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

• 批准号: 1645170
• 负责人: Daniel Bolnick
• 金额: $ 170万
• 依托单位: University of Texas at Austin
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-06-01 至 2019-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1645170&HistoricalAwards=false
• 关键词: IOS; EDGE; Expanding; toolkit; functional

'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.

为了了解人类生物学，研究人员使用非人类物种作为替身或“模型”。因为没有一个物种是人类生物学的完美模型，科学受益于广泛的模式生物组合，每一个都与人类生物学相关。该项目将创造新的方法来研究一种新兴的模式，三棘鱼（Gasterosteus aculeatus）。这种小鱼比传统的实验室模型具有重要的优势。自从大约12,000年前北方的冰川消退以来，许多有益的遗传变异在数千个不同的自然种群中幸存下来。与实验室遗传筛查不同，这些自然变异揭示了生物学创新：例如抵抗寄生虫的新方法。一个大型的研究社区（100个实验室）现在研究刺鱼，以了解行为，发育和免疫学。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，但需要工具来实验性地改变基因功能以进行确认。这笔赠款将支持一个由五名研究人员组成的团队开发针对棘鱼的新基因编辑方法。由于棘鱼在野外也很容易研究，因此这个研究小组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课程培训来自世界各地的本科生、研究生和研究人员。该项目还将建立基础设施（一个储备中心），以使研究有用的种群永久化，并为美洲原住民学生和社区提供研究经验，使他们能够对当地本土动物进行科学研究。海洋种群独立地在许多不同的沿海流域定居，从大规模复制的自然实验中产生了特殊的表型变异。2.祖先等位基因在现代海洋种群中持续存在，使适应性特征的遗传图谱在已知的生态环境中。3.刺鱼很容易在实验室和自然界中大量繁殖和操纵。4.已发表的基因组、转录组和微生物组为强有力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刺鱼适应的遗传学。然而，这些研究主要局限于相关的方法：QTL定位，分歧作图和关联研究。研究人员使用实验性基因操作来验证可疑的候选基因仍然很罕见。为了实现棘鱼的功能基因组研究，该项目将改进基因编辑的方法。首先，研究小组将使用转录组学和ChIP-Seq来改进基因组注释，以更好地定位候选基因。其次，他们将开发更有效的基因编辑方法，通过胚胎显微注射或细胞培养转染或使用病毒介导的基因转移来递送CRISPR-Cas9。最后，研究小组将建立一个储备中心，在那里可以维持天然和转基因品系，并运送给用户，使研究标准化的遗传背景跨越刺鱼？自然多样性。这项工作将通过网络研讨会、方法博客、学生交叉培训和大型实验室课程进行传播。这将为世界各地的本科生，研究生，博士后和同事以及阿拉斯加的美洲原住民社区提供研究培训。

项目成果

Learning objectives for weaving evolutionary thinking into medical education.

将进化思想融入医学教育的学习目标。

• 发表时间: 2017
• 期刊: Medical science educator
• 影响因子: 1.7
• 作者: Bolnick, D.I.

Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution

• DOI: 10.1186/s13059-020-02097-x
• 发表时间: 2020-07-19
• 期刊: GENOME BIOLOGY
• 影响因子: 12.3
• 作者: Peichel, Catherine L.;McCann, Shaugnessy R.;White, Michael A.
• 通讯作者: White, Michael A.