An enduring pipeline to identify and utilize durable late blight disease resistance in potato

马铃薯晚疫病是世界上第三大粮食作物马铃薯上最具破坏性的病害。因此，晚疫病是对全球粮食安全的威胁。最近，我们目睹了欧洲马铃薯晚疫病菌种群的巨大变化，现在由一种侵略性菌株主导，这种菌株克服了许多抗性，包括在头号有机马铃薯Lady Balfour中部署的抗性。此外，农民用来预防晚疫病的许多农药可能很快在欧盟被禁止。农业和科学必须应对病原体种群的快速变化，以确保粮食供应，同时尽量减少对自然资源的影响。该项目旨在通过了解病原体种群动态，提供一个强大而持久的管道，以利用野生茄属物种中自然存在的生物多样性，并快速识别和部署持久的晚疫病抗性（Rpi）基因。致病疫霉的基因组序列非常大，其中74%是非编码DNA重复序列。它已经揭示了500多个候选毒力基因编码的效应蛋白与氨基酸基序（RXLR）所需的运动到植物细胞。迄今发现的马铃薯Rpi蛋白识别的所有致病疫霉效应子都含有该递送基序。RXLR基因位于重复DNA的区域，这可能会受到更高的进化率，也许可以解释为什么这种病原体如此容易克服部署的抗性。我们的第一个关键目标旨在使用微阵列基因表达谱来识别RXLR的“核心集”，这些RXLR被广泛收集的世界范围内的致病疫霉菌株（包括目前威胁欧洲作物的菌株）积极用于感染。这种普遍表达的RXLR为更可能持久的抗性提供了“靶标”。通过对这些来自不同菌株的核心RXLR进行测序，我们将揭示可能进化为逃避耐药性的变异形式。RXLR的核心组及其序列的变体形式将用于筛选潜在持久的晚疫病抗性。SCRI保存了大量的野生马铃薯近缘种，提供了一个遗传变异的活文库，以从马铃薯基因组中的>180个候选者中寻找持久的Rpi基因。将使用不同的当代致病疫霉分离株筛选该收集物和先前鉴定的耐药种属。将筛选涉及该抗性种质的遗传杂交对核心RXLR的反应，寻求抗性和效应子识别之间分离的对应关系。将通过用核心RXLR等位基因变体筛选来评估耐药性的持久性。下一代测序和DNA捕获阵列技术将用于快速鉴定候选Rpi基因，特别是从遗传杂交中的抗性后代中。Rpi候选物将在易感植物中表达，并测试其传递对致病疫霉的抗性的能力。持久的Rpi基因将提供标记，以便在SCRI多品种育种计划中更快地将它们培育成现代马铃薯品种。此外，可以使用转基因技术将克隆的Rpi基因引入商业上重要的马铃薯和番茄栽培品种中。我们将寻求积极与公众接触，讨论对转基因生物的看法。该项目提供了一个合作平台和策略，以产生新的，持久的Rpi基因作为标记，加速育种，并作为基因，可以转基因部署在成品品种。为了击败致病疫霉的高进化潜力，可能需要许多Rpi基因，并且当我们检测到致病疫霉种群中的变化时，必须快速且适当地部署这些基因。因此，我们设想了一个RPI发现管道，该管道将在该项目完成后继续利用我们所掌握的马铃薯生物多样性。

Phytophthora infestans causes late blight, the most devastating disease of potato which is the world's third most important food crop. Consequently, late blight is a threat to global food security. Recently, we have witnessed a dramatic shift in the European P. infestans population, which is now dominated by an aggressive strain that overcomes many resistances, including that deployed in the number one organic potato, Lady Balfour. Moreover, many pesticides that farmers rely on to prevent late blight may soon be banned in the EU. Agriculture and science must respond to rapid pathogen population changes to secure food supply with minimal impact on natural resources. This project aims to provide a powerful and enduring pipeline, driven by understanding pathogen population dynamics, to exploit naturally existing biodiversity in wild Solanum species, and rapidly identify and deploy durable late blight resistance (Rpi) genes. The genome sequence of P. infestans is very large, 74% of which is non-coding DNA repeats. It has revealed more than 500 candidate virulence genes encoding effector proteins with an amino acid motif (RXLR) required for their movement into plant cells. All P. infestans effectors recognised by potato Rpi proteins found so far contain this delivery motif. RXLR genes are located in regions of repetitive DNA, which may be subject to higher rates of evolution, perhaps explaining why this pathogen has so readily overcome deployed resistances. Our first key objective aims to identify, using microarray gene expression profiling, a 'core set' of RXLRs that are actively used for infection by a diverse worldwide collection of P. infestans strains, including those currently threatening European crops. Such universally-expressed RXLRs provide 'targets' for resistances that are more likely to be durable. By sequencing these core RXLRs from the diverse strains, we will reveal variant forms which may have evolved to evade resistance. The core set of RXLRs, and variant forms of their sequences, will be used to screen for potentially durable late blight resistance. A large collection of wild potato relatives is maintained at SCRI, providing a living library of genetic variation to seek durable Rpi genes from the >180 candidates in the potato genome. This collection and previously identified resistant species will be screened with diverse contemporary P. infestans isolates. Genetic crosses involving this resistant germplasm will be screened for responses to core RXLRs, seeking correspondence in segregation between resistance and effector recognition. Durability of resistance will be assessed by screening with core RXLR allelic variants. Next-generation sequencing and DNA capture array technologies will be used to rapidly identify candidate Rpi genes specifically from resistant offspring in genetic crosses. Rpi candidates will be expressed in susceptible plants, and tested for their ability to convey resistance to P. infestans. Durable Rpi genes will provide markers to more rapidly breed them into modern potato cultivars within the SCRI mutlitrait breeding programme. Moreover, cloned Rpi genes can be introduced into commercially important potato and tomato cultivars using transgenic technology. We will seek to actively engage with the public to discuss perceptions of GMOs. This project provides a collaborative platform and strategy to yield novel, durable Rpi genes as markers for accelerated breeding, and as genes that could be deployed transgenically in finished cultivars. To defeat the high evolutionary potential of P. infestans, many Rpi genes may be needed and these must be rapidly and appropriately deployed as we detect changes in the P. infestans population. We thus envisage an Rpi discovery pipeline that will continue to exploit the potato biodiversity at our disposal beyond the completion of this project.