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

Wang, K.; Hua, G.; Li, J.; Yang, Y.; Zhang, C.; Yang, L.; Hu, X.; Scheben, A.; Wu, Y.; Gong, P.; Zhang, S.; Fan, Y.; Zeng, T.; Lu, L.; Gong, Y.; Jiang, R.; Sun, G.; Tian, Y.; Kang, X.; Hu, H.; Li, W.

doi:10.1101/2023.01.28.526061

bioRxiv · 10.1101/2023.01.28.526061

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

Wang, K.·Hua, G.·Li, J.·Yang, Y.·Zhang, C.·Yang, L.·Hu, X.·Scheben, A.·Wu, Y.·Gong, P.·Zhang, S.·Fan, Y.·Zeng, T.·Lu, L.·Gong, Y.·Jiang, R.·Sun, G.·Tian, Y.·Kang, X.·Hu, H.·Li, W.

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Abstract

Structural variations (SVs) are a major source of domestication and improvement traits, however SV profiles of duck and their phenotypic impacts largely hidden. 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 anchoring in a gene body or regulatory region are linked to ducks domestication and improvement. By combining quantitative genetics with molecular experiments, we dissect how TE-derived SVs change gene expression of IGF2BP1 and generate a novel transcript of MITF, shaping bodyweight and white plumage. In the IGF2BP1 locus, the TE-derived SV explains the largest effect on bodyweight 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.

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Wang, K., Hua, G., Li, J., Yang, Y., Zhang, C., Yang, L., Hu, X., Scheben, A., Wu, Y., Gong, P., Zhang, S., Fan, Y., Zeng, T., Lu, L., Gong, Y., Jiang, R., Sun, G., Tian, Y., Kang, X., Hu, H., Li, W.. 2023-01-30. Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution. https://doi.org/10.1101/2023.01.28.526061

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