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Whole-genome resequencing reveals loci under selection during chicken domestication

Author

Listed:
  • Carl-Johan Rubin

    (Uppsala University, Box 582, SE-75123 Uppsala, Sweden)

  • Michael C. Zody

    (Uppsala University, Box 582, SE-75123 Uppsala, Sweden
    Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Jonas Eriksson

    (Uppsala University, Box 582, SE-75123 Uppsala, Sweden)

  • Jennifer R. S. Meadows

    (Uppsala University, Box 582, SE-75123 Uppsala, Sweden)

  • Ellen Sherwood

    (Karolinska Institutet)

  • Matthew T. Webster

    (Uppsala University, Box 582, SE-75123 Uppsala, Sweden)

  • Lin Jiang

    (Uppsala University, Box 582, SE-75123 Uppsala, Sweden)

  • Max Ingman

    (The Rudbeck Laboratory, Uppsala University)

  • Ted Sharpe

    (Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Sojeong Ka

    (Uppsala University)

  • Finn Hallböök

    (Uppsala University)

  • Francois Besnier

    (Swedish University of Agricultural Sciences, Box 597, SE-75124 Uppsala, Sweden)

  • Örjan Carlborg

    (Swedish University of Agricultural Sciences, Box 597, SE-75124 Uppsala, Sweden)

  • Bertrand Bed’hom

    (INRA, AgroParisTech, UMR1313 Animal Genetics and Integrative Biology)

  • Michèle Tixier-Boichard

    (INRA, AgroParisTech, UMR1313 Animal Genetics and Integrative Biology)

  • Per Jensen

    (IFM Biology, Linköping University)

  • Paul Siegel

    (Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0306, USA)

  • Kerstin Lindblad-Toh

    (Uppsala University, Box 582, SE-75123 Uppsala, Sweden
    Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Leif Andersson

    (Uppsala University, Box 582, SE-75123 Uppsala, Sweden
    Swedish University of Agricultural Sciences, Box 597, SE-75124 Uppsala, Sweden)

Abstract

Chicken and egg questions The domestication of the chicken over a period of several thousand years and its later specialization into meat producing (broiler) and egg producing (layer) lines is an informative model of domestication and phenotypic evolution. A study using massively parallel sequencing of domestic chicken and its wild ancestor, the red jungle fowl, reveals a number of 'selective sweeps', where benign genetic variations closely linked to a mutation that dramatically enhances survival increase in frequency relative to other alleles. Most striking of these — found in all domestic chickens — is one at a locus encoding thyroid stimulating hormone receptor, which has a key role in metabolism and vertebrate reproductive timing. This sweep may be related to a classic feature of domesticated animals, the absence of the strict regulation of seasonal reproduction found in wild populations. Several of the selective sweeps detected in broilers overlap genes associated with growth, appetite and metabolic regulation.

Suggested Citation

  • Carl-Johan Rubin & Michael C. Zody & Jonas Eriksson & Jennifer R. S. Meadows & Ellen Sherwood & Matthew T. Webster & Lin Jiang & Max Ingman & Ted Sharpe & Sojeong Ka & Finn Hallböök & Francois Besnier, 2010. "Whole-genome resequencing reveals loci under selection during chicken domestication," Nature, Nature, vol. 464(7288), pages 587-591, March.
    • Handle: RePEc:nat:nature:v:464:y:2010:i:7288:d:10.1038_nature08832
    DOI: 10.1038/nature08832
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    Citations

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    Cited by:

    1. Junli Sun & Tao Chen & Min Zhu & Ran Wang & Yingfei Huang & Qiang Wei & Manman Yang & Yuying Liao, 2022. "Whole-genome sequencing revealed genetic diversity and selection of Guangxi indigenous chickens," PLOS ONE, Public Library of Science, vol. 17(3), pages 1-13, March.
    2. Dandan Wang & Lizhi Tan & Yihao Zhi & Lina Bu & Yangyang Wang & Zhang Wang & Yulong Guo & Weihua Tian & Chunlin Xu & Donghua Li & Zhuanjian Li & Ruirui Jiang & Ruili Han & Guoxi Li & Yongqiang Wang & , 2024. "Genome-wide variation study and inter-tissue communication analysis unveil regulatory mechanisms of egg-laying performance in chickens," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    3. Worapong Singchat & Aingorn Chaiyes & Wongsathit Wongloet & Nattakan Ariyaraphong & Kitipong Jaisamut & Thitipong Panthum & Syed Farhan Ahmad & Warut Chaleekarn & Warong Suksavate & Mitree Inpota & Ch, 2022. "Red Junglefowl Resource Management Guide: Bioresource Reintroduction for Sustainable Food Security in Thailand," Sustainability, MDPI, vol. 14(13), pages 1-19, June.
    4. Xiangjun Yun & Jinrui Wu & Bo Xu & Shijie Lv & Le Zhang & Wenguang Zhang & Shixian Sun & Guixiang Liu & Yazhou Zu & Bin Liu, 2023. "Genome Survey of Stipa breviflora Griseb. Using Next-Generation Sequencing," Agriculture, MDPI, vol. 13(12), pages 1-16, December.
    5. Carli Peters & Kristine K. Richter & Shevan Wilkin & Sören Stark & Basira Mir-Makhamad & Ricardo Fernandes & Farhod Maksudov & Sirojidin Mirzaakhmedov & Husniddin Rahmonov & Stefanie Schirmer & Ksenii, 2024. "Archaeological and molecular evidence for ancient chickens in Central Asia," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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