Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds
Naval-Sanchez, Marina (CSIRO. Agriculture and Food)
Nguyen, Quan (CSIRO. Agriculture and Food)
McWilliam, Sean (CSIRO. Agriculture and Food)
Porto-Neto, Laercio R. (CSIRO. Agriculture and Food)
Tellam, Ross (CSIRO. Agriculture and Food)
Vuocolo, Tony (CSIRO. Agriculture and Food)
Reverter, Antonio (CSIRO. Agriculture and Food)
Perez-Enciso, Miguel (Centre de Recerca en Agrigenòmica)
Brauning, Rudiger (AgResearch Ltd. Invermay Agricultural Centre)
Clarke, Shannon (AgResearch Ltd. Invermay Agricultural Centre)
McCulloch, Alan (AgResearch Ltd. Invermay Agricultural Centre)
Zamani, Wahid (Tarbiat Modares University. Department of Environmental Sciences)
Naderi, Saeid (University of Guilan. Natural Resources Faculty)
Rezaei, Hamid Reza (Gorgan University of Agricultural Sciences and Natural Resources. Environmental Science Department)
Pompanon, Francois (Université Grenoble Alpes. Laboratoire d'Ecologie Alpine)
Taberlet, Pierre (Université Grenoble Alpes. Laboratoire d'Ecologie Alpine)
Worley, Kim C. (Baylor College of Medicine. Human Genome Sequencing Center. Department of Human and Molecular Genetics)
Gibbs, Richard A. (Baylor College of Medicine. Human Genome Sequencing Center. Department of Human and Molecular Genetics)
Muzny, Donna M. (Baylor College of Medicine. Human Genome Sequencing Center. Department of Human and Molecular Genetics)
Jhangiani, Shalini N. (Baylor College of Medicine. Human Genome Sequencing Center. Department of Human and Molecular Genetics)
Cockett, Noelle (Utah State University)
Daetwyler, Hans (La Trobe University. School of Applied Systems Biology)
Kijas, James (CSIRO. Agriculture and Food)

Date:	2018
Abstract:	Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis) to identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species.
Grants:	European Commission 244356
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Computational biology and bioinformatics ; Epigenomics ; Molecular evolution ; Systems biology
Published in:	Nature communications, Vol. 9 Núm. 859 (2018) , ISSN 2041-1723

DOI: 10.1038/s41467-017-02809-1
PMID: 29491421

13 p, 3.1 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
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