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

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 (>46.5X) identified
101,041 SVs, of which substantial proportions were derived from
transposable element (TE) activity. Many TE-derived SVs anchored in a gene
body or regulatory region are linked to domestication and improvement. By
combining quantitative genetics with molecular experiments, we dissect how
TE-derived SVs change gene expression of IGF2BP1 and generate novel
transcripts of MITF, shaping body weight and plumage color. In the IGF2BP1
locus, the TE-derived SV explains the largest effect on body weight among
avian species (27.61% of phenotypic variation). Our findings highlight the
importance of using a pan-genome as a reference in genomics studies and
explore the roles of TE-derived SVs in trait formation and in livestock
breeding.