Open Access Highly Accessed Research article

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

Yuliaxis Ramayo-Caldas1*, Nuria Mach234, Anna Esteve-Codina1, Jordi Corominas1, Anna Castelló1, Maria Ballester1, Jordi Estellé234, Noelia Ibáñez-Escriche5, Ana I Fernández6, Miguel Pérez-Enciso178 and Josep M Folch18

Author affiliations

1 Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Spain

2 INRA, UMR 1313 Génétique Animale et Biologie Intégrative (GABI), Equipe Génétique Immunité Santé, Jouy-en-Josas, F-78352, France

3 AgroParisTech, UMR 1313 GABI, Jouy-en-Josas, F-78352, France

4 CEA, DSV/iRCM/SREIT/LREG, Jouy-en-Josas, F-78352, France

5 Genètica i Millora Animal, IRTA Lleida, Lleida, 25198, Spain

6 Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7, Madrid, 28040, Spain

7 Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

8 Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain

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Citation and License

BMC Genomics 2012, 13:547  doi:10.1186/1471-2164-13-547

Published: 11 October 2012

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.