Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds

Marina Naval-Sanchez, Quan Nguyen, Sean McWilliam, Laercio R. Porto-Neto, Ross Tellam, Tony Vuocolo, Antonio Reverter, Miguel Perez-Enciso, Rudiger Brauning, Shannon Clarke, Alan McCulloch, Wahid Zamani, Saeid Naderi, Hamid Reza Rezaei, Francois Pompanon, Pierre Taberlet, Kim C. Worley, Richard A. Gibbs, Donna M. Muzny, Shalini N. Jhangiani, Noelle Cockett, Hans Daetwyler and James Kijas ()
Additional contact information
Marina Naval-Sanchez: CSIRO Agriculture and Food
Quan Nguyen: CSIRO Agriculture and Food
Sean McWilliam: CSIRO Agriculture and Food
Laercio R. Porto-Neto: CSIRO Agriculture and Food
Ross Tellam: CSIRO Agriculture and Food
Tony Vuocolo: CSIRO Agriculture and Food
Antonio Reverter: CSIRO Agriculture and Food
Miguel Perez-Enciso: Centre for Research in Agricultural Genomics (CRAG)
Rudiger Brauning: AgResearch Ltd, Invermay Agricultural Centre
Shannon Clarke: AgResearch Ltd, Invermay Agricultural Centre
Alan McCulloch: AgResearch Ltd, Invermay Agricultural Centre
Wahid Zamani: Tarbiat Modares University
Saeid Naderi: University of Guilan
Hamid Reza Rezaei: Gorgan University of Agricultural Sciences and Natural resources
Francois Pompanon: Universite Grenoble Alpes
Pierre Taberlet: Universite Grenoble Alpes
Kim C. Worley: Baylor College of Medicine
Richard A. Gibbs: Baylor College of Medicine
Donna M. Muzny: Baylor College of Medicine
Shalini N. Jhangiani: Baylor College of Medicine
Noelle Cockett: Utah State University
Hans Daetwyler: Transport and Resources
James Kijas: CSIRO Agriculture and Food

Nature Communications, 2018, vol. 9, issue 1, 1-13

Abstract: 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.

Date: 2018
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-017-02809-1

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DOI: 10.1038/s41467-017-02809-1

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