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BMC Genomics. 2015 Dec 12;16:1055. doi: 10.1186/s12864-015-2259-9.

Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds.

SanCristobal M1,2,3, Rohart F4,5,6,7, Lascor C8,9,10, Bouffaud M11, Trouilh L12, Martin PG13, Lippi Y14, Tribout T15, Faraut T16,17,18, Mercat MJ19, Milan D20,21,22, Liaubet L23,24,25.

Author information

1
INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326, Castanet-Tolosan, France. magali.san-cristobal@toulouse.inra.fr.
2
Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENSAT, UMR1388 Génétique, F-31326, Castanet-Tolosan, France. magali.san-cristobal@toulouse.inra.fr.
3
Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENVT, UMR1388 Génétique, F-31076, Toulouse, France. magali.san-cristobal@toulouse.inra.fr.
4
INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326, Castanet-Tolosan, France. f.rohart@ua.edu.au.
5
Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENSAT, UMR1388 Génétique, F-31326, Castanet-Tolosan, France. f.rohart@ua.edu.au.
6
Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENVT, UMR1388 Génétique, F-31076, Toulouse, France. f.rohart@ua.edu.au.
7
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.
8
INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326, Castanet-Tolosan, France. ttarttalet-kiki@hotmail.fr.
9
Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENSAT, UMR1388 Génétique, F-31326, Castanet-Tolosan, France. ttarttalet-kiki@hotmail.fr.
10
Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENVT, UMR1388 Génétique, F-31076, Toulouse, France. ttarttalet-kiki@hotmail.fr.
11
INRA, UE450 Testage - porcs, F-35653, Le Rheu, France. marcel.bouffaud@sfr.fr.
12
Plateforme Transcriptome GeT-Biopuces, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), F-31077, Toulouse, France. lidwine.trouilh@insa-toulouse.fr.
13
Plateau Transcriptomic impact of Xenobiotics (TRiX), ToxAlim INRA/INP, F-31027, Toulouse, France. pascal.martin@toulouse.inra.fr.
14
Plateau Transcriptomic impact of Xenobiotics (TRiX), ToxAlim INRA/INP, F-31027, Toulouse, France. yannick.lippi@toulouse.inra.fr.
15
INRA GABI, F-78351, Jouy-en-Josas cedex, France. thierry.tribout@jouy.inra.fr.
16
INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326, Castanet-Tolosan, France. thomas.faraut@toulouse.inra.fr.
17
Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENSAT, UMR1388 Génétique, F-31326, Castanet-Tolosan, France. thomas.faraut@toulouse.inra.fr.
18
Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENVT, UMR1388 Génétique, F-31076, Toulouse, France. thomas.faraut@toulouse.inra.fr.
19
IFIP/BIOPORC, F-35651, Le Rheu Cedex, France. marie-jose.mercat@ifip.asso.fr.
20
INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326, Castanet-Tolosan, France. denis.milan@toulouse.inra.fr.
21
Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENSAT, UMR1388 Génétique, F-31326, Castanet-Tolosan, France. denis.milan@toulouse.inra.fr.
22
Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENVT, UMR1388 Génétique, F-31076, Toulouse, France. denis.milan@toulouse.inra.fr.
23
INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326, Castanet-Tolosan, France. laurence.liaubet@toulouse.inra.fr.
24
Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENSAT, UMR1388 Génétique, F-31326, Castanet-Tolosan, France. laurence.liaubet@toulouse.inra.fr.
25
Physiologie et Systèmes d'Elevage, Université de Toulouse INPT ENVT, UMR1388 Génétique, F-31076, Toulouse, France. laurence.liaubet@toulouse.inra.fr.

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.

PMID:
26651482
PMCID:
PMC4676870
DOI:
10.1186/s12864-015-2259-9
[Indexed for MEDLINE]
Free PMC Article

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