生物
转座因子
遗传学
基因组
羽毛
驯化
基因
表型
基因组学
基因组进化
进化生物学
动物
作者
Kejun Wang,Guoying Hua,Jingyi Li,Yang Yu,Chenxi Zhang,Ling Yang,Xiaoyu Hu,Armin Scheben,Yanan Wu,Pan Gong,Shuangjie Zhang,Yanfeng Fan,Tao Zeng,Lizhi Liu,Yanzhang Gong,Ruirui Jiang,Guirong Sun,Yadong Tian,Xiangtao Kang,Haifei Hu,Wenting Li
出处
期刊:iMeta
[Wiley]
日期:2023-12-17
被引量:3
摘要
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.
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