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

作为人类卡路里消耗的第四大贡献者，马铃薯在世界范围内具有巨大的影响。发展中国家马铃薯产量的巨大比例证明了它的经济意义。因此，马铃薯的全球影响力和影响使其在植物生物学和基因组研究中具有极其重要和相关的意义。没有其他作物系统目前受到密集的基因组研究具有如此高的现实世界的适用性与生物学的独特性。这个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，以便进行比较分析，我们可以利用马铃薯为基础的资源获得最大的收益。该项目将为抗病反应和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，其中已鉴定出许多抗性(R)基因和一般抗性性状；抗性性状的进化资源，包括持久候选抗性基因预测和功能分析的模型和生物信息学工具。通过基因芯片分析茄科植物的发育、对非生物和生物胁迫的响应，将产生转录组资源。我们将通过从茄科植物群落中征集更多生理条件的建议，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。我们将通过一个拓展计划将我们的植物基因组学知识扩展到社区，该计划将包括为高中和大学学生和教师提供植物基因组学培训计划，包括生物信息学和数据挖掘，用于标记开发，追踪美洲土著马铃薯品种的起源，以及马铃薯进化和作物改良育种的研究。茄属植物园及相关的植物遗传多样性、植物育种和植物基因组研究对社会影响的公共教育项目。我们还将有这些组成部分，结合总体项目目标，将导致对马铃薯的全面了解和工作知识，马铃薯是世界上最重要的马铃薯食品之一。合作伙伴：Baker， Buell, Brown, Jahn, Jiang, May, Bradeen, Helgeson, austin - phillipp；公共预测生物信息学工具，用于鉴定候选抗性性状，用于抗性基因的功能测试；联系对象：May；公共茄科功能基因组资源，茄科基因表达数据库；Buell, Baker， jiang通过与植物群落的外部合作分析茄科的基因表达谱contact: Buell使用沉默技术在病原体防御途径中操作的基因功能鉴定contact: Baker genomics为高中生和大学生提供的培训计划。社区茄园和茄园的公共信息联系方式：Baker， Brown， BuellInternet地址（Web或Email）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/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