群体基因组学分析揭示斗鸡的育种历史和人工选择机制

Chickens (Gallus gallus domesticus) are well known to possess the largest phenotypic diversity of any known avian species, largely as a consequence of their long history of domestication for different purposes across the globe. A particular type of domesticated chickens raised for cockfighting—gamefowls (i.e. game cock)—are well-known for their unique aggressiveness and phenotypic adaptations to cockfight, that is, one of the most ancient human blood sports. Accompanying human populations in various dispersals, gamefowls become a global chicken breed distributing wildly. And gamefowls exhibit some unique physical and behavior traits that are markedly different than either common domesticated chickens or the wild ancestor, the red junglefowl (Gallus gallus). Nevertheless, the domestication histories of gamefowls such as their origins, dispersals, as well as the phenotypic evolution, remain poorly understood..In this project, we propose to integrate whole genome re-sequencing and RNA sequencing strategies to investigate the collected samples of global gamefowl populations with the high-throughput next-generation sequencing platform. Incorporating the available data of chicken (including red junglefowl) genomes and transcriptomes, we plan to carry out various analyses to unveil the domestication history of gamefowls. It includes (1) investigating the genomic diversity of global gamefowl populations, discerning the genetic relationships among the gamefowl, indigenous common chicken, and red junglefowl populations and tracing the population history including origin, dispersal, admixture, and demography for gamefowls; (2) detecting the loci and/or genes under directional selection, evaluating and validating the selective signals in transcriptome analyses and the subsequent qRT-PCR, and then inferring the potential genetic mechanisms of artificial selection involved in the breeding of gamefowls..It is expected that, this project will not only provide an essential piece to the genetic jigsaw puzzle of chicken domestication, but also extend the understanding of phenotypic evolution of chicken. The massive genomic and transcriptomic data generated in this project will be valuable in future genetic researches as well as molecular breeding for chicken.

斗鸡是一类专门为打斗而培育的古老鸡种。经过长期选育，斗鸡在体型和行为上演化出有别于其他家鸡和红原鸡的诸多特征。开展斗鸡的基因组学研究可以增进对家鸡遗传多样性和驯化历史的认识，并拓展对家鸡中人工选择及表型演化机制的了解。在本项目中，我们拟采用基于二代测序技术对来自亚非欧三大洲的多个斗鸡群体进行全基因组重测序，并选择部分组织样本进行RNA测序。我们拟运用多种群体基因组学方法分析并结合转录组数据验证的策略，从全基因组水平揭示斗鸡的驯化历史。其内容包括：（1）展示斗鸡群体的基因组多样性分布格局，追溯斗鸡的起源、迁移、混合、有效群体大小变化等群体历史事件，揭示斗鸡的育种历史；（2）检测斗鸡基因组中受到选择作用的位点及其基因片段，并从转录水平对选择信号进行验证，尝试探讨斗鸡驯化和育种中人工选择作用的遗传学机制。

本项目对16个全球斗鸡代表性群体共计121份样本进行全基因组测序，并开展多项群体基因组学分析，展示了斗鸡的遗传多样性分布格局和群体遗传结构，厘清各个地区斗鸡与地方家鸡以及红原鸡之间的遗传关系，阐明家鸡的早期驯化历史。基于选择信号检测分析筛选出斗鸡群体中特异的受选择的基因以及与斗鸡特异表型（如好斗、体态直立、体型高大等）的候选位点。基于转录组数据，探讨了斗鸡特殊行为（如好斗、攻击性强、缺乏恐惧）的遗传基础。在此基础上，本项目将分析结果纳入全球家鸡基因组研究框架之下并开发构建了数据库Chicken2K（http://chicken.ynau.edu.cn/index/home/index）对数据和分析结果进行整合。前期对家鸡早期驯化历史的研究成果已经发表，并引起国内外学者广泛关注。本项目产生的数据、分析结果以及研究成果为研究家鸡的早期驯化、群体扩散历史以及表型多样性进化遗传机制提供了核心框架，也为家鸡的遗传种质资源保护和育种改良提供了重要的参考。