Tomato Chromosome 1 and 10 Sequencing, Coordination and Bioinformatics for the International Solanaceae Genome Initiative

国际茄科基因组计划番茄染色体 1 和 10 测序、协调和生物信息学

• 批准号: 0820612
• 负责人: James Giovannoni
• 金额: $ 1040.72万
• 依托单位: Boyce Thompson Institute Plant Research
• 依托单位国家: 美国
• 项目类别: Cooperative Agreement
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-06-01 至 2015-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0820612&HistoricalAwards=false
• 关键词: Tomato; Chromosome; 10; Sequencing; Coordination

PI: James J. Giovannoni (Boyce Thompson Institute for Plant Research)CoPIs: Bruce A. Roe (University of Oklahoma - Norman), Lukas A. Mueller and Joyce Van Eck (Boyce Thompson Institute for Plant Research), Stephen M. Stack (Colorado State University) The plant family Solanaceae includes tomato, pepper, potato and eggplant and is the most important vegetable family worldwide in terms of both economic value and volume of production. Tomato is also an important model system for studying fruit biology and plant responses to disease with discoveries impacting the production of many other crops. Recent advances in DNA sequencing have made it feasible to sequence the entire genome of an organism and an international consortium of 10 countries has initiated sequencing of tomato as a reference genome for the Solanaceae family of crops. This project represents the US contribution to the tomato genome sequencing effort and specifically encompasses creation of: 1) a low resolution DNA sequence of the entire tomato genome based on state-of-the-art sequencing technologies, 2) high quality DNA sequence of two of the twelve tomato chromosomes (chromosomes 1 and 10) to complement the remaining 10 chromosome sequences being created by our international partners, and 3) creation and enhancement of electronic web-based resources to allow characterization, analysis and delivery of the tomato genome sequence to researchers who will exploit it for biological discovery in tomato and additional crop species important as sources of food, fiber and energy. Availability of a tomato genome sequence will facilitate research and discovery leading to a broader understanding of plant biology, biodiversity and domestication and will impact agricultural improvement efforts directed toward crop sustainability, productivity and quality of tomato and related species.This project encompasses the US contribution to the international tomato genome sequencing effort. Public access to a reference genome sequence for tomato and related vegetable crops (potato, pepper, eggplant) will support and accelerate research activities focused on both basic understanding of plant biology and development of crop varieties with improved yield, performance, quality and sustainability, thus enhancing US and world food security. In addition to the impact of the resulting science, the project will also provide education and training opportunities. Specifically, four Ph.D. scientists (postdoctoral), two graduate students, approximately 20 undergraduate students and 17 computer programmers, research technicians and other professionals will receive training and employment under this project. The project will provide public outreach activities including presentations to K - 12th graders at schools in the vicinity of the participating research laboratories and summer research internship opportunities for ten undergraduate students in addition to those mentioned above. The project partners with ongoing USDA-funded research to convert output of the tomato genome sequencing effort into tools to assist crop breeding in addition to the development of web-based tools for their presentation to interested members of the research community and the general public. Information developed through this project will be deposited in the NCBI public DNA sequence database (GenBank), published in peer-reviewed journals and presented through the Solanaceae Genomics Network database (www.sgn.cornell.edu) that this project will support and expand.

PI: James J. Giovannoni（博伊斯·汤普森植物研究所）CoPIs: Bruce A. Roe（俄克拉何马大学-诺曼），Lukas A. Mueller和Joyce Van Eck（博伊斯·汤普森植物研究所），Stephen M. Stack（科罗拉多州立大学）茄科植物包括番茄、辣椒、土豆和茄子，是世界上经济价值和产量最重要的蔬菜家族。番茄也是研究果实生物学和植物对疾病反应的重要模型系统，其发现影响了许多其他作物的生产。DNA测序的最新进展使得对生物体的整个基因组进行测序成为可能，一个由10个国家组成的国际联盟已经开始对西红柿进行测序，作为茄科作物的参考基因组。该项目代表了美国对番茄基因组测序工作的贡献，具体包括创建：1)基于最先进测序技术的低分辨率番茄全基因组DNA序列，2)12条番茄染色体（1号和10号染色体）中的两条的高质量DNA序列，以补充我们的国际合作伙伴正在创建的其余10条染色体序列，以及3)创建和增强电子网络资源，以便进行鉴定。分析番茄基因组序列并将其传递给研究人员，研究人员将利用该序列在番茄和其他作物物种中进行生物学发现，这些作物物种是食物、纤维和能量的重要来源。番茄基因组序列的可用性将促进研究和发现，从而更广泛地了解植物生物学，生物多样性和驯化，并将影响农业改良工作，以作物的可持续性，番茄和相关物种的生产力和质量。该项目包括美国对国际番茄基因组测序工作的贡献。向公众开放番茄和相关蔬菜作物（马铃薯、辣椒、茄子）的参考基因组序列，将支持和加速研究活动，重点是了解植物生物学的基本知识，以及开发产量、性能、质量和可持续性更高的作物品种，从而加强美国和世界的粮食安全。除了由此产生的科学影响外，该项目还将提供教育和培训机会。具体而言，四名博士（博士后）、两名研究生、大约20名本科生和17名计算机程序员、研究技术人员和其他专业人员将在该项目下接受培训和就业。该项目将提供公众宣传活动，包括在参与研究实验室附近的学校向K - 12年级学生进行演讲，以及为10名本科生提供暑期研究实习机会。该项目与正在进行的美国农业部资助的研究合作，将番茄基因组测序工作的成果转化为辅助作物育种的工具，并开发基于网络的工具，以便向感兴趣的研究界成员和公众展示。通过该项目开发的信息将存储在NCBI公共DNA序列数据库（GenBank）中，发表在同行评议的期刊上，并通过该项目将支持和扩展的茄科基因组学网络数据库（www.sgn.cornell.edu）呈现。