Abstract
BackgroundAmong 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.ResultsA 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2259-9) contains supplementary material, which is available to authorized users.
Highlights
Among transcriptomic studies, those comparing species or populations can increase our understanding of the impact of the evolutionary forces on the differentiation of populations
Are there any differentially expressed genes across breeds of the same species? If yes, what are their biological functions? We propose to explore this problem in the particular context of a domesticated species with a long history of selection pressure from human: the pig
Data The sampled animals came from 5 pig breeds: 24 Duroc (DU), 33 Landrace (LR), 41 Large White dam line (LWF), 10 Large White sire line (LWM) and 39 Piétrain (PI)
Summary
Those comparing species or populations can increase our understanding of the impact of the evolutionary forces on the differentiation of populations. 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. Several recent studies report the existence of differentially expressed genes across species. Hufford et al [14] observed that candidate genes for domestication in maize do not display any specific expression profile, contrary to the genomic patterns (DNA sequence). For the domesticated period of sorghum, Jiang et al [15] observed that gene expression divergence between two lines was mainly determined by DNA sequence divergence. Transcriptomic differences, as well as proteomics and metabolomics were shown between two genetically diverse dry bean germplasm by Mensack et al [20]
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