Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution

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 (December 2023) Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution. iMeta, 3 (1). e154. ISSN 2770-5986 (Public Dataset)

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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.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transposons
CSHL Authors:	Scheben, Armin
Communities:	CSHL labs > Siepel lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	17 December 2023
Date Deposited:	17 Jun 2024 12:56
Last Modified:	17 Jun 2024 12:56
PMCID:	PMC10989122
Related URLs:	Publisher
Dataset ID:	PRJCA011446 https://doi.org/10.5061/dryad.wwpzgmsnt https://github.com/liwenting5959/Duck_pan-genome
URI:	https://repository.cshl.edu/id/eprint/41582

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