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

SanCristobal, Magali, Rohart, Florian, Lascor, Christine, Bouffaud, Marcel, Trouilh, Lidwine, Martin, Pascal G. P., Lippi, Yannick, Tribout, Thierry, Faraut, Thomas, Mercat, Marie-Jose, Milan, Denis and Liaubet, Laurence (2015) Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds. BMC Genomics, 16 1: 1-17. doi:10.1186/s12864-015-2259-9


Author SanCristobal, Magali
Rohart, Florian
Lascor, Christine
Bouffaud, Marcel
Trouilh, Lidwine
Martin, Pascal G. P.
Lippi, Yannick
Tribout, Thierry
Faraut, Thomas
Mercat, Marie-Jose
Milan, Denis
Liaubet, Laurence
Title Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2015-12-12
Year available 2015
Sub-type Article (original research)
DOI 10.1186/s12864-015-2259-9
Open Access Status DOI
Volume 16
Issue 1
Start page 1
End page 17
Total pages 17
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2016
Language eng
Formatted 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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

 
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