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

• Published in: BMC genomics Vol. 16; no. 1; p. 1055
• Main Authors: SanCristobal, Magali, Rohart, Florian, Lascor, Christine, Bouffaud, Marcel, Trouilh, Lidwine, Martin, Pascal G.P., Lippi, Yannick, Tribout, Thierry, Faraut, Thomas, Mercat, Marie-José, Milan, Denis, Liaubet, Laurence
• Format: Journal Article
• Language: English
• Published: London BioMed Central 12.12.2015; BioMed Central Ltd
• Subjects: Analysis; Animal Genetics and Genomics; Animals; Biomedical and Life Sciences; Breeding; Female; Gene expression; Gene Expression Profiling - methods; Gene Expression Profiling - veterinary; Gene Expression Regulation; Genes; Genetic research; Genomics; Life Sciences; Livestock; Male; Microarrays; Microbial Genetics and Genomics; Muscle proteins; Muscle, Skeletal - metabolism; Muscles; Non-human and non-rodent vertebrate genomics; Oligonucleotide Array Sequence Analysis - methods; Oligonucleotide Array Sequence Analysis - veterinary; Plant Genetics and Genomics; Proteomics; Research Article; Signal Transduction; Statistical methods; Sus scrofa - classification; Sus scrofa - genetics; Sus scrofa - metabolism; Swine; Production Trait; Differentially Express Gene; Differentially Express; Muscle Mass; Pairwise Analysis; population transcriptomic; selection; domestication; pattern; european pig breed; vitamin-d; evolution; skeletal muscle; mechanism; gene expression
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-015-2259-9

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.