Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution
文献类型： 外文期刊
作者： Wang, Kejun 1 ; Hua, Guoying 3 ; Li, Jingyi 4 ; Yang, Yu 5 ; Zhang, Chenxi 1 ; Yang, Lan 1 ; Hu, Xiaoyu 1 ; Scheben, Armin 6 ; Wu, Yanan 7 ; Gong, Ping 5 ; Zhang, Shuangjie 9 ; Fan, Yanfeng 9 ; Zeng, Tao 10 ; Lu, Lizhi 10 ; Gong, Yanzhang 4 ; Jiang, Ruirui 1 ; Sun, Guirong 1 ; Tian, Yadong 1 ; Kang, Xiangtao 1 ; Hu, Haifei 11 ; Li, Wenting 1 ;
作者机构： 1.Henan Agr Univ, Coll Anim Sci & Technol, Henan Key Lab Innovat & Utilizat Chicken Germplasm, Zhengzhou, Peoples R China
2.Shennong Lab, Zhengzhou, Peoples R China
3.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch, Guangdong Lab Lingnan Modern Agr, Shenzhen, Peoples R China
4.Huazhong Agr Univ, Coll Anim Sci & Technol, Intelligent Husb Dept, Key Lab Agr Anim Genet Breeding & Reprod,Minist E, Wuhan, Peoples R China
5.Wuhan Acad Agr Sci, Wuhan, Peoples R China
6.Cold Spring Harbor Lab, Simons Ctr Quantitat Biol, Cold Spring Harbor, NY USA
7.Henan Agr Univ, Coll Vet Med, Dept Prevent Vet Med, Zhengzhou, Peoples R China
8.Int Joint Res Ctr Natl Anim Immunol, Zhengzhou, Henan, Peoples R China
9.Jiangsu Inst Poultry Sci, Qual Safety & Proc Lab, Yangzhou, Peoples R China
10.Zhejiang Acad Agr Sci, Inst Anim Husb & Vet Sci, State Key Lab Managing Biot & Chem Threats Qual &, Hangzhou, Peoples R China
11.Guangdong Acad Agr Sci, Rice Res Inst, Guangdong Key Lab New Technol Rice Breeding, Guangzhou, Peoples R China
12.Guangdong Acad Agr Sci, Guangdong Rice Engn Lab, Guangzhou, Peoples R China
13.Henan Agr Univ, Coll Anim Sci & Technol, Dept Anim Genet & Breeding, Henan Key Lab Innovat & Utilizat Chicken Germplasm, Zhengzhou 450046, Peoples R China
14.Guangdong Acad Agr Sci, Rice Res Inst, Guangdong Key Lab New Technol Rice Breeding, Guangzhou 510640, Peoples R China
15.Guangdong Acad Agr Sci, Guangdong Rice Engn Lab, Guangzhou 510640, Peoples R China
关键词： IGF2BP1; MITF; pan-genome; structural variation; transposable element
期刊名称：IMETA （ 影响因子：33.2； 五年影响因子：33.2 ）
ISSN： 2770-5986
年卷期： 2024 年 3 卷 1 期
页码：
收录情况： SCI
摘要： 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 similar to 40.98 Mb new sequences. This pan-genome together with high-depth sequencing data (similar to 46.5x) 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.
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