IOS EDGE: Expanding the toolkit for functional genetics in threespine stickleback to place genomics into its natural context

IOS EDGE：扩展三刺鱼功能遗传学工具包，将基因组学置于其自然环境中

基本信息

批准号：
1915134
负责人：
Daniel Bolnick
金额：
$ 123.21万
依托单位：
University of Connecticut
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2018
资助国家：
美国
起止时间：
2018-09-01 至 2022-05-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1915134&HistoricalAwards=false
关键词：
IOS EDGE Expanding toolkit functional

项目摘要

'To learn about human biology, researchers use non-human species as stand-ins, or 'models'. Because no single species is a perfect model of human biology, science benefits from a broad portfolio of model organisms, each with its own relevance to human biology. This project will create new methods to study an emerging model, the threespine stickleback (Gasterosteus aculeatus). This small fish offers an important advantage over traditional lab models. Since the glaciers retreated in the northern hemisphere ~12,000 years ago, many beneficial genetic variants have survived in thousands of distinct natural populations. Unlike laboratory genetic screens, which reveal mutations in genes causing abnormal development or physiology, these natural variants reveal biological innovations: new ways of resisting parasites, for instance. A large community of researchers (100 labs) now studies stickleback to understand behavior, development, and immunology. The research team has identified candidate genes affecting important traits like brain and bone development, but require tools to experimentally alter gene function for confirmation. This grant will support a team of five researchers developing new gene-editing methods for stickleback. Because stickleback are easily studied in the wild as well, this research team can take the unique step of linking laboratory genetics back to gene function in their natural environment. The researchers will train undergraduates, graduate students, and researchers from around the world, via new online communities and in-person courses. The project will also build infrastructure (a stock center) to perpetuate research-useful populations and provide research experiences for Native American students and communities, exposing them to scientific studies of local native animals.Stickleback are a leading model in organismal biology for several reasons: 1. Marine populations independently colonized many diverse coastal watersheds, yielding exceptional phenotypic variation from a massively replicated natural experiment. 2. Ancestral alleles persist in modern oceanic populations, enabling genetic mapping of adaptive traits in known ecological contexts. 3. Stickleback are easy to breed and manipulate in large numbers in the lab and in nature. 4. Published genomes, transcriptomes, and microbiomes provide references for robust candidate gene identification and probe development. Consequently, hundreds of researchers study the genetics of stickleback adaptation. However, this research is largely confined to correlative approaches: QTL mapping, divergence mapping, and association studies. It remains rare for researchers to validate suspected candidate genes using experimental gene manipulation. To enable functional genomic studies of stickleback, this project will refine methods for gene editing. First, the research team will use transcriptomics and ChIP-Seq to improve genome annotation, to better locate candidate genes. Second, they will develop methods for more efficient gene editing with CRISPR-Cas9 delivered via embryo microinjection or cell culture transfection, or using viral-mediated gene transfer. Finally, the team will construct a stock center where natural and transgenic lines can be maintained and shipped to users, enabling studies on standardized genetic backgrounds spanning sticklebacks? natural diversity. The work will be disseminated via webinars, methods blogs, cross training of students, and a large lab course. This will provide research training to undergraduates, graduate students, postdocs, and colleagues around the world, as well as Native American communities in Alaska.

“了解人类生物学，研究人员将非人类物种用作替代品或“模型”。由于没有单一物种是人类生物学的完美模型，因此科学受益于模型生物的广泛组合，每种都与人类生物学相关。该项目将创建新的方法来研究新兴模型，即三杆粘背（Gasterosteus aculeatus）。这种小鱼比传统实验室模型具有重要的优势。自从北半球撤退的冰川大约12，000年前，许多有益的遗传变异已在数千种不同的自然种群中幸存下来。与实验室遗传筛查揭示了引起异常发育或生理学的基因突变不同，这些自然变体揭示了生物创新：例如，抵抗寄生虫的新方法。一个大型研究人员社区（100个实验室）现在研究障碍，以了解行为，发展和免疫学。研究小组已经确定了影响大脑和骨骼发育等重要特征的候选基因，但需要工具才能实验改变基因功能以确认。该赠款将支持由五名研究人员组成的团队，开发新的基因编辑方法来进行Stickleback。由于在野外也很容易研究Stickleback，因此该研究团队可以采取独特的步骤将实验室遗传学与自然环境中的基因功能联系起来。研究人员将通过新的在线社区和面对面的课程培训来自世界各地的大学生，研究生和研究人员。该项目还将建立基础架构（储备中心），以使研究可用的人群永存，并为美国原住民的学生和社区提供研究经验，使它们接受对当地本地动物的科学研究。Stickleback是生物学的主要模型，原因是几种原因：1。海洋人群独立于沿海地区独立地殖民了自然的众所周知，从而产生了众多的自然量，从而产生了一个自然的种如候。 2。祖先等位基因在现代海洋种群中持续存在，在已知的生态环境中实现了适应性特征的遗传图。 3.粘式背部在实验室和自然界中易于繁殖和操纵。 4。发表的基因组，转录组和微生物组为可靠的候选基因鉴定和探针开发提供了参考。因此，数百名研究人员研究了粘性适应的遗传学。但是，这项研究在很大程度上仅限于相关方法：QTL映射，分歧映射和关联研究。研究人员使用实验基因操纵验证可疑的候选基因仍然很少。为了实现粘性的功能基因组研究，该项目将完善基因编辑的方法。首先，研究小组将使用转录组学和CHIP-SEQ来改善基因组注释，以更好地定位候选基因。其次，他们将开发使用通过胚胎微注射或细胞培养转染或使用病毒介导的基因转移的CRISPR-CAS9进行更有效基因编辑的方法。最后，团队将建立一个库存中心，可以将天然和转基因线保持并运送给用户，从而可以研究标准化的遗传背景，以跨越粘性？自然多样性。这项工作将通过网络研讨会，方法博客，学生交叉培训以及大型实验室课程进行传播。这将为世界各地的大学生，研究生，博士后和同事以及阿拉斯加原住民社区提供研究培训。