title: Differences in muscle transcriptome among pigs phenotypically extreme for fatty acid composition.
abstract: BACKGROUND
  Besides having an impact on human health, the porcine muscle fatty acid profile determines meat quality and taste. The RNA-Seq technologies allowed us to explore the pig muscle transcriptome with an unprecedented detail. The aim of this study was to identify differentially-expressed genes between two groups of 6 sows belonging to an Iberian × Landrace backcross with extreme phenotypes according to FA profile.
  
  
  RESULTS
  We sequenced the muscle transcriptome acquiring 787.5 M of 75 bp paired-end reads. About 85.1% of reads were mapped to the reference genome. Of the total reads, 79.1% were located in exons, 6.0% in introns and 14.9% in intergenic regions, indicating expressed regions not annotated in the reference genome. We identified a 34.5% of the intergenic regions as interspersed repetitive regions. We predicted a total of 2,372 putative proteins. Pathway analysis with 131 differentially-expressed genes revealed that the most statistically-significant metabolic pathways were related with lipid metabolism. Moreover, 18 of the differentially-expressed genes were located in genomic regions associated with IMF composition in an independent GWAS study in the same genetic background. Thus, our results indicate that the lipid metabolism of FAs is differently modulated when the FA composition in muscle differs. For instance, a high content of PUFA may reduce FA and glucose uptake resulting in an inhibition of the lipogenesis. These results are consistent with previous studies of our group analysing the liver and the adipose tissue transcriptomes providing a view of each of the main organs involved in lipid metabolism.
  
  
  CONCLUSIONS
  The results obtained in the muscle transcriptome analysis increase the knowledge of the gene regulation of IMF deposition, FA profile and meat quality, in terms of taste and nutritional value. Besides, our results may be important in terms of human health.
authors.affiliation: Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
authors.forename: Anna
authors.initials: A
authors.lastname: Puig-Oliveras
authors.affiliation: Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France.
authors.forename: Yuliaxis
authors.initials: Y
authors.lastname: Ramayo-Caldas
authors.affiliation: Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
authors.forename: Jordi
authors.initials: J
authors.lastname: Corominas
authors.affiliation: Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France; Génétique Animale et Biologie Intégrative UMR1313 (GABI), AgroParisTech, Jouy-en-Josas, France; Laboratoire de Radiobiologie et Etude du Génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Jouy-en-Josas, France.
authors.forename: Jordi
authors.initials: J
authors.lastname: Estellé
authors.affiliation: Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.
authors.forename: Dafne
authors.initials: D
authors.lastname: Pérez-Montarelo
authors.affiliation: Computational and Systems Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Animal, Food and Health SciencesQLD, Brisbane, Australia.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Hudson
authors.affiliation: Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain; Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologies Agroalimentàries (IRTA), Lleida, Spain.
authors.forename: Joaquim
authors.initials: J
authors.lastname: Casellas
authors.affiliation: Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
authors.forename: Josep M
authors.initials: JM
authors.lastname: Folch
authors.forename: Maria
authors.initials: M
authors.lastname: Ballester
mesh_terms: D000818:Animals; D005227:Fatty Acids / Q000378:metabolism*; D005260:Female; D020869:Gene Expression Profiling; D018482:Muscle, Skeletal / Q000378:metabolism*; D034421:Sus scrofa; D013552:Swine; D059467:Transcriptome / Q000235:genetics*
chemical_list: D005227:Fatty Acids