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

马铃薯是世界上第三大粮食作物，而疫霉则是马铃薯最具毁灭性的疾病。因此，晚疫病对全球粮食安全构成威胁。最近，我们目睹了欧洲病原菌种群的巨大变化，现在由一种具有侵略性的菌株主导，这种菌株克服了许多抗性，包括在排名第一的有机马铃薯“巴尔弗夫人”中使用的抗性。此外，许多农民用来预防晚疫病的农药可能很快就会在欧盟被禁止。农业和科学必须对病原体数量的快速变化作出反应，以便在对自然资源影响最小的情况下确保粮食供应。本项目旨在通过对病原菌种群动态的了解，为利用野生茄属植物自然存在的生物多样性，快速鉴定和部署持久的晚疫病抗性（Rpi）基因提供一个强大而持久的途径。大肠杆菌的基因组序列非常大，其中74%为非编码DNA重复序列。它已经发现了500多个候选毒力基因，编码具有氨基酸基序（RXLR）的效应蛋白，这些效应蛋白是它们进入植物细胞所必需的。迄今为止发现的所有马铃薯Rpi蛋白识别的病原菌效应物都含有这种传递基序。RXLR基因位于重复DNA的区域，这可能受到更高的进化速率的影响，这也许解释了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是利用微阵列基因表达谱鉴定一组“核心”RXLRs，这些RXLRs被世界范围内各种各样的病原菌感染，包括那些目前威胁欧洲作物的病原菌。这种普遍表达的rxlr为更有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，我们将揭示可能已经进化以逃避耐药性的变体形式。RXLRs的核心组及其序列的变体形式将用于筛选潜在的持久的晚疫病抗性。SCRI保存了大量的野生马铃薯近缘基因，为从马铃薯基因组中bbbb180候选基因中寻找持久的Rpi基因提供了一个活的遗传变异库。这一收集和先前确定的耐药物种将与不同的当代病原菌分离株进行筛选。将筛选涉及该抗性种质的遗传杂交对核心rxlr的反应，寻找抗性和效应识别之间的对应分离。抗性的持久性将通过筛选核心RXLR等位基因变体来评估。下一代测序和DNA捕获阵列技术将用于从遗传杂交的抗性后代中快速鉴定候选Rpi基因。候选Rpi将在易感植物中表达，并测试其传递对病原菌抗性的能力。耐久的Rpi基因将为在SCRI多品种育种计划中更快地将其培育成现代马铃薯品种提供标记。此外，克隆的Rpi基因可以通过转基因技术引入具有重要商业价值的马铃薯和番茄品种。我们将寻求与公众积极接触，讨论对转基因生物的看法。该项目提供了一个协作平台和策略，以产生新的、持久的Rpi基因，作为加速育种的标记，并作为可在成品品种中转基因部署的基因。为了打败疟原虫的高进化潜力，可能需要许多Rpi基因，当我们检测到疟原虫种群的变化时，这些基因必须迅速和适当地部署。因此，我们设想了一个Rpi发现管道，该管道将在本项目完成后继续开发马铃薯生物多样性。

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.