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

柄锈菌属真菌引起锈病，影响全世界的小麦、大麦和燕麦生产。培育具有抗病基因的品种是防治作物病害的有效策略。这些基因通常编码识别特定病原体蛋白（称为无毒（Avr）蛋白）并触发防御反应的免疫受体。然而，这种方法被病原体进化破坏，以通过改变其Avr基因来逃避识别，因此有效的抗性基因部署需要了解病原体种群中的Avr基因变异。我们试图了解宿主免疫基因和病原体毒力基因之间的相互作用如何影响病原体种群的进化以克服宿主抗性。我们专注于三个相关的柄锈菌属真菌感染不同的谷类作物宿主：禾柄锈菌f。侵染小麦的小麦锈病（茎锈病）、侵染大麦的大麦柄锈菌（褐锈病）和侵染小麦的冠状柄锈菌（Puccinia coronata f.）感染燕麦的燕麦条锈菌（冠锈病）。这些目前对比水平的性与克隆性，并提供了一个机会，比较和对比相关的病原体物种和它们的主机和不同水平的性与克隆reproduction.Critical问题要回答的是：什么类型的基因组变异（拷贝数变异，单核苷酸多态性，转座因子插入）的基础上，这些谷物锈病种群的毒力差异？在全球育种计划中重要的作物R基因识别的锈菌Avr基因有哪些？这些基因座的纯合性/杂合性水平及其突变毒力的倾向是什么？Avr效应子在感染过程中执行哪些功能，哪些对病原体适应性最关键？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鉴定Avr基因候选者;目标2：通过功能测定鉴定Avr基因候选者;目标3：检查Avr基因多样性和锈菌种群的进化;目标4：确定Avr蛋白在锈菌感染中的作用。

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.