Quantitative Trait Locus Editing for Crop Improvement

用于作物改良的定量性状基因座编辑

• 批准号: 1444511
• 负责人: Adam Bogdanove
• 金额: $ 550万
• 依托单位: Cornell University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-05-01 至 2021-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1444511&HistoricalAwards=false
• 关键词: Quantitative; Trait; Locus; Editing; Crop

Milestone achievements in crop research now enable difficult challenges to be addressed rapidly and effectively using innovative approaches. These achievements include DNA sequences and measurements of traits relevant to productivity and quality for large numbers of varieties within individual crop species, powerful computational approaches and data management tools, increasingly detailed molecular understanding of plant biology including responses to the environment, and new methods to precisely test the function of particular DNA sequences. Building on these resources and tools, this project will address the longstanding challenge of identifying DNA sequences responsible for traits that vary in a quantitative way, called "quantitative trait loci" (QTL), and making them amenable for crop improvement. While QTL are key determinants of crop productivity, they have been exceedingly difficult to study, and very little is known about them. This project focuses on QTL for disease resistance, disease susceptibility, and tolerance to acid soils in the globally important crop species, rice. The project will isolate DNA sequences associated with high levels of these traits and test whether those sequences are responsible by moving them into rice varieties that show low trait levels and measuring the result. The project will improve understanding of crop resistance to stresses caused by pests and poor soil conditions and lead to improved crop productivity. More broadly, the project will establish effective ways to connect variation across individuals with the DNA sequences that cause that variation, which will be useful not only for plant research, but other life sciences, including medicine. The project will further benefit society by integrating its research objectives with educational activities and materials that will engage and inform the public and increase participation by members of underrepresented groups. These include a combined classroom and research experience program for small-college undergraduates, training workshops for plant biologists, multi-media educational resources to engage middle and high school students, and a project web site (www.ricediversity.org) for public access to project-related materials, publications, and data. Moreover, the project will foster the development of diverse junior personnel into independent scientistsCompilations of genomic and other genotypic as well as phenotypic and associated metadata for large numbers of rice, powerful informatics approaches and data management tools, the unprecedented ability to precisely edit plant genomes to probe gene function, and increasingly detailed molecular understanding of rice responses to biotic and abiotic stresses, together provide a foundation for this project. This project applies large-scale statistical genetics and genome editing technology to examine distinct QTL for disease resistance, disease susceptibility, and acid soil tolerance. Building on genomic and phenotypic data, computational methods, and infrastructure generated under previous NSF awards and elsewhere, including the recently released genome sequences of 3,000 rice accessions, the project will connect genotype to phenotype for each trait, using genome editing to functionally evaluate isolated genetic polymorphism in new genetic backgrounds. Co-variation will also be examined for each trait to test for genetic background effects on allele viability, and in the case of disease susceptibility and resistance, allelic variation in pathogen-targeted genes will be queried for evidence of purifying or positive selection. Findings will be used to expand the tools and the collection of genotypic and phenotypic data associated with the project, and tailor these resources for the community, while improving understanding of and the ability to enhance plant resistance to biotic and abiotic stresses. Under the outreach objectives of the project, the combined classroom and research experience program for small-college undergraduates will integrate computational and molecular biology aspects of the proposed research and include summer internships in the research laboratories at Cornell. The training workshops will focus specifically on genome editing for plant biologists, especially those from underserved and underrepresented groups; the multimedia educational resources will include stories, podcasts, and interactive web modules and will be distributed through major media outlets; the project web site (www.ricediversity.org) for scientists, the general public, and educators will provide access to project-related materials, protocols, publications, and data (data will be released on or before publication of analytical results). Finally, the development of diverse junior personnel into capable, creative, and collaborative independent scientists will be fostered by a multi-institutional, cross-disciplinary research environment.

作物研究的里程碑式成就现在使人们能够使用创新方法快速有效地应对困难的挑战。这些成就包括DNA序列和与单个作物物种中大量品种的生产力和质量相关的性状的测量，强大的计算方法和数据管理工具，对植物生物学（包括对环境的反应）日益详细的分子理解，以及精确测试特定DNA序列功能的新方法。在这些资源和工具的基础上，该项目将解决长期存在的挑战，即确定负责以定量方式变化的性状的DNA序列，称为“数量性状基因座”（QTL），并使其适合作物改良。 虽然QTL是作物生产力的关键决定因素，但它们的研究非常困难，而且对它们的了解很少。该项目的重点是在全球重要的作物品种，水稻抗病性，疾病易感性，耐酸性土壤的QTL。该项目将分离出与高水平这些性状相关的DNA序列，并通过将这些序列转移到表现出低水平性状的水稻品种中并测量结果来测试这些序列是否与此相关。该项目将提高对作物抵抗虫害和土壤条件差造成的压力的认识，从而提高作物生产力。更广泛地说，该项目将建立有效的方法，将个体之间的变异与导致这种变异的DNA序列联系起来，这不仅对植物研究有用，而且对包括医学在内的其他生命科学也有用。该项目将通过将其研究目标与教育活动和材料相结合，使公众参与和了解情况，并增加代表性不足群体成员的参与，从而进一步造福社会。这些措施包括一个综合的教室和研究经验计划，为小型大学本科生，植物生物学家的培训研讨会，多媒体教育资源，使初中和高中学生，和一个项目网站（www.ricediversity.org）为公众访问项目相关的材料，出版物和数据。此外，该项目还将促进将各种初级人员培养成独立的科学家，包括大量水稻的基因组和其他基因型以及表型和相关元数据的研究、强大的信息学方法和数据管理工具、精确编辑植物基因组以探测基因功能的前所未有的能力，以及对水稻对生物和非生物胁迫的反应越来越详细的分子理解，共同为这个项目奠定了基础。该项目应用大规模统计遗传学和基因组编辑技术来检测抗病性、疾病易感性和酸性土壤耐受性的不同QTL。该项目基于先前NSF奖项和其他地方产生的基因组和表型数据、计算方法和基础设施，包括最近发布的3,000份水稻种质的基因组序列，将每个性状的基因型与表型联系起来，使用基因组编辑功能评估新遗传背景中孤立的遗传多态性。还将检查每个性状的共变异，以测试对等位基因活力的遗传背景效应，并且在疾病易感性和抗性的情况下，将查询病原体靶向基因中的等位基因变异，以获得纯化或阳性选择的证据。研究结果将用于扩展与该项目相关的工具和基因型和表型数据的收集，并为社区定制这些资源，同时提高对增强植物对生物和非生物胁迫抗性的理解和能力。根据该项目的推广目标，针对小型大学本科生的综合课堂和研究经验计划将整合拟议研究的计算和分子生物学方面，并包括在康奈尔大学研究实验室的暑期实习。培训讲习班将特别侧重于植物生物学家的基因组编辑，特别是那些来自服务不足和代表性不足群体的生物学家;多媒体教育资源将包括故事、播客和互动网络模块，并将通过主要媒体渠道分发;www.ricediversity.org科学家、公众和教育工作者的项目网站（www.example.com）将提供与项目有关的材料、协议、出版物、和数据（数据将在分析结果发表之时或之前发布）。最后，多元化的初级人员发展成为有能力的，创造性的和协作的独立科学家将由多机构，跨学科的研究环境。