title: RNA-seq based detection of differentially expressed genes in the skeletal muscle of Duroc pigs with distinct lipid profiles.
abstract: We have used a RNA-seq approach to investigate differential expression in the skeletal muscle of swine (N = 52) with divergent lipid profiles i.e. HIGH (increased intramuscular fat and muscle saturated and monounsaturated fatty acid contents, higher serum lipid concentrations and fatness) and LOW pigs (leaner and with an increased muscle polyunsaturated fatty acid content). The number of mRNAs and non-coding RNAs (ncRNAs) expressed in the porcine gluteus medius muscle were 18,104 and 1,558, respectively. At the nominal level of significance (P-value ≤ 0.05), we detected 1,430 mRNA and 12 non-coding RNA (ncRNA) transcripts as differentially expressed (DE) in the gluteus medius muscle of HIGH vs LOW pigs. This smaller contribution of ncRNAs to differential expression may have biological and technical reasons. We performed a second analysis, that was more stringent (P-value ≤ 0.01 and fold-change ≥ 1.5), and only 96 and 0 mRNA-and ncRNA-encoding genes happened to be DE, respectively. The subset of DE mRNA genes was enriched in pathways related with lipid (lipogenesis and triacylglycerol degradation) and glucose metabolism. Moreover, HIGH pigs showed a more lipogenic profile than their LOW counterparts.
authors.affiliation: Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.|CAPES Foundation, Ministry of Education of Brazil, Brasilia D. F., Zip Code 70.040-020, Brazil.
authors.forename: T F
authors.initials: TF
authors.lastname: Cardoso
authors.affiliation: Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
authors.forename: A
authors.initials: A
authors.lastname: Cánovas
authors.affiliation: Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui 08140, Spain.
authors.forename: O
authors.initials: O
authors.lastname: Canela-Xandri
authors.affiliation: Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
authors.forename: R
authors.initials: R
authors.lastname: González-Prendes
authors.affiliation: Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.|Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Amills
authors.affiliation: Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui 08140, Spain.
authors.forename: R
authors.initials: R
authors.lastname: Quintanilla
mesh_terms: D000818:Animals; D053263:Gene Regulatory Networks; D050356:Lipid Metabolism / Q000235:genetics*; D018482:Muscle, Skeletal / Q000378:metabolism*; D010641:Phenotype; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism; D022661:RNA, Untranslated / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013552:Swine; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger; D022661:RNA, Untranslated; D012313:RNA