Format

Send to

Choose Destination
Nat Commun. 2018 Feb 28;9(1):859. doi: 10.1038/s41467-017-02809-1.

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

Author information

1
CSIRO Agriculture and Food, 306 Carmody Road, St. Lucia, 4067, QLD, Australia.
2
Centre for Research in Agricultural Genomics (CRAG), Bellaterra, 08193, Spain.
3
ICREA, Carrer de Lluís Companys 23, Barcelona, 08010, Spain.
4
AgResearch Ltd, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, Otago, New Zealand.
5
Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Mazandaran, 46414-356, Iran.
6
Natural Resources Faculty, University of Guilan, Guilan, 41335-1914, Iran.
7
Environmental Science Department, Gorgan University of Agricultural Sciences and Natural resources, Gorgan, 49138-15739, Iran.
8
Laboratoire d'Ecologie Alpine, Universite Grenoble Alpes, Grenoble, 38041, France.
9
Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
10
Utah State University, 1435 Old Main Hill, Logan, UT, 84322-1435-1435, USA.
11
Department of Economic Development, Jobs, Transport and Resources, Bundoora, 3083, VIC, Australia.
12
School of Applied Systems Biology, La Trobe University, Bundoora, 3083, VIC, Australia.
13
CSIRO Agriculture and Food, 306 Carmody Road, St. Lucia, 4067, QLD, Australia. James.Kijas@csiro.au.

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.

PMID:
29491421
PMCID:
PMC5830443
DOI:
10.1038/s41467-017-02809-1
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Nature Publishing Group Icon for PubMed Central
Loading ...
Support Center