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: 1915154
• 负责人: Paul Lefebvre
• 金额: $ 62.22万
• 依托单位: University of Minnesota-Twin Cities
• 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 2024-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1915154&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，这些资源将极大地提高对光合生物中数千个基因功能的理解。光合生物几乎为地球上的所有生命提供了食物和能量，但它们的大多数基因仍然没有表征。该项目将扩大研究基因功能在单细胞模型光合藻藻中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与可观察到的特征之间的关系，并将基因以前所未有的规模分配到遗传途径。由此产生的突变体将通过衣原体资源中心向研究社区提供，并且可以在网站上搜索所得数据。该项目产生的基本知识和资源将为生物技术，农业和健康的进步奠定基础。将成千上万个基因放置在途径中将确定光合生物中途径工程的新机会。在特定环境中增长或不足生长的突变体将揭示遗传靶标，以增强农作物对广泛应力的抗性。纤毛缺陷的突变体将提高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来增强研究和教育的基础设施。该项目将直接有助于对许多本科生，大学毕业生和博士后研究员的培训，并将在使用所产生的资源时进步对无数年轻研究人员进行培训。该项目基于团队在开发现有的Chlamydomonas突变资源和广泛的预段研究方面的成功基础，该研究表明，通过衡量了该突变型的众所周知，这是众所周知的，该研究均可在池塘中评估了众所周知的估计率。 DNA条形码。对基因型 - 表型关系的高信心需要三个独立的高信心等位基因破坏感兴趣的基因。该项目的第一个目的是通过提高现有突变体的映射准确性并产生其他突变体来增加9％的基因百分比。第二个目的是通过识别整个基因组中的高信任基因型 - 表型关系来系统地将基因分配给途径。 70,000个突变体的表型将在数百个条件下确定，其中一半将由社区选择。基因将基于以下原理聚类为途径，即在相同途径中受影响的突变体在广泛的条件下显示出相似的表型模式。第三个目的是使研究界广泛可用的突变体和数据。该项目产生的突变体将通过提供目前未代表的基因的覆盖范围来补充衣原体资源中心的现有收藏。插入位点，突变体和基因表型以及基因途径分配将在线搜索。该项目将通过生成全面的基因型 - 表型图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的分子功能及其编码的蛋白质方面取得快速进步。该奖项由系统和合成生物学计划和遗传机制计划共同资助。 基础设施。 这三个计划均在生物科学局中。该奖项反映了NSF的法定任务，并被认为是使用基金会的知识分子优点和更广泛影响的评论标准的评估值得支持的。