Evolution and Domestication of Core Eudicot Defense Mechanisms against a Common Generalist Pathogen

植物防御变异的研究通常集中在宿主或特定病原体内的单个大效基因上，这些基因只与其他基因相互作用。然而，对大多数通用病原体的抗性是定量的，不能使用少数基因典型不同的个体进行调查。该项目将开始对核心植物谱系内部和跨核心植物谱系的基因组多样性进行首次直接调查之一，这些基因组多样性可能是由一种广谱通才真菌的基因组多样性塑造的，这种真菌可以感染大多数（如果不是全部）植物。这将导致新的生物学和统计学方法的发展，以处理跨系统发育谱系的基因组多样性，并提供一个独特的多植物物种数据集，目前仅适用于葡萄孢杆菌。所有数据和分析方案都将公开，在获得适当许可之前，微生物分离物将应要求提供。在培训方面，该项目将为高中生、本科生和研究生提供研究机会。这些学生将接受复杂性状的现代定量遗传学培训，为他们未来在工业界或学术界的职业生涯做好准备。由于这是尝试在两个相互作用的物种中进行数量遗传学的第一个实例之一，这将使他们在理论和计算应用方面处于该领域的前沿。本科生将在这个项目的框架内开发和设计他们自己的项目。任何由这项研究产生的出版物都可能包括至少一名本科生作为共同作者，他在设计和解释实验中不可或缺。此外，首席研究员将参与教学，包括在大学课堂环境和正在进行的推广工作，以教育社区成员关于植物代谢，植物防御进化和定量基因组学。植物/病原体的相互作用决定了植物的适合度/产量。大多数关于植物/病原体相互作用的研究都集中在由病原体引起的流行病上，这些病原体只感染一种或几种类似于人类流感的物种。然而，这导致缺乏对地方性病原体的研究，如灰葡萄孢菌或普通感冒，它们可以感染大多数宿主基因型，但只造成低水平的经济损失。这些多面手病原体在植物谱系中施加进化压力，然而这种跨谱系压力很少被系统地解决。例如，目前尚不清楚是否存在一个共同的植物防御网络，可以在所有植物中对这些通用病原体起作用。为了验证这一问题，该项目旨在：1)利用高通量平台测量6种独立驯化的植物物种（生菜、番茄、葡萄、大豆和芸苔属）的病变发展情况，其中包括100个基因组测序的葡萄灰霉病菌分离株；2)利用全基因组关联图谱数据集确定病原体内部的致病网络，使其能够感染这些不同的宿主；3)利用新的共种共表达网络方法鉴定和验证这些网络的植物基因靶点，以测试病原体的防御机制是否在植物间是保守的或变异的，以及这些防御机制是否受到人类驱动的驯化的影响；4)在这些植物/病原体组合中进行转录组分析，以确定在菊科谱系中保守或变异的转录反应。通过在每个植物物种中包括驯化和野生基因型，该项目将提供一个共同的参考框架，以研究驯化如何可能或可能不始终影响植物防御。从长远来看，这一信息将有助于更好地理解选择压力是如何推动生物谱系对多面手病原体的防御进化的。

Plant defense variation studies typically focus on single large effect genes within a host or specialist pathogen that interact only with each other. However, resistance to most generalist pathogens is quantitative and cannot be investigated using few genotypically distinct individuals. This project will begin one of the first direct surveys of how genomic diversity within and across core plant lineages may be shaped by genomic diversity in a broad spectrum generalist fungus that can infect most if not all plants. This will lead to the development of novel biological and statistical methods to handle genomic diversity across phylogenetic lineages and provide a unique multi-plant species dataset that is currently only feasible with Botrytis cincerea. All data and analysis protocols will be publicly available and microbial isolates will be available upon request pending the acquisition of the appropriate permits. With regard to training, the project will provide research opportunities for high school, undergraduate, and graduate students. These students will be trained in modern quantitative genetics of complex traits to prepare them for future careers in industry or academics. As this is the one of the first instances of attempting to do quantitative genetics in two interacting species, this will place them at the forefront of the field in both theory and computational applications. Undergraduates will develop and devise their own projects within the frame of this project. Any publication resulting from this research will likely include at least one undergraduate student as a co-author who was integral in designing and interpreting the experiments. In addition, the principal investigator will be involved in teaching, both in a university classroom setting and in ongoing outreach efforts to educate community members about plant metabolism, plant defense evolution, and quantitative genomics. Plant/pathogen interactions determine plants fitness/yield. Most research on plant/pathogen interactions focuses on epidemic diseases from pathogens that infect only one or a few species similar to the human flu. However, this has led to a paucity of research on pathogens that are endemic, like Botrytis cinerea or the common cold, which can infect most host genotypes but only cause a low level of economic loss. These generalist pathogens place evolutionary pressure across plant lineages, yet this cross-lineage pressure is rarely systematically addressed. For example, it is currently not known if there is a common plant defense network against these generalist pathogens that can function in all plants. To test this question, this project aims to: 1) measure lesion development with a high-throughput platform across six plant species that have independently undergone domestication (lettuce, tomato, grape, soy and Brassicas) with 100 genome sequenced isolates of the pathogen, Botrytis cinerea; 2) use the genome wide association mapping dataset to identify pathogenicity networks within the pathogen that allow it to infect these diverse hosts; 3) identify and validate plant gene targets of these networks using a new co-species co-expression network approach to test if the pathogen targets defense mechanisms that are conserved or variant across plants and if these defense mechanisms have been affected by human driven domestication; and 4) conduct transcriptome profiling across these plant/pathogen combinations to identify conserved or variant transcriptional responses across the eudicot lineages. By including domestic and wild genotypes in each plant species this project will provide a common reference frame in which to study how domestication may or may not consistently influence plant defenses. In the longer term, this information will provide for a better understanding of how selection pressures drive the evolution of defenses within eudicot lineages towards generalist pathogens.