Exploiting Tomato Genomics Resources to Investigate Basal Plant Defenses Against Pathogens

利用番茄基因组资源研究植物对病原菌的基础防御反应（an Collmer, Cornell university, magdalen Lindeberg, Cornell university） gregory B. Martin， Boyce Thompson植物研究所项目摘要本项目旨在开发和利用3个基因组资源来解决番茄对模式病原菌丁香假单胞菌（Pseudomonas syringae pv）自然抗性的基本问题。番茄DC3000。这些资源包括一组76个来自易感亲本但对DC3000感染表现出不同程度抗性的番茄渗入系，一组约140个功能失活的已知改变疾病易感性的番茄基因，以及一组约16个DC3000毒力效应蛋白，这些蛋白由病原体注入宿主细胞，可用于鉴定相互作用的番茄蛋白。将用一组细菌和感染过程试验对渗入系进行分析，并通过基于图谱的克隆分离出5或6个最有希望的基因座。当番茄基因组序列可用时，功能失活基因和编码效应相互作用基因将被放置在番茄连锁图谱和物理图谱上。通过比较这些多种方法鉴定的番茄基因座集，将产生防御系统的功能概况，揭示哪些方面是最可变的，并促进基于自然防御机制的更有效和持久的抗病能力的发展。该项目的具体目标是：(1)利用番茄渗入系中所代表的自然变异，寻找控制丁香假单胞菌反应的新寄主位点。(2)对控制丁香假单胞菌应答的PSR位点进行分子表征。(3)建立番茄p基因基因组激活模型。丁香相互作用，结合效应-靶标物理相互作用，有助于提高作物对病原体的抗性。(4)扩大功能基因组学社区网络资源（http://pseudomonas-syringae.org）和教育推广活动。由于几个原因，该项目可能产生具有广泛影响的重要成果。农作物容易受到细菌和许多其他微生物病原体的影响，而一些由此产生的疾病实际上是无法控制的。抗性育种是重要的控制策略，通常利用单一的显性抗性基因。但是这种抗药性在田间常常被病原体变异所击败。植物有额外的“基础”防御，可以更好地利用，但由于植物-病原体相互作用和这些防御的高度多因子性质，人们对这些防御知之甚少，而且很难利用。基础防御的数量性状位点可以通过使用具有抗性自然变异的渗入系、仔细的表型分析和缺乏毒力因子亚群的病原体突变体（这可以揭示潜在抗性位点的表型）来确定。因为这项研究涉及基因组学、农业、基因工程生物和疾病，它可以为各个层次的学生提供广泛的课程。因此，这个项目有广泛的高中外展和本科生研究经验组成部分。

Exploiting tomato genomics resources to investigate plant basal defense responses to pathogensAlan Collmer, Cornell UniversityMagdalen Lindeberg, Cornell UniversityGregory B. Martin, Boyce Thompson Institute for Plant ResearchProject Abstract This project seeks to develop and exploit three genome-enabled resources to address fundamental questions about natural resistance in tomato against the model pathogen Pseudomonas syringae pv. tomato DC3000. These resources are a set of 76 tomato introgression lines that are from susceptible parents but show various levels of resistance to DC3000 infection, a collection of ca. 140 functionally inactivated tomato genes that are known to alter disease susceptibility, and a set of ca. 16 DC3000 virulence effector proteins that are injected by the pathogen into host cells and can be used to identify interacting tomato proteins. The introgression lines will be analyzed with a panel of bacteria and infection-process assays, and 5 or 6 of the most promising loci will be isolated by map-based cloning. The functionally inactivated genes and genes encoding effector interactors will be placed on the tomato linkage map and on the physical map as tomato genome sequence becomes available. Comparing the sets of tomato loci identified by these multiple approaches will produce a functional profile of the defense system, reveal what aspects are most variable, and foster development of more effective and durable disease resistance based on natural defense mechanisms. The specific objectives of the project are to: (1) Exploit natural variation represented in tomato introgression lines to identify new host loci controlling responses to P. syringae. (2) Molecularly characterize PSR loci controlling responses to P. syringae. (3) Develop a genome-enabled model for tomato-P. syringae interactions that incorporates effector-target physical interactions and is useful for developing enhanced crop resistance to pathogens. (4) Expand functional genomics community web resources (http://pseudomonas-syringae.org) and educational outreach activities.The project could have important outcomes with broad impact for several reasons. Crop plants are susceptible to bacteria and many other microbial pathogens, and some of the resulting diseases are virtually impossible to control. Breeding for resistance is an important control strategy and commonly exploits single, dominant resistance (R) genes. But such resistance is often defeated in the field by pathogen variants. Plants have additional "basal" defenses that could be better exploited but are poorly understood and difficult to work with because of the highly multifactorial nature of plant-pathogen interactions and these defenses. The quantitative trait loci underlying basal defenses can be identified through the use of introgression lines with natural variations in resistance, careful phenotypic analyses, and pathogen mutants lacking subsets of virulence factors (which can unmask phenotypes for underlying resistance loci), as proposed here. Because this research deals with genomics, agriculture, genetically engineered organisms, and disease, it can offer broad lessons for students at all levels. Therefore, this project has extensive high school outreach and undergraduate research experience components.