EXCELMEAT Workshop
Biosensing Pork Quality
Lleida, 25 October 2012
RNA-Seq liver transcriptome profile in pigs with extreme phenotypes
of intramuscular fatty acid composition
Yuliaxis Ramayo-Caldas1, Nuria Mach2,3,4, Anna Esteve-Codina1, Jordi Corominas1, Anna
Castelló1, Maria Ballester1, Jordi Estellé2,3,4, Noelia Ibáñez-Escriche5, Ana I. Fernández6,
Miguel Pérez-Enciso1,7,8, Josep M. Folch1,8
1
Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra
08193, Spain, 2INRA, UMR 1313 Génétique Animale et Biologie Intégrative (GABI), Equipe Génétique
Immunité Santé, Jouy-en-Josas, F-78352, France, 3AgroParisTech, UMR 1313 GABI, Jouy-en-Josas, F78352, France, 4CEA, DSV/iRCM/SREIT/LREG, Jouy-en-Josas, F-78352, France, 5Genètica i Millora
Animal, IRTA Lleida, Lleida, 25198, Spain, 6Departamento de Mejora Genética Animal, INIA, Ctra. De
la Coruña km. 7, Madrid, 28040, Spain, 7Institut Català de Recerca i Estudis Avançats (ICREA),
Barcelona, Spain, 8Departament de Ciència Animal i dels Aliments, Facultat de Veterinària,
Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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. 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. 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. A differential expression analysis 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.