Donkey genomes provide new insights into domestication and selection for coat color

Changfa Wang; Haijing Li; Yu Guo; Jinming Huang; Yan Sun; Jiumeng Min; Jinpeng Wang; Xiaodong Fang; Zicheng Zhao; Shuai Wang; Yanlin Zhang; Qingfeng Liu; Qiang Jiang; Xiuge Wang; Yijun Guo; Chunhong Yang; Yinchao Wang; Fang Tian; Guilong Zhuang; Yanna Fan; Qican Gao; Yuhua Li; Zhihua Ju; Jianbin Li; Rongling Li; Minghai Hou; Guiwen Yang; Guiqin Liu; Wenqiang Liu; Jiao Guo; Shanshan Pan; Guangyi Fan; Wei Zhang; Ruitao Zhang; Jie Yu; Xinhao Zhang; Qi Yin; Chuanliang Ji; Yuanchun Jin; Guidong Yue; Mei Liu; Jiake Xu; Shimin Liu; Jordi Jordana; Antonia Noce; Marcel Amills; Dong Dong Wu; Shuaicheng Li; Xiangshan Zhou; Jifeng Zhong

doi:10.1038/s41467-020-19813-7

Donkey genomes provide new insights into domestication and selection for coat color

Changfa Wang, Haijing Li, Yu Guo, Jinming Huang, Yan Sun, Jiumeng Min, Jinpeng Wang, Xiaodong Fang, Zicheng Zhao, Shuai Wang, Yanlin Zhang, Qingfeng Liu, Qiang Jiang, Xiuge Wang, Yijun Guo, Chunhong Yang, Yinchao Wang, Fang Tian, Guilong Zhuang, Yanna FanQican Gao, Yuhua Li, Zhihua Ju, Jianbin Li, Rongling Li, Minghai Hou, Guiwen Yang, Guiqin Liu, Wenqiang Liu, Jiao Guo, Shanshan Pan, Guangyi Fan, Wei Zhang, Ruitao Zhang, Jie Yu, Xinhao Zhang, Qi Yin, Chuanliang Ji, Yuanchun Jin, Guidong Yue, Mei Liu, Jiake Xu, Shimin Liu, Jordi Jordana, Antonia Noce, Marcel Amills, Dong Dong Wu^*, Shuaicheng Li^*, Xiangshan Zhou^*, Jifeng Zhong^*

^*Corresponding author for this work

Department of Computer Science

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

83 Citations (Scopus)

93 Downloads (CityUHK Scholars)

Abstract

Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition.

Original language	English
Article number	6014
Journal	Nature Communications
Volume	11
Online published	8 Dec 2020
DOIs	https://doi.org/10.1038/s41467-020-19813-7
Publication status	Published - 2020

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This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format.

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Wang, C., Li, H., Guo, Y., Huang, J., Sun, Y., Min, J., Wang, J., Fang, X., Zhao, Z., Wang, S., Zhang, Y., Liu, Q., Jiang, Q., Wang, X., Guo, Y., Yang, C., Wang, Y., Tian, F., Zhuang, G., ... Zhong, J. (2020). Donkey genomes provide new insights into domestication and selection for coat color. Nature Communications, 11, Article 6014. https://doi.org/10.1038/s41467-020-19813-7

@article{c72ac1843ca7412e9107f2fe5ea68db5,

title = "Donkey genomes provide new insights into domestication and selection for coat color",

abstract = "Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition.",

author = "Changfa Wang and Haijing Li and Yu Guo and Jinming Huang and Yan Sun and Jiumeng Min and Jinpeng Wang and Xiaodong Fang and Zicheng Zhao and Shuai Wang and Yanlin Zhang and Qingfeng Liu and Qiang Jiang and Xiuge Wang and Yijun Guo and Chunhong Yang and Yinchao Wang and Fang Tian and Guilong Zhuang and Yanna Fan and Qican Gao and Yuhua Li and Zhihua Ju and Jianbin Li and Rongling Li and Minghai Hou and Guiwen Yang and Guiqin Liu and Wenqiang Liu and Jiao Guo and Shanshan Pan and Guangyi Fan and Wei Zhang and Ruitao Zhang and Jie Yu and Xinhao Zhang and Qi Yin and Chuanliang Ji and Yuanchun Jin and Guidong Yue and Mei Liu and Jiake Xu and Shimin Liu and Jordi Jordana and Antonia Noce and Marcel Amills and Wu, {Dong Dong} and Shuaicheng Li and Xiangshan Zhou and Jifeng Zhong",

