Studying Co-evolution in agriculture to inform NLR deployment

马铃薯是世界上最重要的非谷类粮食作物，其生产受到病原体的威胁，这些病原体严重降低作物产量和质量。最重要的病原体是晚疫病，这是导致爱尔兰马铃薯饥荒的有机体。目前世界上大部分地区的晚疫病控制方法主要是基于使用化学喷雾剂，这可能对环境有害且昂贵。认识到栽培马铃薯可以通过引入来自野生物种的抗病基因来保护免受病原体如晚疫病的侵害，导致了许多功能性植物核苷酸结合、富含亮氨酸重复序列的抗性基因（NLR）的分子表征。这些功能性NLR在马铃薯品种中的部署模式在很大程度上仍然未知，这阻碍了农业背景下有效的抗性育种策略和病原体共进化研究。为此，我们改进了一种新的工具，称为dRenSeq，以检测马铃薯中特征化NLR的存在。这使我们能够跟踪，第一次，在品种和（前）育种材料的功能NLR的当前，历史和地理部署模式。通过最近建立的病原体富集测序（PenSeq）技术，我们还能够研究晚疫病病原体效应子多样性，包括通过NLR检测导致抗性的无毒基因的变化。因此，我们现在已经达到了一个位置，研究NLR基因部署同源病原体Avr基因多样化的影响。我们的初步数据表明，在英国和美国种植的最具商业价值的马铃薯品种含有最多四个已经被击败的NLR，特异性针对晚疫病病原体P. infestans。这两个国家NLR基因部署的不同模式分别反映在美国和英国现存致病疫霉基因型中同源Avr基因的多样性。与育种高度相关，我们发现了最近表征的NLR，这些NLR对致病疫霉仍然有效，并且已经存在于先进的育种前材料甚至在荷兰试验的品种中。重要的是，这些“新”抗性尚未在商业马铃薯生产中广泛使用，并且尚未在品种中堆叠。迄今为止，只有有限数量的致病疫霉分离株存在，可以克服这些新的NLR在隔离。该建议旨在发现病原体适应机制，使不同的和地理上不同的谱系的致病疫霉克服农业中的宿主抗性。这些知识将通过与我们的全球商业合作伙伴的育种计划应用于生产更持久的抗性品种，其中包含互补和有效的NLR堆栈。有效的NLR的组合将延长个体抗性的寿命并减少对化学应用的需求。

Potato is the world's most important non-cereal food crop and production is threatened by pathogens that severely reduce crop yield and quality. The most important pathogen is late blight, the organism that caused the Irish potato famine. Current control methods for late blight in most parts of the world are based mainly on the use of chemical sprays which can be environmentally hazardous and expensive. The realisation that cultivated potatoes could be protected from pathogens such as late blight by the introduction of disease resistance genes from wild species, led to the molecular characterisation of numerous functional plant nucleotide-binding, leucine-rich-repeat resistance genes (NLRs). The deployment patterns of these functional NLRs in potato varieties remain largely unknown, which obstructs effective resistance breeding strategies and pathogen co-evolution studies in an agricultural context. To this effect we refined a novel tool, referred to as dRenSeq, to detect the presence of characterised NLRs in potatoes. This enables us to track, for the first time, the current, historical and geographical deployment patterns of functional NLRs in varieties and (pre)-breeding material. Through recently established Pathogen enrichment Sequencing (PenSeq) technology, we are in a position to also study the late blight pathogen effector diversity including changes to bonafide avirulence genes which lead to resistance upon detection by NLRs. Therefore, we have now reached a position to study the impact of NLR gene deployment on the cognate pathogen Avr gene diversification. Our preliminary data suggest that the most commercially valuable potato varieties grown in the UK and US contain a maximum of four already defeated NLRs specific against the late blight pathogen, P. infestans. The distinct patterns of NLR gene deployment in both countries is mirrored by the diversity of the cognate Avr genes in virulent extant US and UK P. infestans genotypes, respectively. Highly relevant for breeding, we identified recently characterised NLRs that remain effective against P. infestans and that already exist in advanced pre-breeding material or even varieties which have been trialed in the Netherlands. Critically, these 'new' resistances have not been used extensively in commercial potato production and have not yet been stacked in varieties. To date, only a limited number of P. infestans isolates exist that can overcome these new NLRs in isolation. This proposal aims to discover the pathogen adaptation mechanisms that enable different and geographically distinct lineages of P. infestans to overcome host resistance in agriculture. This knowledge will be applied, through breeding programs with our global commercial partners, to produce more durable resistant varieties containing complementary and effective NLR stacks. The combination of effective NLRs will prolong the longevity of individual resistances and reduce the need for chemical applications.