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

奖项摘要作为人类卡路里消耗的第四大贡献者，土豆在世界范围内有着巨大的影响。其经济意义体现在发展中国家的马铃薯产量所占比例很大。因此，马铃薯的全球影响力和影响使其对植物生物学和基因组研究极其重要和相关。目前正在进行密集基因组研究的其他作物系统都没有具有如此高度的现实世界适用性和生物独特性。本项目致力于进一步了解马铃薯生物学的重要特征：块茎发育、抗病、杂合性和多倍体。由于马铃薯与其他重要的茄科物种如番茄高度相关，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，并利用我们以马铃薯为基础的资源以获得最大收益。该项目将提供一套全面的资源，用于绘制抗病反应和关键发育特征和途径的基因组和转录组图谱。这些综合资源包括：对马铃薯和其他茄科植物基因组区域进行有针对性的基因组序列分析，在这些区域已经确定了大量的抗性(R)基因和一般抗性特性；抗性特性的进化资源，包括用于预测和分析持久候选抗性基因的模型和生物信息学工具。通过对茄科植物发育的基因芯片分析，以及对非生物和生物胁迫的响应，将产生一个转录组资源。我们将通过向茄科群落征集有关其他生理条件的建议，将这些阵列的使用扩展到项目之外。所有数据将以快速的方式公开，以允许整个茄科社区访问这些数据。该数据库将为茄科植物的基因表达模式提供第一个全面的资源。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，其中将包括针对高中生和大学生和教师的植物基因组学培训计划，其中包括生物信息学和数据挖掘，用于标记开发，以追踪美洲原住民马铃薯品种的起源，以及研究马铃薯进化和育种，以促进作物改良。茄子花园和相关的公共教育计划，涉及植物遗传多样性、植物育种和植物基因组研究对社会的影响。我们还将拥有这些组件中的每一个，结合总体项目目标，将导致对马铃薯这一世界上最重要的双子叶食品之一的全面了解和工作知识。交付内容：已注释的R基因区域序列、R基因和R基因候选(SOLAR)内容的公共茄科数据集：Baker，Buell，Brown，Jahn，酱，May，Bradeen，Helgeson，Austin-Phillips公共预测生物信息学工具，用于鉴定候选抗性性状，进行抗性基因功能测试。联系：MayPublic功能性基因组茄科资源，茄科基因表达数据库，表达产物联系：Buell，Baker，Contact通过与植物界的外部合作进行茄科的基因表达谱研究联系：利用沉默技术对参与病原菌防御途径的基因进行功能鉴定联系：面向高中生和大学生的面包师基因组学培训计划。社区茄子园和茄子上的公共信息联系：贝克，布朗，贝尔项目信息的互联网地址(网络或电子邮件)：1.国家科学基金会马铃薯基因组计划http://www.bakerlab.usda.gov/NSFPotatoGenome/2.TIGR：国家科学基金会马铃薯功能基因组http://www.tigr.org/tdb/potato/3.茄科基因组网络http://soldb.cit.cornell.edu/index.html

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