全基因组水平揭示家鸡的起源和人工选择机制

When, where and how animals were domesticated is a fundamental and crucial question in biological research. Chicken, is one of the leading domestic animals globally in terms of numbers and variability, yet questions regarding where, when, and which subspecies of Red junglefowl procured its domestication remain controversial. To resolve this puzzle, we plan to perform whole genome sequencing for 150 Red junglefowls and 350 domestic chickens from Southern Asia, Southeastern Asia, and Eastern Asia, covering all the disputed origins for domestic chicken, and leverage a series of population genomics and bioinformatic method to clarify the origin of domestic chicken. Based on the inferred population history of domestic chicken, we will compare genomes of domestic chicken with their direct ancestor and employ biological experiments to reveal the genetic basis of evolutionary changes in chicken during domestication. Additionally, we plan to facilitate better use and sharing of chicken genomic resources by constructing the first chicken population SNP database using combining the genomic data and result generated in this and previous projects. Thus, this study is a systematic project that will not only resolve the origin but also reveal the evolutionary events following domestication of chicken. This study provides a model for other domestic animal research and would facilitate the protection and utilization of chicken genomic resources.

家养动物在何时何地以及如何被成功驯化是生物学领域最基本的科学问题。家鸡作为饲养数量最多、表型多样性最为丰富的家养动物之一，在何时何地由哪个红原鸡亚种驯化而来仍未有定论。本项目拟对覆盖东亚、东南亚和南亚等有争议的家鸡起源地的150只红原鸡和350只家鸡的基因组进行测序，利用群体遗传学方法和生物信息学方法深度研究探讨家鸡的起源相关问题。基于家鸡的群体历史，我们将家鸡和最近野生祖先的基因组进行比较分析，并结合功能实验，来揭示家鸡在驯化过程中的人工选择机制。本项目通过阐明家鸡的起源和驯化问题，为家养动物“起源-驯化”提供研究范式，为家鸡资源的保护和利用提供重要理论参考。

家鸡是目前饲养数量最多，表型变异最丰富的家养动物。即便如此，目前对其起源和驯化机制并不清楚。本项目通过测定和分析了大规模家鸡和野生近缘种的全基因组数据，对家鸡的起源和驯化进行了详细研究。我们研究了原鸡的系统发育和群体历史，证实家鸡起源于分布于我国云南、泰国北部和缅甸的滇南亚种的红原鸡（Gallus gallus spadiceus），而并不是之前认为的起源于多个红原鸡亚种。我们的结果支持“驯化代价”假说，说明家鸡的早期驯化存在强烈的瓶颈效应。驯化以后，家鸡基因组中积累了大量的有害突变。这些有害突变大部分以隐形和杂合状态存在，揭露了目前育种策略的弊端。通过基因组分析和功能试验结合，否定了之前认为的TSHR是家鸡早期的驯化基因。同时，我们发现了一些和生殖、生长发育相关的基因在家鸡受强烈选择信号，可能参与了家鸡的驯化过程。我们的结果为野生原鸡的多样性保护和家鸡品种的培育改良提供依据。