Dataset Information

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.

SUBMITTER: Wang C

PROVIDER: S-EPMC7723042 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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

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

Nature communications 20201208 1

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 mater ...[more]

PMID: 33293529

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Project description:Background: Earlobe color is a typical external trait in chicken. There are some previous studies showing that the chicken white/red earlobe color is a polygenic and sex-linked trait in some breeds, but its molecular genetic and histological mechanisms still remain unclear. Methods: We herein utilized histological section, genome-wide association study (GWAS) and RNA-seq, further to investigate the potential histological and molecular genetic mechanisms of white/red earlobe formation in Qiangyuan Partridge chicken (QYP). Results: through histological section analysis, we found the dermal papillary layer of red earlobes had many more blood vessels than that of white earlobes. And we identified a total of 44 SNPs from Chromosome 1, 2, 3, 4, 9, 10, 11, 13, 19, 20, 23 and Z, that was significantly associated with the chicken white/red earlobe color from GWAS, along with 73 significantly associated genes obtained (e.g., PIK3CB, B4GALT1 and TP63), supporting the fact that the white/red earlobe color was also polygenic and sex-linked in QYP. Importantly, PIK3CB and B4GALT1 are both involved in the biological process of angiogenesis, which may directly give rise to the chicken white earlobe formation through regulating blood vessel density in chicken earlobe. Additionally, through contrast of RNA-seq profiles between white earlobe skins and red earlobe skins, we further identified TP63 and CDH1 differentially expressed. Combined with the existing knowledge of TP63 in epithelial development and tumor angiogenesis, we propose that down-regulated TP63 in white earlobes may play roles in thickening the skin and decreasing the vessel numbers in dermal papillary layer, thereby contributing to the white earlobe formation via paling the redness of the skin in QYP, but the specific mechanism remains further clarified. Conclusion: our findings advance the existing understanding of the white earlobe formation, as well as provide new clues to understand the molecular mechanism of chicken white/red earlobe color formation.

Dataset Information

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

Publications

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

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