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Zhu F, Yin ZT, Wang Z, Smith J, Zhang F, Martin F, Ogeh D, Hincke M, Lin FB, Burt DW, Zhou ZK, Hou SS, Zhao QS, Li XQ, Ding SR, Li GS, Yang FX, Hao JP, Zhang Z, Lu LZ, Yang N, Hou ZC. Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. Nat Commun 2021; 12:5932. [PMID: 34635656 PMCID: PMC8505442 DOI: 10.1038/s41467-021-26272-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 09/21/2021] [Indexed: 01/23/2023] Open
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.
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Affiliation(s)
- Feng Zhu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Zhong-Tao Yin
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Zheng Wang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Jacqueline Smith
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Fan Zhang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Denye Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maxwell Hincke
- Department of Cellular and Molecular Medicine, Department of Innovation in Medical Education, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, KIH 8M5, Canada
| | - Fang-Bing Lin
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - David W Burt
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Zheng-Kui Zhou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Shui-Sheng Hou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Qiang-Sen Zhao
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Xiao-Qin Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Si-Ran Ding
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Guan-Sheng Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Fang-Xi Yang
- Beijing Golden-Star Inc., Beijing, 100076, China
| | - Jing-Pin Hao
- Beijing Golden-Star Inc., Beijing, 100076, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Li-Zhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.
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