RESEARCH-PGR: Leveraging Natural Variation in Tomato to Identify, Characterize, and Deploy New Sources of Disease Resistance

Pi：Gregory Martin(博伊斯·汤普森植物研究所)Copis：Susan Strickler和Zhang jun Fei(博伊斯·汤普森植物研究所)；Alan Collmer和Magdalen Lindeberg(康奈尔大学)；Samuel Hutton(佛罗里达大学)；Dilip Panthee(北卡罗来纳州立大学)近30年来对植物免疫系统和病原体感染过程的分子基础进行了深入的研究，使人们对某些模式植物物种的潜在机制有了广泛的了解。该领域现在可以利用这一知识来探索有助于植物免疫的自然遗传变异，并将其应用于作物改良。该项目利用番茄与一种引起细菌性斑点的病原体的相互作用，细菌性斑点病是一种经济上重要的疾病，降低了新鲜市场和加工番茄的适销性和产量。这种相互作用是了解抗病能力的强大系统，因为植物和病原体在实验上都很容易驯化。此外，在番茄的野生近缘中存在着大量的天然遗传变异，所有这些都可以与栽培番茄杂交。该项目的目标是利用这种自然变异来识别在植物免疫中发挥作用的基因，使用分子方法表征这些基因，并将它们引入生鲜市场育种系，这些系是两个公共番茄改良计划中的重要亲本。该项目的一个重要方面是改进和推广VEGEVADERS，这是一个娱乐和教育高中生和更广泛的公众关于植物与病原体相互作用的科学和重要性的游戏。提高新鲜番茄市场和加工番茄的抗病能力可以减少农药的使用，从而节省种植者的资金，减少疾病控制对环境的影响，并为消费者提供农药残留较少的食品。农作物病害具有重大的经济和环境影响，因为它们降低了产量，需要广泛使用杀虫剂。这个项目的主要目标是利用番茄及其野生近缘的自然变异以及广泛的基因组序列数据来发现有助于模式触发免疫(PTI)的新基因/位点。这些基因的分子功能将通过CRISPR介导的突变和其他方法进行研究，选定的基因/座位将被导入两个基础的鲜食番茄育种系。该项目的目标是：1)利用病原菌诱导子和具有不同效应谱的紫丁香病工程菌株，筛选200个番茄家系、育种系和野生种材料进行PTI的自然变异；2)寻找新的PTI相关基因座/基因，并开发用于两个番茄育种计划的DNA标记；3)培育150个候选免疫相关基因发生CRISPR改变的番茄品系，并鉴定它们对PTI的反应；4)将新的抗病来源引入两个新鲜番茄育种系，并研究PTI相关基因座/基因的分子功能；5)增强基于植物-微生物相互作用的游戏VEGEVADERS，扩大功能基因组学网络资源，开发植物育种研讨会，并促进教育推广。本科生、研究生和博士后将接受生物信息学、植物育种、植物病理学和功能基因组学方面的培训。该项目产生的知识将增强对植物免疫系统的了解，并使番茄品种具有更好的抗病能力。所有数据和资源都将根据要求向公众开放，并可通过长期数据和种质储存库获取。

PI: Gregory Martin (Boyce Thompson Institute for Plant Research)CoPIs: Susan Strickler and Zhangjun Fei (Boyce Thompson Institute for Plant Research); Alan Collmer and Magdalen Lindeberg (Cornell University); Samuel Hutton (University of Florida); and, Dilip Panthee (North Carolina State University)Nearly 30 years of intensive research on the molecular basis of the plant immune system and pathogen infection processes has generated a broad understanding of their underlying mechanisms in certain model plant species. The field is now positioned to use this knowledge to explore the natural genetic variation that contributes to plant immunity and to apply it to crop improvement. This project takes advantage of the interaction of tomato with a pathogen that causes bacterial speck, an economically important disease that decreases the marketability and yield of fresh-market and processing tomatoes. This interaction is a powerful system for understanding disease resistance because both the plant and the pathogen are experimentally tractable. In addition, a vast source of natural genetic variation exists in wild relatives of tomato, all of which can be crossed to cultivated tomato. The goal of this project is to leverage this natural variation to identify genes that play a role in plant immunity, characterize these genes using molecular methods, and introduce them into fresh-market breeding lines that are important parents in two public tomato improvement programs. An important aspect of the project is the improvement and promotion of VEGEVADERS, a game to entertain and teach high school students and the broader public about the science and importance of plant-pathogen interactions. The enhancement of disease resistance in fresh-market and processing tomatoes could lead to decreased use of pesticides thus saving growers money, reducing the impact of disease control on the environment and providing food for consumers with fewer pesticide residues. Diseases of crop plants have major economic and environmental impacts because they decrease yields and require extensive pesticide applications. The overarching goal of this project is to take advantage of the natural variation present in tomato and its wild relatives along with the extensive genome sequence data available to discover new genes/loci that contribute to pattern-triggered immunity (PTI). The molecular functions of these genes will be investigated by using CRISPR-mediated mutations and other approaches and selected genes/loci will be introgressed into two foundational fresh-market tomato breeding lines. Specifically, the objectives of the project are to: 1) screen 200 tomato heirlooms, breeding lines, and wild species accessions for natural variation for PTI using pathogen elicitors and engineered P. syringae strains with different effector repertoires; 2) identify novel PTI-associated loci/genes and develop DNA markers for use in two tomato breeding programs; 3) develop 150 tomato lines with CRISPR-mediated alterations in candidate immunity-associated genes and characterize them for PTI responses; 4) introduce novel sources of disease resistance into two fresh-market tomato breeding lines and investigate the molecular functions of PTI-associated loci/genes; and 5) enhance VEGEVADERS, a game based on plant-microbe interactions, expand functional genomics web resources, develop a plant breeding workshop, and promote educational outreach. Undergraduates, graduate students, and postdocs will be trained in bioinformatics, plant breeding, plant pathology, and functional genomics. Knowledge generated in the project will both enhance the understanding of the plant immune system and lead to tomato varieties with improved disease resistance. All data and resources will be accessible to the public upon request and through long-term data and germplasm repositories.