Exploiting Tomato Genomics Resources to Investigate Basal Plant Defenses Against Pathogens

利用番茄基因组学资源研究植物对病原菌的基础防御反应Alan Collmer，Cornell University Magdalen Lindeberg，Cornell University Gregory B.马丁，博伊斯汤普森植物研究所项目摘要该项目旨在开发和利用三个基因组使能的资源，以解决有关番茄对模式病原体假单胞菌pv.番茄DC 3000。这些资源是一组76个番茄渐渗系，它们来自感病亲本，但对DC 3000感染表现出不同水平的抗性，是一组ca. 140个功能失活的番茄基因，已知改变疾病的易感性，和一组CA。16 DC 3000毒力效应蛋白，其由病原体注射到宿主细胞中并且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测定分析渐渗系，并通过图位克隆分离5或6个最有希望的基因座。功能失活的基因和编码效应相互作用物的基因将被放置在番茄连锁图谱上，并且当番茄基因组序列变得可用时被放置在物理图谱上。通过比较这些多种方法鉴定的番茄基因座的集合将产生防御系统的功能概况，揭示哪些方面是最可变的，并促进基于天然防御机制的更有效和持久的抗病性的发展。本项目的具体目标是：（1）利用番茄渐渗系中的自然变异来鉴定控制番茄疫霉反应的新宿主基因座。(2)分子表征控制对P. dingae的响应的PSR基因座。(3)开发一个基因组启动的番茄-番茄疫霉相互作用模型，该模型结合了效应物-靶标物理相互作用，可用于增强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。农作物易受细菌和许多其他微生物病原体的影响，一些由此产生的疾病实际上是不可能控制的。抗性育种是一种重要的控制策略，通常利用单一的显性抗性（R）基因。但这种抗性在田间常常被病原体变体击败。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素性，人们对它们的了解很少，也很难进行研究。基础防御的数量性状基因座可以通过使用具有抗性天然变异的渐渗系、仔细的表型分析和缺乏毒力因子子集的病原体突变体（其可以揭示潜在抗性基因座的表型）来鉴定，如本文所提出的。由于这项研究涉及基因组学，农业，转基因生物和疾病，它可以为各级学生提供广泛的课程。因此，这个项目有广泛的高中推广和本科研究经验的组成部分。

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.