数字农科院2.0

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;Hua, Guoying;Li, Jingyi;Yang, Yu;Zhang, Chenxi;Yang, Lan;Hu, Xiaoyu;Scheben, Armin;Wu, Yanan;Gong, Ping;Zhang, Shuangjie;Fan, Yanfeng;Zeng, Tao;Lu, Lizhi;Gong, Yanzhang;Jiang, Ruirui;Sun, Guirong;Tian, Yadong;Kang, Xiangtao;Hu, Haifei;Li, Wenting

作者机构：

关键词： （2-0-3）IGF2BP1;MITF;pan-genome;structural variation;transposable element

期刊名称： iMeta

ISSN： 2770-5986

年卷期： 2024 年

页码：

收录情况： SCIE（2024版）

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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