中国科学院昆明动物研究所机构知识库

在从东南亚地区的野生丛林鸡驯化后，鸡伴随着人类来到世界各地，成为所有家畜中最丰富、最广泛和多样化的一种。几千年来，自然选择和人工选择的共同作用在鸡的基因组上留下了印记，吸引了众多学者的研究，以获得对养鸡资源保护和复杂人类疾病的建模解决方案的认识。加快利用诸如二代测序技术（NGS)等新近出现的技术进步来鉴定家鸡独特的适应性和发育性性状的遗传基础是势在必行的。NGS技术已经能够发现基因及其分子机制，例如人和家畜适应高海拔环境，如西藏和埃塞俄比亚高原，适应尼日利亚狗的强紫外线和热带寄生虫，以及猪的大小和毛色等正选择的基因。本地鸡在资源贫乏地区的家庭生计中扮演着不可或缺的角色。这些鸡表现出的对严酷的热带环境、疾病以及次优营养等的杰出适应力。然而，它们的遗传背景仍然不清楚。同样，在中国这样的亚洲国家，本土鸡肉在营养、健康和经济增长方面也起到了相当的作用。例如，像元宝这样的微型鸡在中国古代不仅作为食物来源，而且作为财富的象征。迄今为止，“三黄鸡”在华南地区任然是一种特殊的美味佳肴和药用食品。然而，鸡体型大小的遗传控制仍然不是十分明了的。同时，尽管对三黄鸡的需求不断增加，但是关于重要本地鸡（如“三黄鸡”)的遗传结构的认识非常零碎。我们的研究集中于利用表型、基因组和转录的方法，来解开支持土著鸡适应不利环境压力的分子和表型机制，例如非洲热带地区的高温，以及家鸡选育中的重要经济性状候选基因和机制。本文总结了我们的研究成果，为促进鸡的研究和育种提供了重要的思路和资源。第一章中，我们对各土鸡鸡的起源、扩散、用途、以及由此引起的基因组和表型变化进行了全面的文献综述，这些变化使得土鸡成为研究、育种和保护的重要目标。我们还提供了进化选择的背景，以及如何破译选择的印记和重要的适应性突变位点。最后，我们提出了一些重要的研究方向和目标，以及一些我们在本研究中已经解决了的问题。在第二章中，我们完成了对肯尼亚鸡的土著鸡表型数据和所有可从互联网上下载得到的数据的广泛收集和分析。我们分析了一种以区域为基础的地方鸡的分化模式，它提示了对环境因素的适应。我们强调必须对地方鸡进行全面的遗传特征鉴定，加强表型鉴定方法来鉴定重要的遗传资源并运用于鸡的遗传育种。在第三章中，我们报告了来自肯尼亚斯瓦希里海岸的土著鸡和中国同类鸡的比较基因组和转录组学研究，以鉴定可能的热带印度洋区域适应性的候选正选择基因。这一分析是认识土著鸡适应非洲南亚热带气候的一个重要步骤，在非洲地区，土著鸡具有改善营养健康和改善数百万贫困家庭经济状况的巨大潜力。在第四章中，我们揭示了关键候选基因POU1F1和IGF1的发现，这些基因是世界最小的鸡品种Serama小体型形成的基础。我们还报道了另外三个不同地域的小型鸡品种。这些发现揭示了基因控制复杂的经济性状的可行性，如身体大小性状。在第五章中，我们首次报道了中国黄羽鸡(YFCs)的全基因组序列，俗称“三黄鸡”，并描述了它们的遗传结构和与其他中国家鸡的进化关系。我们还利用具有良好注释的高质量基因组变体的公共遗传资源数据库来支持未来研究、育种和保护中国的“三黄鸡”。最后，本文总结了本研究的主要研究成果和存在的局限性以及对未来发展的展望。

After their domestication from wild junglefowls in the southeast Asian region, chickens accompanied man to all parts of the globe, becoming one of the most abundant, wide-spread, and diversiform of all domestic animals. The joint hands of natural and artificial selection have for several millennia wrote changes on the chicken genome, attracting a high level of multi-disciplinary research to gain insights for aviculture, resource conservation, and modeling solutions to complex human diseases. Expedited leverage of the newly available technological advancements like next generation sequencing (NGS) to identify the genetic underpinnings of unique adaptive and developmental chicken-traits is imperative. NGS has enabled the discovery of genes and molecular mechanisms conveying adaptation of human and domestic animals to high altitude environments like the Tibetan and Ethiopian highlands, to strong UV and tropical parasites in Nigerian dogs, as well as the positively selected genes controlling body size and coat color in pigs.Indigenous chicken play an integral role in the livelihoods of households in resource poor settings. Compared to commercial chickens, these chickens demonstrate an outstanding resilience to harsh tropical environments, diseases, and sub-optimal nutrition and healthcare. However, their genetic background remains poorly illuminated. Similarly, indigenous chicken have played a pertinent role in the nutrition, health, and economic growth in Asian countries like China. For instance, miniature chickens like Yuanbao were used in ancient China, not only as source of food, but also as a symbol of wealth. To date, the “three-yellow chickens” are highly esteemed in southern China as a special delicacy and a medicinal food. However, the genetic control of chicken body size has remained elusive. At the same time, knowledge on the genetic architecture of important indigenous chickens like the “three-yellow-chickens” is very patchy, despite the incremental demand for these chickens. Our research focused on using phenotypic, genomic, and transcriptomic approaches to unravel the molecular and phenotypic regimes that support adaptation of indigenous chicken to places where they are highly valuable yet experience adverse environments stress, for instance the Afrotropics, and to delineate candidate genes and mechanisms involved in breeding for economically important chicken traits. In chapter one, we provide a comprehensive literature review of origin, dispersal, utilities, and consequent genomic and phenotypic changes in indigenous chicken that make them important targets for research, breeding, and conservation. We also provide a background of evolutionary selection and how to decipher the footprints of selection and important adaptive variants that can be utilized in aviculture. We lastly explain the important research gaps and the objectives that we have addressed in this research.In chapter two, we describe an extensive collection and analysis of indigenous chicken phenotypic data encompassing Kenyan chicken and all data available from internet sources. We describe a region-based differentiation pattern of indigenous chicken, which hints at likely responses to environmental factors and management practices. We highlight the necessity for comprehensive genetic characterization of indigenous chickens to augment phenotypic approaches in identifying important genetic resources for chicken breeding. In the third chapter, we report the comparative genomic and transcriptomic assessment of indigenous chicken from the Kenyan Swahili coast and their Chinese counterparts to identify candidate positively selected genes that are likely conferring adaptation to tropical Indian Ocean ream. This analysis is an important step towards understanding ways of designing suitable breeds for the Afrotropics, where indigenous chicken have a huge potential to improve the nutritional health and mitigate the rampant poverty among millions of households.In chapter four, we describe the discovery of key candidate genes, POU1F1 and IGF1, underlying the development of the world’s smallest chicken variety, the Serama. These genes are functionally associated with growth. We also report an interesting parallelism in the breeding of three allopatric bantam chickens. These findings shed important light on the genetic control of complex economically viable traits like body size. In the fifth chapter, we report the first comprehensive whole-genome sequencing of yellow-feathered chickens (YFCs) from China, commonly known as “three-yellow-chickens”, and describe their genetic structure and evolutionary relationship with other Chinese chickens. We also avail a public genetic resource with well annotated high quality genomic variants to support future research, breeding, and conservation of the esteemed Chinese YFCs.This thesis ends by a summarization of the key findings and limitations of our research and suggestions for future research.