Duck pan‐genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution
Kejun Wang,
Guoying Hua,
Jingyi Li,
Yu Yang,
Chenxi Zhang,
Lan Yang,
Xiaoyu Hu,
Armin Scheben,
Yanan Wu,
Ping Gong,
Shuangjie Zhang,
Yanfeng Fan,
Tao Zeng,
Lizhi Lu,
Yanzhang Gong,
Ruirui Jiang,
Guirong Sun,
Yadong Tian,
Xiangtao Kang,
Haifei Hu,
Wenting Li
Affiliations
Kejun Wang
Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and Technology Henan Agricultural University Zhengzhou China
Guoying Hua
Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
Jingyi Li
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Intelligent Husbandry Department, College of Animal Science and Technology Huazhong Agricultural University Wuhan China
Yu Yang
Wuhan Academy of Agricultural Science Wuhan China
Chenxi Zhang
Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and Technology Henan Agricultural University Zhengzhou China
Lan Yang
Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and Technology Henan Agricultural University Zhengzhou China
Xiaoyu Hu
Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and Technology Henan Agricultural University Zhengzhou China
Armin Scheben
Simons Center for Quantitative Biology Cold Spring Harbor Laboratory Cold Spring Harbor New York USA
Yanan Wu
Department of preventive veterinary medicine, College of Veterinary Medicine Henan Agricultural University Zhengzhou China
Ping Gong
Wuhan Academy of Agricultural Science Wuhan China
Shuangjie Zhang
Quality Safety and Processing Laboratory Jiangsu Institute of Poultry Sciences Yangzhou China
Yanfeng Fan
Quality Safety and Processing Laboratory Jiangsu Institute of Poultry Sciences Yangzhou China
Tao Zeng
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Animal Husbandry and Veterinary Science Zhejiang Academy of Agricultural Sciences Hangzhou China
Lizhi Lu
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Animal Husbandry and Veterinary Science Zhejiang Academy of Agricultural Sciences Hangzhou China
Yanzhang Gong
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Intelligent Husbandry Department, College of Animal Science and Technology Huazhong Agricultural University Wuhan China
Ruirui Jiang
Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and Technology Henan Agricultural University Zhengzhou China
Guirong Sun
Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and Technology Henan Agricultural University Zhengzhou China
Yadong Tian
Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and Technology Henan Agricultural University Zhengzhou China
Xiangtao Kang
Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and Technology Henan Agricultural University Zhengzhou China
Haifei Hu
Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding and Guangdong Rice Engineering Laboratory Guangdong Academy of Agricultural Sciences Guangzhou China
Wenting Li
Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and Technology Henan Agricultural University Zhengzhou China
Abstract Structural variations (SVs) are a major source of domestication and improvement traits. We present the first duck pan‐genome constructed using five genome assemblies capturing ∼40.98 Mb new sequences. This pan‐genome together with high‐depth sequencing data (∼46.5×) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE‐derived SVs anchoring in a gene body or regulatory region are linked to duck's domestication and improvement. By combining quantitative genetics with molecular experiments, we, for the first time, unraveled a 6945 bp Gypsy insertion as a functional mutation of the major gene IGF2BP1 associated with duck bodyweight. This Gypsy insertion, to our knowledge, explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). In addition, we also examined another 6634 bp Gypsy insertion in MITF intron, which triggers a novel transcript of MITF, thereby contributing to the development of white plumage. Our findings highlight the importance of using a pan‐genome as a reference in genomics studies and illuminate the impact of transposons in trait formation and livestock breeding.
