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

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, Xiao-Qin Li, Si-Ran Ding, Guan-Sheng Li, Fang-Xi Yang, Jing-Pin Hao, Ziding Zhang, Li-Zhi Lu, Ning Yang and Zhuo-Cheng Hou ()
Additional contact information
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
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

Nature Communications, 2021, vol. 12, issue 1, 1-11

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-26272-1

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