Potato Functional Genomics: Aplication to Analysis of Growth, Development, Metabolism and Responses to Biotic and Abiotic Stress

马铃薯功能基因组学：应用于分析生长、发育、代谢以及对生物和非生物胁迫的反应

• 批准号: 0218166
• 负责人: Barbara Baker
• 金额: --
• 依托单位: University of California-Berkeley
• 依托单位国家: 美国
• 项目类别: Cooperative Agreement
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-10-01 至 2008-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0218166&HistoricalAwards=false
• 关键词: Potato; Functional; Genomics; Aplication; Analysis

Award AbstractAs the fourth most important contributor to human calorie consumption, the potato bears an enormous influence worldwide. Its economic significance is evidenced by the large output percentage of potato by the developing world. Thus, the global influence and impact of potato makes it extremely important and relevant to plant biology and genome research. No other crop system currently being subjected to intensive genomic research possesses such a high degree of real-world applicability juxtaposed with biological uniqueness. This project is focused on furthering the understanding of important features of potato biology: tuber development, disease resistance, heterozygosity, and polyploidy. As potato is highly related to other important Solanaceae species such as tomato, we will incorporate other Solanaceae species into our studies such that comparative analyses can be performed and that we can leverage our potato-based resources for maximal gain. This project will provide a comprehensive set of resources for genome and transcriptome profiling of disease resistance responses and key developmental traits and pathways. These comprehensive resources include: targeted genome sequence analysis of potato and other Solanaceae genomic regions where numerous resistance (R) genes and general resistance traits have been identified; an evolutionary resource for resistance traits including models and bioinformatic tools for prediction and functional analysis of durable candidate resistance genes. A transcriptome resource will be generated by microarray analysis of Solanaceae development, and response to abiotic and biotic stress. We will extend the use of these arrays outside the project by soliciting proposals focused on additional physiological conditions from the Solanaceae community. All data will be made public in a rapid fashion to allow the entire Solanaceae community access to the data. This database will provide the first comprehensive resource for gene expression patterns in the Solanaceae family. We will extend our knowledge of plant genomics to the community through an outreach program that will include a training program for high school and college students and instructors in plant genomics including bioinformatics and data mining for marker development for tracing the origin of Native American potato varieties and for studies on potato evolution and breeding for crop improvement.Solanacae gardens and associated public educational programs on plant genetic diversity, plant breeding and the impact of plant genome research on society. We will also have Each of these components, in conjunction with the overarching project objectives, will lead to a comprehensive understanding and working knowledge of potato, one of the most important dicot foods in the world.Deliverables:Public Solanaceae dataset of annotated R gene region sequence, R genes and R gene candidates (SOLAR)Conatcts: Baker, Buell, Brown, Jahn, Jiang, May, Bradeen, Helgeson, Austin-PhillipsPublic predictive bioinformatic tools to identify candidate resistance traits for functional testing of resistance genesContact: MayPublic functional genomic Solanaceae resource, Solanaceae Gene Expression Database, of expression profilesContacts: Buell, Baker, JiangGene expression profiling of Solanaceae through external collaborations with the plant communityContact: BuellFunctional identification of genes operating in pathogen defense pathways using silencingContact: BakerGenomics training program for high school and college students. Community Solanum gardens and public information on SolanumContacts: Baker, Brown, BuellInternet Addresses (Web or Email) for Project Information:1. NSF Potato Genome Project http://www.bakerlab.usda.gov/NSFPotatoGenome/2. TIGR: NSF Potato Functional Genomics http://www.tigr.org/tdb/potato/ 3. Solanaceae Genome Network http://soldb.cit.cornell.edu/index.html

奖项摘要作为人类卡路里消耗的第四大贡献者，马铃薯在全世界范围内具有巨大的影响力。 发展中国家马铃薯的高产量比例证明了其经济重要性。 因此，马铃薯的全球影响力和影响力使其对于植物生物学和基因组研究极其重要和相关。 目前正在接受深入基因组研究的其他作物系统没有一个具有如此高的现实世界适用性和生物学独特性。 该项目的重点是进一步了解马铃薯生物学的重要特征：块茎发育、抗病性、杂合性和多倍体。 由于马铃薯与番茄等其他重要的茄科物种高度相关，因此我们将把其他茄科物种纳入我们的研究中，以便进行比较分析，并利用我们的马铃薯资源获得最大收益。 该项目将为抗病反应以及关键发育特征和途径的基因组和转录组分析提供一套全面的资源。 这些综合资源包括：马铃薯和其他茄科基因组区域的靶向基因组序列分析，其中已鉴定出大量抗性（R）基因和一般抗性性状；抗性特征的进化资源，包括用于持久候选抗性基因的预测和功能分析的模型和生物信息学工具。通过对茄科发育以及对非生物和生物胁迫的反应进行微阵列分析，将产生转录组资源。 我们将通过向茄科社区征求针对其他生理条件的提案，将这些阵列的使用扩展到项目之外。 所有数据都将快速公开，以便整个茄科社区都能访问这些数据。该数据库将提供第一个关于茄科基因表达模式的综合资源。我们将通过一项外展计划将我们的植物基因组学知识扩展到社区，该计划包括针对高中生和大学生以及植物基因组学教师的培训计划，包括用于追踪美洲原住民马铃薯品种起源的标记开发的生物信息学和数据挖掘，以及用于研究马铃薯进化和育种以促进作物改良的茄科花园以及有关植物遗传多样性、植物育种和植物基因组研究对社会影响的相关公共教育计划。 我们还将把这些组成部分中的每一个与总体项目目标结合起来，使人们对马铃薯这一世界上最重要的双子叶植物食品有一个全面的了解和使用知识。 交付成果：带注释的 R 基因区域序列、R 基因和 R 候选基因的公共茄科数据集 (SOLAR)联系人：Baker、Buell、Brown、Jahn、Jiang、May、Bradeen、 Helgeson，Austin-Phillips公共预测生物信息工具，用于识别候选抗性性状，用于抗性基因的功能测试联系人：5月公共功能基因组茄科资源，茄科基因表达数据库，表达谱联系人：Buell，Baker，Jiang通过与植物界的外部合作进行茄科基因表达谱联系： Buell 使用沉默对病原体防御途径中的基因进行功能性鉴定联系方式：面向高中生和大学生的 BakerGenomics 培训计划。社区 Solanum 花园和 Solanum 公共信息联系人：Baker、Brown、Buell 项目信息的互联网地址（网页或电子邮件）：1。 NSF 马铃薯基因组计划 http://www.bakerlab.usda.gov/NSFPotatoGenome/2。 TIGR：NSF 马铃薯功能基因组学 http://www.tigr.org/tdb/potato/ 3. 茄科基因组网络 http://soldb.cit.cornell.edu/index.html