year = "2020",

doi = "10.1038/s41467-020-19813-7",

language = "English",

volume = "11",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Springer Nature",

}

Wang, C, Li, H, Guo, Y, Huang, J, Sun, Y, Min, J, Wang, J, Fang, X , Zhao, Z , Wang, S, Zhang, Y, Liu, Q, Jiang, Q, Wang, X, Guo, Y, Yang, C, Wang, Y, Tian, F, Zhuang, G, Fan, Y, Gao, Q, Li, Y, Ju, Z, Li, J, Li, R, Hou, M, Yang, G, Liu, G, Liu, W, Guo, J, Pan, S, Fan, G, Zhang, W, Zhang, R, Yu, J, Zhang, X, Yin, Q, Ji, C, Jin, Y, Yue, G, Liu, M, Xu, J, Liu, S, Jordana, J, Noce, A, Amills, M, Wu, DD, Li, S, Zhou, X & Zhong, J 2020, 'Donkey genomes provide new insights into domestication and selection for coat color', Nature Communications, vol. 11, 6014. https://doi.org/10.1038/s41467-020-19813-7

TY - JOUR

T1 - Donkey genomes provide new insights into domestication and selection for coat color

AU - Wang, Changfa

AU - Li, Haijing

AU - Guo, Yu

AU - Huang, Jinming

AU - Sun, Yan

AU - Min, Jiumeng

AU - Wang, Jinpeng

AU - Fang, Xiaodong

AU - Zhao, Zicheng

AU - Wang, Shuai

AU - Zhang, Yanlin

AU - Liu, Qingfeng

AU - Jiang, Qiang

AU - Wang, Xiuge

AU - Guo, Yijun

AU - Yang, Chunhong

AU - Wang, Yinchao

AU - Tian, Fang

AU - Zhuang, Guilong

AU - Fan, Yanna

AU - Gao, Qican

AU - Li, Yuhua

AU - Ju, Zhihua

AU - Li, Jianbin

AU - Li, Rongling

AU - Hou, Minghai

AU - Yang, Guiwen

AU - Liu, Guiqin

AU - Liu, Wenqiang

AU - Guo, Jiao

AU - Pan, Shanshan

AU - Fan, Guangyi

AU - Zhang, Wei

AU - Zhang, Ruitao

AU - Yu, Jie

AU - Zhang, Xinhao

AU - Yin, Qi

AU - Ji, Chuanliang

AU - Jin, Yuanchun

AU - Yue, Guidong

AU - Liu, Mei

AU - Xu, Jiake

AU - Liu, Shimin

AU - Jordana, Jordi

AU - Noce, Antonia

AU - Amills, Marcel

AU - Wu, Dong Dong

AU - Li, Shuaicheng

AU - Zhou, Xiangshan

AU - Zhong, Jifeng

PY - 2020

Y1 - 2020

N2 - Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition.

AB - Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition.

UR - http://www.scopus.com/inward/record.url?scp=85097292421&partnerID=8YFLogxK

UR - https://www.scopus.com/record/pubmetrics.uri?eid=2-s2.0-85097292421&origin=recordpage

U2 - 10.1038/s41467-020-19813-7

DO - 10.1038/s41467-020-19813-7

M3 - RGC 21 - Publication in refereed journal

C2 - 33293529

SN - 2041-1723

VL - 11

JO - Nature Communications

JF - Nature Communications

M1 - 6014

ER -

Donkey genomes provide new insights into domestication and selection for coat color

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