Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition.
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.
Centre de Recerca en Agrigenòmica, Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra 08193, Spain. yuliaxis.ramayo@uab.es
Yuliaxis
Y
Ramayo-Caldas
Nuria
N
Mach
Anna
A
Esteve-Codina
Jordi
J
Corominas
Anna
A
Castelló
Maria
M
Ballester
Jordi
J
Estellé
Noelia
N
Ibáñez-Escriche
Ana I
AI
Fernández
Miguel
M
Pérez-Enciso
Josep M
JM
Folch
D000818:Animals; D001947:Breeding; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D005227:Fatty Acids / Q000032:analysis*; D005260:Female; D050356:Lipid Metabolism / Q000235:genetics; D008099:Liver / Q000378:metabolism*; D018482:Muscle, Skeletal / Q000737:chemistry*; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D017423:Sequence Analysis, RNA; D013552:Swine / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
D005227:Fatty Acids