/AP2008-01450/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//AGL2008-04818-C03-01/ES/GENES CANDIDATOS E IDENTIFICACION GENOMICA DE LOCI Y RUTAS GENETICAS QUE AFECTAN A LA CALIDAD DE LA CARNE EN CERDOS/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MEC//CSD2007-00036/ES/Centro de Genómica Básica y de orientación Agroalimentaria/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//AGL2011-29821-C02-02/ES/APLICACION DE METODOS DE SECUENCIACION PARALELA MASIVA Y GENOMICA AL ESTUDIO DE VARIANTES GENICAS QUE REGULAN:CRECIMIENTO,CONFORMACION Y CALIDAD DE CARNE EN CERDO.SUBPROYECTO2/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//BES-2009-018223-2/ES/BES-2009-018223-2/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//BES-2008-005772/ES/BES-2008-005772/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Ciencia Animal - Departament de Ciència Animal es_ES
dc.description.bibliographicCitation Ramayo-Caldas, Y.; Mach, N.; Esteve-Codina, A.; Corominas, J.; Castelló, A.; Ballester, M.; Estellé, J.... (2012). Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition. BMC Genomics. 13:1-18. https://doi.org/10.1186/1471-2164-13-547 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1186/1471-2164-13-547 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 18 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 13 es_ES
dc.identifier.pmid 23051667 es_ES
dc.identifier.pmcid PMC3478172 es_ES
dc.relation.pasarela S\395265 es_ES
dc.contributor.funder Ministerio de Educación es_ES
dc.contributor.funder Ministerio de Ciencia e Innovación es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
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