Collaborative Research: A community resource for genome-scale identification of genotype-phenotype relationships in a model photosynthetic eukaryote

合作研究：用于在模型光合真核生物中基因组规模鉴定基因型-表型关系的社区资源

• 批准号: 1914989
• 负责人: Martin Jonikas
• 金额: $ 387.64万
• 依托单位: Princeton University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-15 至 2024-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1914989&HistoricalAwards=false
• 关键词: Collaborative; Research; community; resource; genome

This project will generate physical and data resources that will dramatically advance understanding of the functions of thousands of genes in photosynthetic organisms. Photosynthetic organisms provide food and energy for nearly all life on Earth, yet most of their genes remain uncharacterized. This project will expand the availability of mutants needed to study the functions of genes in the single-celled model photosynthetic alga Chlamydomonas reinhardtii. The new project will use the newly generated mutants to identify relationships between genes and observable characteristics and will allow genes to be assigned to genetic pathways on an unprecedented scale. The resulting mutants will be available to the research community via the Chlamydomonas Resource Center, and the resulting data will be searchable on a website. The basic knowledge and resources generated by this project will lay the groundwork for advances in biotechnology, agriculture, and health. The placement of thousands of genes into pathways will identify new opportunities for pathway engineering in photosynthetic organisms. Mutants with enhanced or deficient growth in specific environments will reveal genetic targets for enhancing resistance of crops to a broad range of stresses. Mutants with defects in cilia will advance our structural and molecular understanding of these organelles, which play key roles in development and disease. The project will enhance infrastructure for research and education by providing urgently needed high-quality disruption mutants for many genes. The project will directly contribute to the training of many undergraduates, college graduates, and a postdoctoral fellow, and will advance the training of countless young researchers as they use the resources produced.The project builds on the team's success in developing the existing Chlamydomonas mutant resource and extensive preliminary studies demonstrating that mutant phenotypes can be assessed in pools, where each mutant's growth rate is tracked by measuring the abundance of its unique DNA barcode. High confidence in a genotype-phenotype relationship requires three independent high-confidence alleles disrupting the gene of interest. The first aim of this project is to increase from 9% to 84% the percentage of genes covered with three high-confidence disruptions by improving the mapping accuracy of existing mutants and by generating additional mutants. The second aim is to systematically assign genes to pathways by identifying high-confidence genotype-phenotype relationships across the genome. The phenotypes of 70,000 mutants will be determined under hundreds of conditions, half of which will be selected by the community. Genes will be clustered into pathways based on the principle that mutants affected in in the same pathway show a similar pattern of phenotypes across a broad range of conditions. The third aim is to make the resulting mutants and data broadly available to the research community. Mutants generated by the project will complement the Chlamydomonas Resource Center's existing collection by providing coverage for genes not currently represented. Insertion sites, mutant and gene phenotypes, and gene pathway assignments will be searchable online. This project will transform our understanding of photosynthetic organisms by producing a comprehensive genotype-phenotype map. The availability of mutants and phenotypes will allow the community to make rapid progress on determining the molecular functions of uncharacterized genes and the proteins they encode.This award was jointly funded by the Systems and Synthetic Biology Program and the Genetic Mechanisms Program in the Division of Molecular and Cellular Biosciences and by the Infrastructure Capacity for Biology Program / Collections in Support of Biological Research in the Division of Biological Infrastructure. All three programs are in the Biological Sciences Directorate.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

该项目将产生物理和数据资源，这将极大地促进对光合生物中数千种基因功能的理解。光合生物为地球上几乎所有的生命提供食物和能量，但它们的大部分基因仍未被确定。该项目将扩大研究单细胞模式光合藻类莱茵衣藻基因功能所需突变体的可用性。新项目将使用新产生的突变体来识别基因和可观察特征之间的关系，并将允许基因以前所未有的规模分配给遗传途径。最终的突变体将通过衣藻资源中心提供给研究界，结果数据将在网站上搜索。该项目产生的基本知识和资源将为生物技术、农业和卫生方面的进步奠定基础。将成千上万的基因植入途径将为光合生物的途径工程提供新的机会。在特定环境中增强或缺乏生长的突变体将揭示增强作物对广泛胁迫的抗性的遗传靶标。具有纤毛缺陷的突变体将促进我们对这些细胞器的结构和分子理解，这些细胞器在发育和疾病中起着关键作用。该项目将通过为许多基因提供急需的高质量破坏突变体，加强研究和教育的基础设施。该项目将直接为许多本科生、大学毕业生和一名博士后的培训做出贡献，并将促进无数年轻研究人员的培训，因为他们使用所产生的资源。该项目建立在团队成功开发现有衣藻突变资源和广泛的初步研究的基础上，这些研究表明可以在池中评估突变表型，通过测量其独特DNA条形码的丰度来跟踪每个突变的生长速度。高置信度的基因型-表型关系需要三个独立的高置信度等位基因干扰感兴趣的基因。该项目的第一个目标是通过提高现有突变体的定位精度和产生额外的突变体，将三种高可信度中断覆盖的基因百分比从9%提高到84%。第二个目标是通过在基因组中识别高置信度的基因型-表型关系，系统地将基因分配到通路上。将在数百种条件下确定70,000个突变体的表型，其中一半将由社区选择。基因将根据在同一途径中受影响的突变在广泛的条件下表现出相似的表型模式的原则聚集成通路。第三个目标是使结果突变体和数据广泛地提供给研究界。该项目产生的突变体将通过覆盖目前未代表的基因，补充衣藻资源中心现有的收集。插入位点，突变和基因表型，以及基因通路分配将可在线搜索。这个项目将通过制作一个全面的基因型-表型图谱来改变我们对光合生物的理解。突变体和表型的可用性将使社区在确定未表征基因及其编码的蛋白质的分子功能方面取得快速进展。该奖项由分子与细胞生物科学部的系统与合成生物学项目和遗传机制项目以及生物基础设施部支持生物研究的生物项目基础设施能力/集合共同资助。这三个项目都在生物科学理事会。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。