Genomics, Proteomics & Bioinformatics (Jun 2023)
The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation
- Guobin Chang,
- Xiaoya Yuan,
- Qixin Guo,
- Hao Bai,
- Xiaofang Cao,
- Meng Liu,
- Zhixiu Wang,
- Bichun Li,
- Shasha Wang,
- Yong Jiang,
- Zhiquan Wang,
- Yang Zhang,
- Qi Xu,
- Qianqian Song,
- Rui Pan,
- Lingling Qiu,
- Tiantian Gu,
- Xinsheng Wu,
- Yulin Bi,
- Zhengfeng Cao,
- Yu Zhang,
- Yang Chen,
- Hong Li,
- Jianfeng Liu,
- Wangcheng Dai,
- Guohong Chen
Affiliations
- Guobin Chang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Xiaoya Yuan
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Qixin Guo
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Xiaofang Cao
- Novogene Bioinformatics Institute, Beijing 100080, China
- Meng Liu
- Novogene Bioinformatics Institute, Beijing 100080, China
- Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Bichun Li
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Shasha Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Yong Jiang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Zhiquan Wang
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Yang Zhang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Qi Xu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Qianqian Song
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Rui Pan
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Lingling Qiu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Tiantian Gu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Xinsheng Wu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Yulin Bi
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Zhengfeng Cao
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Yu Zhang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Yang Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Hong Li
- Novogene Bioinformatics Institute, Beijing 100080, China
- Jianfeng Liu
- College of Animal Science and Technology, China Agricultural University, Beijing 100091, China
- Wangcheng Dai
- Zhenjiang Tiancheng Agricultural Science and Technology Co., Ltd, Zhenjiang 210034, China
- Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Corresponding author.
- Journal volume & issue
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Vol. 21,
no. 3
pp. 483 – 500
Abstract
The Chinese crested (CC) duck is a unique indigenous waterfowl breed, which has a crest cushion that affects its survival rate. Therefore, the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability. In the present study, we first generated a chromosome-level genome of CC ducks. Comparative genomics revealed that genes related to tissue repair, immune function, and tumors were under strong positive selection, indicating that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks. We also assembled a Chinese spot-billed (Csp-b) duck genome, and detected the structural variations (SVs) in the genome assemblies of three ducks (i.e., CC duck, Csp-b duck, and Peking duck). Functional analysis revealed that several SVs were related to the immune system of CC ducks, further strongly suggesting that genetic compensation in the anti-tumor and immune systems supports the survival of CC ducks. Moreover, we confirmed that the CC duck originated from the mallard ducks. Finally, we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation. Overall, the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.
