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原鸡和本土乡村鸡的全基因组重测序揭示了该物种基因组动态的新见解。

Whole-Genome Resequencing of Red Junglefowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species.

作者信息

Lawal Raman A, Al-Atiyat Raed M, Aljumaah Riyadh S, Silva Pradeepa, Mwacharo Joram M, Hanotte Olivier

机构信息

Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.

Genetics and Biotechnology, Animal Science Department, Agriculture Faculty, Mutah University, Karak, Jordan.

出版信息

Front Genet. 2018 Jul 20;9:264. doi: 10.3389/fgene.2018.00264. eCollection 2018.

Abstract

The red junglefowl is the main progenitor of domestic chicken, the commonest livestock species, outnumbering humans by an approximate ratio of six to one. The genetic control for production traits have been well studied in commercial chicken, but the selection pressures underlying unique adaptation and production to local environments remain largely unknown in indigenous village chicken. Likewise, the genome regions under positive selection in the wild red junglefowl remain untapped. Here, using the pool heterozygosity approach, we analyzed indigenous village chicken populations from Ethiopia, Saudi Arabia, and Sri Lanka, alongside six red junglefowl, for signatures of positive selection across the autosomes. Two red junglefowl candidate selected regions were shared with all domestic chicken populations. Four candidates sweep regions, unique to and shared among all indigenous domestic chicken, were detected. Only one region includes annotated genes ( and ). Candidate regions that were unique to each domestic chicken population with functions relating to adaptation to temperature gradient, production, reproduction and immunity were identified. Our results provide new insights on the consequence of the selection pressures that followed domestication on the genome landscape of the domestic village chicken.

摘要

原鸡是家鸡的主要祖先,家鸡是最常见的家畜物种,数量比人类多出约六比一。商业鸡种中生产性状的遗传控制已得到充分研究,但本地土鸡独特适应和适应本地环境的生产背后的选择压力在很大程度上仍不为人知。同样,野生原鸡中受到正选择的基因组区域仍未被开发。在这里,我们使用混合杂合性方法,分析了来自埃塞俄比亚、沙特阿拉伯和斯里兰卡的本地土鸡种群,以及六只原鸡,以寻找常染色体上正选择的特征。两个原鸡候选选择区域与所有家鸡种群共有。检测到四个候选扫荡区域,这些区域是所有本地家鸡所特有的且在它们之间共享。只有一个区域包含注释基因(和)。确定了每个家鸡种群特有的与适应温度梯度、生产、繁殖和免疫相关功能的候选区域。我们的结果为驯化后选择压力对本地家鸡基因组景观的影响提供了新的见解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a708/6062655/a775d21e4bef/fgene-09-00264-g0001.jpg

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