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.