Research PGR: Co-transcriptome networks to identify conserved and lineage specific plant resistance against a generalist pathogen

为了生存和繁殖，任何生物体都必须防止由病毒、细菌和真菌等病原体引起的疾病。了解控制寄主和病原体之间这场战斗的机制对于了解生态学和进化以及努力提高农业系统的生产力是必要的。这些宿主-病原体的相互作用跨越了广泛的系统，从专门的一个宿主与一个病原体对峙的系统到更一般的系统，其中一个病原体可能攻击广泛的宿主。大多数机械知识局限于专门的系统，这个项目将致力于加深我们对通用宿主-病原体系统的知识。通过使用一种几乎在任何植物上都能致病的真菌病原体，该项目将测试植物对常见攻击者的防御机制的多样性。植物是通过共同的防御系统、新的个性化机制还是共同和新的防御机制的混合来保护自己？这些信息将提高我们对进化何时产生新解决方案的理解，而不是对现有解决方案进行轻微调整，以提高抗病能力。这些知识可以用来理解防御是如何以及何时发生的，提高作物对疾病的抵抗力，也有助于指导我们设计新的生物系统。植物-病原菌相互作用的理论是通过对受谱系特有的大效应基因控制的寄主-病原菌相互作用的广泛研究而形成的。这些理论决定了植物是如何被培育成抗病的。然而，大效应模型不能描述宿主-通用型病原体之间的相互作用，这种相互作用由分布在不同机制上的众多小到中等效应基因主导。宿主-多面手相互作用的多基因性质使任何机械论见解从一个宿主到另一个宿主的翻译变得复杂，因为机制可以是特定的或保守的。识别这些保守的机制将提高跨物种转换机制的能力。这项工作将利用一组通用病原菌灰霉病菌来测量代表8个玫瑰花科和星形科谱系的16种双子叶植物的病变发展，以确定特定于谱系的抗性机制与保守的抗性机制。结合共转录组的方法，我们将测量宿主和病原体的转录组反应，并确定保守的或谱系特定的调控网络。通过制定规则来预测保守的和谱系特有的抗性机制，该项目将提高将科学发现从一个物种预测到另一个物种的能力。番茄、生菜和拟南芥中已识别的保守和谱系特异的抗性机制将通过基因组编辑来验证它们对抗病的影响。该项目还将为第一代和转学大学生提供STEM的综合介绍，这些学生在更广泛的外展工作中经常被忽视。他们将接受基因网络现代定量分析方面的培训，为未来在工业或学术界的职业生涯做好准备。该奖项由综合组织系统分部的植物基因组研究计划和植物生物相互作用计划共同资助。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

To live and reproduce, any organism must prevent disease caused by pathogens like viruses, bacteria and fungi. Understanding the mechanisms controlling this battle between host and pathogens is necessary for understanding ecology and evolution and efforts to improve productivity in agricultural systems. These host-pathogens interactions span a wide range of systems from specialized where one host faces off with one pathogen to more general systems where a pathogen may attack a wide range of hosts. Most mechanistic knowledge is limited to the specialized systems and this project will work to deepen our knowledge of generalist host-pathogen systems. By using a fungal pathogen, Botrytis cinerea, that causes disease on nearly any plant, this project will test the diversity of plant defense mechanisms to a common attacker. Do plants defend themselves with a common defense system, novel individualized mechanisms or a blend of common and novel defense mechanisms? This information will improve our understanding of when evolution generates novel solutions versus slight tweaks to existing solutions to improve disease resistance. This knowledge can be used to understand how and when evolution of defense has occurred, improve crops resistance to disease and also help guide our efforts to engineer new biological systems. Theories of plant-pathogen interactions are molded by extensive research on host-specialist pathogen interactions controlled by lineage-specific large-effect genes. Those theories shape how plants are bred for disease resistance. However, large-effect models do not describe host-generalist pathogen interactions, dominated by numerous small to moderate effect genes distributed across diverse mechanisms. The polygenic nature of host-generalist interactions complicates the translation of any mechanistic insights from one host to another as mechanisms can be lineage specific or conserved. Identifying these conserved mechanisms will improve the ability translate mechanisms across species. This work will identify resistance mechanisms that are lineage specific versus conserved using a collection of the generalist pathogen Botrytis cinerea to measure lesion development across 16 dicot plant species representing eight rosid and asterid lineages. Incorporating a co-transcriptome approach, we will measure the host and pathogens transcriptome responses and identify conserved or lineage-specific regulatory networks. By developing rules to predict conserved and lineage-specific resistance mechanisms, this project will increase the ability to predictively translate scientific discoveries from one species to another. The identified conserved and lineage specific resistance mechanisms in Tomato, Lettuce and Arabidopsis will be validated for their influence on disease resistance via genome editing. This project will also provide an integrative introduction to STEM for first generation and transfer college students that are often overlooked in broader outreach efforts. They will be trained in modern quantitative analysis of gene networks to prepare them for future careers in industry or academics. This award was co-funded by the Plant Genome Research Program and the Plant Biotic Interactions Program in the Division of Integrative Organismal Systems.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.