Exploiting Tomato Genomics Resources to Investigate Basal Plant Defenses Against Pathogens

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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.