title: A co-association network analysis of the genetic determination of pig conformation, growth and fatness.
abstract: BACKGROUND
  Several QTLs have been identified for major economically relevant traits in livestock, such as growth and meat quality, revealing the complex genetic architecture of these traits. The use of network approaches considering the interactions of multiple molecules and traits provides useful insights into the molecular underpinnings of complex traits. Here, a network based methodology, named Association Weight Matrix, was applied to study gene interactions and pathways affecting pig conformation, growth and fatness traits.
  
  
  RESULTS
  The co-association network analysis underpinned three transcription factors, PPARγ, ELF1, and PRDM16 involved in mesoderm tissue differentiation. Fifty-four genes in the network belonged to growth-related ontologies and 46 of them were common with a similar study for growth in cattle supporting our results. The functional analysis uncovered the lipid metabolism and the corticotrophin and gonadotrophin release hormone pathways among the most important pathways influencing these traits. Our results suggest that the genes and pathways here identified are important determining either the total body weight of the animal and the fat content. For instance, a switch in the mesoderm tissue differentiation may determinate the age-related preferred pathways being in the puberty stage those related with the miogenic and osteogenic lineages; on the contrary, in the maturity stage cells may be more prone to the adipocyte fate. Hence, our results demonstrate that an integrative genomic co-association analysis is a powerful approach for identifying new connections and interactions among genes.
  
  
  CONCLUSIONS
  This work provides insights about pathways and key regulators which may be important determining the animal growth, conformation and body proportions and fatness traits. Molecular information concerning genes and pathways here described may be crucial for the improvement of genetic breeding programs applied to pork meat production.
authors.affiliation: Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain; Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain.
authors.forename: Anna
authors.initials: A
authors.lastname: Puig-Oliveras
authors.affiliation: Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain; Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain.
authors.forename: Maria
authors.initials: M
authors.lastname: Ballester
authors.affiliation: Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain; Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain.
authors.forename: Jordi
authors.initials: J
authors.lastname: Corominas
authors.affiliation: Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain; Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Revilla
authors.affiliation: Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), 78350, Jouy-en-Josas, France; Génétique Animale et Biologie Intégrative UMR1313 (GABI), AgroParisTech, 78350, Jouy-en-Josas, France; Laboratoire de Radiobiologie et Etude du Génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 78350, 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), 28040, Madrid, Spain.
authors.forename: Ana I
authors.initials: AI
authors.lastname: Fernández
authors.affiliation: Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain; Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain; Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), 78350, Jouy-en-Josas, France; Génétique Animale et Biologie Intégrative UMR1313 (GABI), AgroParisTech, 78350, Jouy-en-Josas, France; Laboratoire de Radiobiologie et Etude du Génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 78350, Jouy-en-Josas, France.
authors.forename: Yuliaxis
authors.initials: Y
authors.lastname: Ramayo-Caldas
authors.affiliation: Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain; Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain.
authors.forename: Josep M
authors.initials: JM
authors.lastname: Folch
mesh_terms: D000818:Animals; D001835:Body Weight / Q000235:genetics*; D001947:Breeding; D002417:Cattle; D004843:Epistasis, Genetic; D016678:Genome; D050356:Lipid Metabolism / Q000235:genetics; D008460:Meat; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*; D013552:Swine