%0 Journal Article
%T Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution.
%A Wang K
%A Hua G
%A Li J
%A Yang Y
%A Zhang C
%A Yang L
%A Hu X
%A Scheben A
%A Wu Y
%A Gong P
%A Zhang S
%A Fan Y
%A Zeng T
%A Lu L
%A Gong Y
%A Jiang R
%A Sun G
%A Tian Y
%A Kang X
%A Hu H
%A Li W
%J Imeta
%V 3
%N 1
%D 2024 Feb
%M 38868520
暂无%R 10.1002/imt2.154
%X 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.