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

识别和利用马铃薯持久晚疫病抗性的持久管道

• 批准号: BB/H018697/1
• 负责人: Paul Birch
• 金额: $ 50.68万
• 依托单位: University of Dundee
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2011
• 资助国家: 英国
• 起止时间: 2011 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FH018697%2F1
• 关键词: enduring; pipeline; identify; utilize; durable

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.

植物疫情导致晚期疫苗，这是马铃薯最具破坏性的疾病，这是世界第三重要的食品作物。因此，晚枯萎病是对全球粮食安全的威胁。最近，我们目睹了欧洲P. Infestans人口发生的巨大转变，该人口现在以一种积极的压力为主，它克服了许多抵抗，其中包括部署在第一名有机马铃薯夫人Balfour中的抵抗力量。此外，农民所依靠的许多农药可能很快在欧盟被禁止。农业和科学必须对病原体种群的快速变化做出反应，以确保粮食供应，对自然资源的影响最小。该项目旨在提供一条强大而持久的管道，这是在理解病原体种群动态，利用野生茄种中自然存在的生物多样性并迅速识别和部署耐用的晚期疫病抗性（RPI）基因的驱动的。炎症假单胞菌的基因组序列非常大，其中74％是非编码DNA重复序列。它揭示了500多个候选毒力基因编码具有氨基酸基序（RXLR）的效应蛋白的毒力基因，以使其流入植物细胞。到目前为止发现，所有被马铃薯RPI蛋白识别的P. infestans效应子都包含此分娩基序。 RXLR基因位于重复DNA的区域，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很容易克服部署的抗药性。我们的第一个主要目标旨在使用微阵列基因表达分析来识别RXLR的“核心”集合，这些RXLR被多种多样的全球P. Infestans菌株（包括当前威胁到欧洲农作物的人）积极地用于感染。这种普遍表达的RXLR为更可能耐用的电阻提供了“目标”。通过对来自各种菌株的这些核心RXLR进行测序，我们将揭示可能已进化为逃避抗性的变体形式。 RXLR的核心集和其序列的变体形式将用于筛选潜在耐用的晚疫病抗性。 SCRI在SCRI上保持了大量的野马亲戚，提供了一个活着的遗传变异库，可以从土豆基因组中的180名候选人中寻求耐用的RPI基因。该集合和先前确定的抗性物种将通过不同的当代疫苗分离株进行筛选。将筛选涉及这种抗性种质的遗传杂交对核心RXLR的反应，从而在抗性和效应子识别之间寻求对应关系。电阻的耐用性将通过使用核心RXLR等位基因变体进行筛选来评估。下一代测序和DNA捕获阵列技术将用于快速识别候选RPI基因，专门从遗传杂交中的抗性后代中。 RPI候选者将在易感植物中表达，并测试其传递抗药性的能力。耐用的RPI基因将在Scri Mutlitrait育种计划中更快地将它们繁殖为现代马铃薯品种。此外，可以使用转基因技术将克隆的RPI基因引入商业重要的马铃薯和番茄品种。我们将寻求与公众积极互动，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，以产生新颖，耐用的RPI基因作为加速育种的标志，并作为可以在成品品种中转基因部署的基因。为了击败Infestans的高进化潜力，可能需要许多RPI基因，并且在检测到Iffestans人群的变化时，这些基因必须迅速而适当地部署。因此，我们设想了一条RPI发现管道，该管道将继续利用马铃薯生物多样性，以便在该项目完成之外。

项目成果

Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

• DOI: 10.1371/journal.pone.0060058
• 发表时间: 2013
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Leggett RM;Ramirez-Gonzalez RH;Verweij W;Kawashima CG;Iqbal Z;Jones JD;Caccamo M;Maclean D
• 通讯作者: Maclean D

Identification and localisation of the NB-LRR gene family within the potato genome.

• DOI: 10.1186/1471-2164-13-75
• 发表时间: 2012-02-15
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Jupe F;Pritchard L;Etherington GJ;Mackenzie K;Cock PJ;Wright F;Sharma SK;Bolser D;Bryan GJ;Jones JD;Hein I
• 通讯作者: Hein I

Relocalization of Late Blight Resistance Protein R3a to Endosomal Compartments Is Associated with Effector Recognition and Required for the Immune Response

• DOI: 10.1105/tpc.112.104992
• 发表时间: 2012-12-01
• 期刊: PLANT CELL
• 影响因子: 11.6
• 作者: Engelhardt, Stefan;Boevink, Petra C.;Birch, Paul R. J.
• 通讯作者: Birch, Paul R. J.

The early days of late blight.

• DOI: 10.7554/elife.00954
• 发表时间: 2013-06-18
• 期刊: eLife
• 影响因子: 7.7
• 作者: Birch PR;Cooke DE
• 通讯作者: Cooke DE

Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations.

• DOI: 10.1111/tpj.12307
• 发表时间: 2013-11
• 期刊: The Plant journal : for cell and molecular biology
• 作者: Jupe F;Witek K;Verweij W;Sliwka J;Pritchard L;Etherington GJ;Maclean D;Cock PJ;Leggett RM;Bryan GJ;Cardle L;Hein I;Jones JD
• 通讯作者: Jones JD