Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition
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Author
Mach, Nuria
Esteve-Codina, Anna
Corominas, Jordi
Castelló, Anna
Ballester, Maria
Estellé, Jordi
Fernández, Ana I.
Pérez-Enciso, Miguel
Folch, Josep M
Publication date
2012-10-11ISSN
1471-2164
Abstract
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.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
575 - General genetics. General cytogenetics
663/664 - Food and nutrition. Enology. Oils. Fat
Pages
18
Publisher
BMC
Is part of
BMC Genomics
Citation
Ramayo-Caldas, Yuliaxis, Núria Mach, Anna Esteve‐Codina, Jordi Corominas, Anna Castelló, María Ballester, Jordi Estellé, et al. 2012. “Liver Transcriptome Profile in Pigs With Extreme Phenotypes of Intramuscular Fatty Acid Composition.” BMC Genomics 13 (1): 547. doi:10.1186/1471-2164-13-547.
Grant agreement number
MICINN/Programa Nacional de Proyectos de Investigación Fundamental/AGL2008-04818-C03/ES/GENES CANDIDATOS E IDENTIFICACION GENOMICA DE LOCI Y RUTAS GENETICAS QUE AFECTAN A LA CALIDAD DE LA CARNE EN CERDOS/GAN
MICINN/Programa Nacional de Proyectos de Investigación Fundamental/AGL2011-29821-C02/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/
MEC/Programa nacional de medios de transporte/CSD2007-00036/ES/Centro de Genómica Básica y de orientación Agroalimentaria/
MICINN/Programa Nacional de Formación de Recursos Humanos/BES-2009-018223/ES/ /
MICINN/Programa Nacional de Formación de Recursos Humanos/BES-2008-005772/ES/ /
Program
Genètica i Millora Animal
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2838]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/