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、张军Fei（博伊斯·汤普森植物研究所）；康奈尔大学的艾伦·科尔默、莫德林·林德伯格；塞缪尔·赫顿（佛罗里达大学）；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研究，对某些模式植物物种的潜在机制有了广泛的了解。该领域现在的定位是利用这些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。该项目利用了番茄与引起细菌斑点的病原体的相互作用，细菌斑点是一种重要的经济疾病，会降低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性的一个强大系统，因为植物和病原体在实验上都是可处理的。此外，在番茄的野生近缘种中存在着大量的自然遗传变异，这些变异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起作用的基因，使用分子方法表征这些基因，并将它们引入新鲜市场的育种系，这些育种系是两个公共番茄改良计划的重要亲本。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。增强新鲜市场和加工番茄的抗病性可以减少农药的使用，从而为种植者节省资金，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，因为它们会降低产量并需要大量使用农药。该项目的总体目标是利用番茄及其野生近缘种存在的自然变异以及广泛的基因组序列数据，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介导突变和其他方法进行研究，选定的基因/位点将渗入到两个基本的新鲜市场番茄育种品系中。具体而言，该项目的目标是：1)使用病原体激发子和具有不同效应库的丁香假单抗菌株筛选200个番茄传家宝、育种系和野生物种，以确定PTI的自然变异；2)鉴定新的pti相关位点/基因，并开发用于两个番茄育种项目的DNA标记；3)开发150个具有crispr介导的候选免疫相关基因改变的番茄品系，并对其PTI反应进行表征；4)在两种新鲜市场番茄育种品系中引入新的抗病来源，研究pti相关位点/基因的分子功能；5)加强基于植物与微生物相互作用的VEGEVADERS游戏，扩展功能基因组学网络资源，开发植物育种研讨会，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。项目中产生的知识将增强对植物免疫系统的理解，并导致番茄品种具有更好的抗病性。所有数据和资源均可应要求通过长期数据和种质资源库向公众开放。

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.