title: Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds.
abstract: BACKGROUND
  Among transcriptomic studies, those comparing species or populations can increase our understanding of the impact of the evolutionary forces on the differentiation of populations. A particular situation is the one of short evolution time with breeds of a domesticated species that underwent strong selective pressures. In this study, the gene expression diversity across five pig breeds has been explored in muscle. Samples came from: 24 Duroc, 33 Landrace, 41 Large White dam line, 10 Large White sire line and 39 Piétrain. From these animals, 147 muscle samples obtained at slaughter were analyzed using the porcine Agilent 44 K v1 microarray.
  
  
  RESULTS
  A total of 12,358 genes were identified as expressed in muscle after normalization and 1,703 genes were declared differential for at least one breed (FDR < 0.001). The functional analysis highlighted that gene expression diversity is mainly linked to cellular signaling pathways such as the PI3K (phosphoinositide 3-kinase) pathway. The PI3K pathway is known to be involved in the control of development of the skeletal muscle mass by affecting extracellular matrix - receptor interactions, regulation of actin cytoskeleton pathways and some metabolic functions. This study also highlighted 228 spots (171 unique genes) that differentiate the breeds from each other. A common subgroup of 15 genes selected by three statistical methods was able to differentiate Duroc, Large White and Piétrain breeds.
  
  
  CONCLUSIONS
  This study on transcriptomic differentiation across Western pig breeds highlighted a global picture: mainly signaling pathways were affected. This result is consistent with the selection objective of increasing muscle mass. These transcriptional changes may indicate selection pressure or simply breed differences which may be driven by human selection. Further work aiming at comparing genetic and transcriptomic diversities would further increase our understanding of the consequences of human impact on livestock species.
authors.affiliation: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326, Castanet-Tolosan, France. magali.san-cristobal@toulouse.inra.fr.|Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENSAT, UMR1388 Génétique, F-31326, Castanet-Tolosan, France. magali.san-cristobal@toulouse.inra.fr.|Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENVT, UMR1388 Génétique, F-31076, Toulouse, France. magali.san-cristobal@toulouse.inra.fr.
authors.forename: Magali
authors.initials: M
authors.lastname: SanCristobal
authors.affiliation: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326, Castanet-Tolosan, France. f.rohart@ua.edu.au.|Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENSAT, UMR1388 Génétique, F-31326, Castanet-Tolosan, France. f.rohart@ua.edu.au.|Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENVT, UMR1388 Génétique, F-31076, Toulouse, France. f.rohart@ua.edu.au.|Australian Institute for Bioengineering and Nanotechnology (AIBN), Corner College and Cooper Rds (Bldg 75), The University of Queensland, Brisbane Qld, 4072, Australia. f.rohart@ua.edu.au.
authors.forename: Florian
authors.initials: F
authors.lastname: Rohart
authors.affiliation: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326, Castanet-Tolosan, France. ttarttalet-kiki@hotmail.fr.|Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENSAT, UMR1388 Génétique, F-31326, Castanet-Tolosan, France. ttarttalet-kiki@hotmail.fr.|Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENVT, UMR1388 Génétique, F-31076, Toulouse, France. ttarttalet-kiki@hotmail.fr.
authors.forename: Christine
authors.initials: C
authors.lastname: Lascor
authors.affiliation: INRA, UE450 Testage - porcs, F-35653, Le Rheu, France. marcel.bouffaud@sfr.fr.
authors.forename: Marcel
authors.initials: M
authors.lastname: Bouffaud
authors.affiliation: Plateforme Transcriptome GeT-Biopuces, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), F-31077, Toulouse, France. lidwine.trouilh@insa-toulouse.fr.
authors.forename: Lidwine
authors.initials: L
authors.lastname: Trouilh
authors.affiliation: Plateau Transcriptomic impact of Xenobiotics (TRiX), ToxAlim INRA/INP, F-31027, Toulouse, France. pascal.martin@toulouse.inra.fr.
authors.forename: Pascal G P
authors.initials: PG
authors.lastname: Martin
authors.affiliation: Plateau Transcriptomic impact of Xenobiotics (TRiX), ToxAlim INRA/INP, F-31027, Toulouse, France. yannick.lippi@toulouse.inra.fr.
authors.forename: Yannick
authors.initials: Y
authors.lastname: Lippi
authors.affiliation: INRA GABI, F-78351, Jouy-en-Josas cedex, France. thierry.tribout@jouy.inra.fr.
authors.forename: Thierry
authors.initials: T
authors.lastname: Tribout
authors.affiliation: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326, Castanet-Tolosan, France. thomas.faraut@toulouse.inra.fr.|Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENSAT, UMR1388 Génétique, F-31326, Castanet-Tolosan, France. thomas.faraut@toulouse.inra.fr.|Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENVT, UMR1388 Génétique, F-31076, Toulouse, France. thomas.faraut@toulouse.inra.fr.
authors.forename: Thomas
authors.initials: T
authors.lastname: Faraut
authors.affiliation: IFIP/BIOPORC, F-35651, Le Rheu Cedex, France. marie-jose.mercat@ifip.asso.fr.
authors.forename: Marie-José
authors.initials: MJ
authors.lastname: Mercat
authors.affiliation: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326, Castanet-Tolosan, France. denis.milan@toulouse.inra.fr.|Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENSAT, UMR1388 Génétique, F-31326, Castanet-Tolosan, France. denis.milan@toulouse.inra.fr.|Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENVT, UMR1388 Génétique, F-31076, Toulouse, France. denis.milan@toulouse.inra.fr.
authors.forename: Denis
authors.initials: D
authors.lastname: Milan
authors.affiliation: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326, Castanet-Tolosan, France. laurence.liaubet@toulouse.inra.fr.|Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENSAT, UMR1388 Génétique, F-31326, Castanet-Tolosan, France. laurence.liaubet@toulouse.inra.fr.|Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENVT, UMR1388 Génétique, F-31076, Toulouse, France. laurence.liaubet@toulouse.inra.fr.
authors.forename: Laurence
authors.initials: L
authors.lastname: Liaubet
mesh_terms: D000818:Animals; D001947:Breeding; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods* / Q000662:veterinary; D005786:Gene Expression Regulation; D008297:Male; D018482:Muscle, Skeletal / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000662:veterinary; D015398:Signal Transduction; D034421:Sus scrofa / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D013552:Swine