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

Research output: Contribution to journalArticleResearchpeer-review


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 languageAmerican English
Pages (from-to)6014
JournalNature Communications
Issue number1
Publication statusPublished - Dec 2020

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