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，严重降低了作物的产量和质量。最重要的病原体是晚疫病，这种生物导致了爱尔兰马铃薯饥荒。目前在世界大多数地区防治晚疫病的方法主要是使用化学喷雾剂，这可能对环境有害且价格昂贵。人们认识到，通过从野生物种引入抗病基因，栽培马铃薯可以免受晚疫病等病原体的侵害，这导致了许多功能性植物核苷酸结合、富含亮氨酸的重复抗性基因（NLRs）的分子特征。这些功能性NLRs在马铃薯品种中的分布模式在很大程度上仍然未知，这阻碍了有效的抗性育种策略和农业背景下病原体共同进化的研究。为此，我们改进了一种新的工具，称为dRenSeq，用于检测马铃薯中特征nlr的存在。这使我们能够首次跟踪功能性nlr在品种和（预）育种材料中的当前、历史和地理分布模式。通过最近建立的病原体富集测序（PenSeq）技术，我们也能够研究晚疫病病原体效应物的多样性，包括在NLRs检测后导致抗性的真实无毒基因的变化。因此，我们现在可以研究NLR基因部署对同源病原体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中，最多含有四种已经被击败的抗晚疫病病原体（P. infestans）的NLRs。两国NLR基因分布的不同模式分别反映在美国和英国现存致病性病原菌基因型中同源Avr基因的多样性上。与育种高度相关的是，我们最近确定了具有特征的nlr，这些nlr仍然有效地对抗鼠疫杆菌，并且已经存在于先进的育种前材料中，甚至已经在荷兰进行了试验的品种中。关键的是，这些“新”抗性尚未广泛用于商业马铃薯生产，也尚未在品种中堆叠。迄今为止，只有数量有限的疟原虫分离株能够单独克服这些新的NLRs。本研究旨在发现病原菌适应机制，使不同地理位置的病原菌谱系能够克服农业中宿主的抗性。通过与全球商业伙伴的育种项目，我们将运用这些知识，生产出含有互补和有效的NLR组合的更耐久的抗性品种。有效nlr的组合将延长单个抗性的寿命，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.