Posted by: shrikantmantri | March 12, 2010

Nature: Whole-genome resequencing reveals loci under selection during chicken domestication

Nature advance online publication 10 March 2010 | 


; Received 22 September 2009; Accepted 8 January 2010; Published online 10 March 2010

Whole-genome resequencing reveals loci under selection during chicken domestication

Carl-Johan Rubin1,10, Michael C. Zody1,2,10, Jonas Eriksson1, Jennifer R. S. Meadows1, Ellen Sherwood3, Matthew T. Webster1, Lin Jiang1, Max Ingman4, Ted Sharpe2, Sojeong Ka5, Finn Hallböök5, Francois Besnier6, Örjan Carlborg6, Bertrand Bed’hom7, Michèle Tixier-Boichard7, Per Jensen8, Paul Siegel9, Kerstin Lindblad-Toh1,2 & Leif Andersson1,6

  1. Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-75123 Uppsala, Sweden
  2. Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
  3. Department of Cell and Molecular Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden
  4. Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala, Sweden
  5. Department of Neuroscience, Uppsala University, SE-75124 Uppsala, Sweden
  6. Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 597, SE-75124 Uppsala, Sweden
  7. INRA, AgroParisTech, UMR1313 Animal Genetics and Integrative Biology, F-78350 Jouy-en-Josas, France
  8. IFM Biology, Linköping University, SE-58183 Linköping, Sweden
  9. Virginia Polytechnic Institute and State University, Department of Animal and Poultry Sciences, Blacksburg, Virginia 24061-0306, USA
  10. These authors contributed equally to this work.

Correspondence to: Leif Andersson1,6 Correspondence and requests for materials should be addressed to L.A. (Email:

This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence.


Domestic animals are excellent models for genetic studies of phenotypic evolution1, 2, 3. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor4. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.


Posted via email from Sharing significant bytes —(Shrikant Mantri)


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