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Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication

Author

Listed:
  • Feng Zhu

    (China Agricultural University)

  • Zhong-Tao Yin

    (China Agricultural University)

  • Zheng Wang

    (China Agricultural University)

  • Jacqueline Smith

    (University of Edinburgh, Easter Bush)

  • Fan Zhang

    (China Agricultural University)

  • Fergal Martin

    (European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton)

  • Denye Ogeh

    (European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton)

  • Maxwell Hincke

    (Faculty of Medicine, University of Ottawa)

  • Fang-Bing Lin

    (China Agricultural University)

  • David W. Burt

    (University of Edinburgh, Easter Bush
    The University of Queensland)

  • Zheng-Kui Zhou

    (Chinese Academy of Agricultural Sciences)

  • Shui-Sheng Hou

    (Chinese Academy of Agricultural Sciences)

  • Qiang-Sen Zhao

    (China Agricultural University)

  • Xiao-Qin Li

    (China Agricultural University)

  • Si-Ran Ding

    (China Agricultural University)

  • Guan-Sheng Li

    (China Agricultural University)

  • Fang-Xi Yang

    (Beijing Golden-Star Inc.)

  • Jing-Pin Hao

    (Beijing Golden-Star Inc.)

  • Ziding Zhang

    (China Agricultural University)

  • Li-Zhi Lu

    (Zhejiang Academy of Agricultural Sciences)

  • Ning Yang

    (China Agricultural University)

  • Zhuo-Cheng Hou

    (China Agricultural University)

Abstract

Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for thousands of new protein-coding genes and recover a major percentage of the presumed “missing genes” in birds. We obtain the entire genomic sequences for the C-type lectin (CTL) family members that regulate eggshell biomineralization. Our population and comparative genomics analyses provide more than 36 million sequence variants between duck populations. Furthermore, a mutant cell line allows confirmation of the predicted anti-adipogenic function of NR2F2 in the duck, and uncovered mutations specific to Pekin duck that potentially affect adipose deposition. Our study provides insights into avian evolution and the genetics of oviparity, and will be a rich resource for the future genetic improvement of commercial traits in the duck.

Suggested Citation

  • Feng Zhu & Zhong-Tao Yin & Zheng Wang & Jacqueline Smith & Fan Zhang & Fergal Martin & Denye Ogeh & Maxwell Hincke & Fang-Bing Lin & David W. Burt & Zheng-Kui Zhou & Shui-Sheng Hou & Qiang-Sen Zhao & , 2021. "Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26272-1
    DOI: 10.1038/s41467-021-26272-1
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    References listed on IDEAS

    as
    1. Guojie Zhang, 2015. "Bird sequencing project takes off," Nature, Nature, vol. 522(7554), pages 34-34, June.
    2. Yingyao Zhou & Bin Zhou & Lars Pache & Max Chang & Alireza Hadj Khodabakhshi & Olga Tanaseichuk & Christopher Benner & Sumit K. Chanda, 2019. "Metascape provides a biologist-oriented resource for the analysis of systems-level datasets," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    3. Zhengkui Zhou & Ming Li & Hong Cheng & Wenlei Fan & Zhengrong Yuan & Qiang Gao & Yaxi Xu & Zhanbao Guo & Yunsheng Zhang & Jian Hu & Hehe Liu & Dapeng Liu & Weihuang Chen & Zhuqing Zheng & Yong Jiang &, 2018. "An intercross population study reveals genes associated with body size and plumage color in ducks," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
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