2021-BBSRC/NSF-BIO: Host Immunity as a Driver of Virulence Evolution in Cereal Rust Fungi

锈菌属真菌会引起锈病，影响世界各地的小麦、大麦和燕麦生产。培育抗病(R)基因的品种是防治作物病害的有效策略。这些基因通常编码免疫受体，识别特定的病原体蛋白，称为无毒蛋白(AVR)，并触发防御反应。然而，这种方法被病原菌通过改变其AVR基因来逃避识别的进化所破坏，因此有效的抗性基因部署需要了解病原菌群体中AVR基因的变异。我们试图了解寄主免疫基因和病原菌毒力基因之间的相互作用如何影响病原菌种群的进化，以克服寄主抗性。我们重点研究了三种相关的真菌，它们侵染不同的谷类作物寄主：小麦锈菌f.sp.侵染小麦的小黑麦(Tritici)、侵染大麦的黑锈菌(Puccinia Hordei)和侵染大麦的冠锈菌(Puccinia coronata f.sp.)燕麦(冠锈病)侵染燕麦。这些表现出性别和克隆的不同水平，并提供了一个机会来比较和对比相关病原菌物种和它们的寄主以及不同水平的有性和克隆复制。需要回答的关键问题是：在这些谷物锈菌种群中，哪些类型的基因组变异(拷贝数变异、单核苷酸多态、转座元件插入)导致了毒力差异？由作物R基因识别的哪些锈菌AVR基因在全球育种计划中具有重要意义？这些基因座的纯合性/杂合性水平以及它们突变成毒力的倾向是什么？AVR效应器在感染过程中执行哪些功能？哪些功能对病原体的适合性最关键？这些问题将通过以下四个工作目标来解决：目标1：通过基因组序列比较确定AVR基因候选；目标2：通过功能分析验证AVR基因候选；目标3：检测锈菌种群中AVR基因的多样性和进化；目标4：确定AVR蛋白在锈病侵染中的作用。

Fungi of the genus Puccinia cause rust diseases affecting wheat, barley and oat production worldwide. An effective strategy to prevent crop diseases is to breed cultivars with disease resistance (R) genes. These genes typically encode immune receptors that recognise specific pathogen proteins, called avirulence (Avr) proteins, and trigger defence responses. However, this approach is undermined by pathogen evolution to evade recognition by changing their Avr genes, so effective resistance gene deployment requires knowledge of Avr gene variation in pathogen populations. We seek to understand how the interactions between host immunity genes and pathogen virulence genes influences the evolution of pathogen populations to overcome host resistance. We focus on three related Puccinia species of fungi that infect different cereal crop hosts: Puccinia graminis f. sp. tritici (stem rust) infecting wheat, Puccinia hordei (brown rust) infecting barley, and Puccinia coronata f. sp. avenae (crown rust) infecting oats. These present contrasting levels of sexuality versus clonality and provide an opportunity to compare and contrast between related pathogen species and their hosts and different levels of sexual versus clonal reproduction.Critical questions to answer are: What types of genomic variation (copy number variation, single nucleotide polymorphisms, transposable element insertions) underlie virulence differences in these cereal rust populations? What are the rust Avr genes recognized by the crop R genes that are important in global breeding programs? What is the level of homozygosity/ heterozygosity at these loci and their propensity to mutate to virulence? What functions do Avr effectors perform during infection and which are most critical for pathogen fitness? These questions will be addressed through the following four work objectives:Objective 1: Identify Avr gene candidates through genome sequence comparisons.Objective 2: Validate Avr gene candidates through functional assays.Objective 3: Examine Avr gene diversity and evolution in rust populations.Objective 4: Determine the role of Avr proteins in rust infection.