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

基本信息

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

项目摘要

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，从而极大地促进对光合生物中数千个基因功能的理解。光合生物为地球上几乎所有生命提供食物和能量，但它们的大部分基因仍未被表征。该项目将扩大研究单细胞模型光合藻类莱茵衣藻基因功能所需的突变体的可用性。新项目将使用新生成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。由此产生的突变体将通过衣藻资源中心提供给研究界，并且所得数据可在网站上搜索。该项目产生的基础知识和资源将为生物技术、农业和健康的进步奠定基础。将数千个基因放入通路中将为光合生物中的通路工程找到新的机会。在特定环境中生长增强或不足的突变体将揭示增强作物对广泛胁迫的抵抗力的遗传目标。纤毛缺陷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发挥着关键作用。该项目将通过为许多基因提供急需的高质量破坏突变体来加强研究和教育基础设施。该项目将直接为许多本科生、大学毕业生和博士后的培训做出贡献，并将在使用所产生的资源时促进无数年轻研究人员的培训。该项目建立在该团队成功开发现有衣藻突变体资源的基础上广泛的初步研究表明，可以在池中评估突变体表型，通过测量其独特 DNA 条形码的丰度来跟踪每个突变体的生长速率。基因型-表型关系的高置信度需要三个独立的高置信度等位基因破坏感兴趣的基因。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生成额外的突变体，将被三个高置信度破坏覆盖的基因百分比从 9% 增加到 84%。第二个目标是通过识别整个基因组中高可信度的基因型-表型关系来系统地将基因分配给通路。 70,000 个突变体的表型将在数百种条件下确定，其中一半将由社区选择。基因将被聚类到途径中，其原理是受同一途径影响的突变体在广泛的条件下表现出相似的表型模式。第三个目标是将产生的突变体和数据广泛提供给研究界。该项目产生的突变体将通过覆盖目前未代表的基因来补充衣藻资源中心的现有收集。插入位点、突变体和基因表型以及基因途径分配都可以在线搜索。该项目将通过生成全面的基因型-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能够在确定未表征的基因及其编码的蛋白质的分子功能方面取得快速进展。该奖项由分子部门的系统和合成生物学计划和遗传机制计划联合资助和细胞生物科学以及生物基础设施部门支持生物研究的生物学计划/馆藏的基础设施能力。所有三个项目均属于生物科学理事会。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。