Exploring and Exploiting Epigenetic Plant Immunity

作物保护对全球粮食供应链至关重要。尽管自绿色革命以来取得了重大技术进步，但植物病害继续对粮食安全构成威胁。由于立法限制农药和转基因作物的使用，迫切需要开发替代作物保护方法。这一目标已成为联合王国可持续强化议程的关键优先事项。在作物保护领域，定量抗病是一个很有吸引力的概念。与依赖单一抗性基因的定性抗性不同，数量抗性依赖于多种相互作用的基因和机制。因此，它对病原体的共同进化更有弹性，并对多种病原体分离物和物种提供广谱保护。然而，尽管有这些优势，数量抗性尚未充分发挥其潜力，因为与传统保护策略相比，其调节复杂，有时效果可变。例如，虽然定量耐药性减缓了疾病进展，但它往往太弱，无法完全预防强毒病原体的感染。诱导抗性（IR）是一种适应性免疫反应，使植物能够提高其先天的数量抗性水平。IR通常在从生物压力中恢复后发展，基于一种称为启动的免疫记忆形式，它能够更快和/或更强地防御未来病原体的攻击。我们之前已经表明，模式植物拟南芥的长期IR具有表观遗传基础，涉及DNA甲基化的全基因组减少，这可以传递给后代。虽然暴露于疾病胁迫后的表观遗传IR （epi-IR）可能是可变的，但我们发现直接操纵拟南芥表观基因组可以产生接近完全水平的对霜霉病的保护。控制这种人工epi-IR反应的表观遗传位点在多代内是稳定的，并且与植物生长的重大减少无关，使其在作物保护方面的开发具有吸引力。然而，作物的基因组比拟南芥大，这使得它们更容易受到全基因组DNA甲基化减少的影响。因此，为了进一步推进这一研究，我们建议开发一种更精确和可调节的方法来引入植物基因组的表观遗传变异。这不仅对作物保护和育种具有很高的翻译价值，而且为探索表观遗传改变的DNA位点启动防御基因的复杂机制提供了有价值的研究工具。基于初步的概念验证结果，我们的项目将利用我们实验室的专业知识和资源，开发一种新的工具，用于可调节地引入植物基因组的表观遗传变异。这种可调节的表皮突变将优化拟南芥和莴苣的表皮- ir抗霜霉病。然后，我们将使用该方法筛选表观遗传基因调控受损的拟南芥突变体，以了解其发展和保留epi-IR的能力，随后进行下一代测序分析，以揭示全基因组范围内的基础机制。同时，我们将利用我们的方法，选择具有高水平抗霜霉病epi-IR的表观遗传修饰生菜品系。这些品系将被鉴定出与商业相关的性状，并用于产生表观遗传重组自交系，以便将epi-IR从对生长和结实率的潜在不良影响中分离出来。该项目将与ENZA合作进行，ENZA是一家全球作物育种公司，占英国生菜种子市场的50%。这一伙伴关系将由一名业务发展经理监督，以确保有效的知识交流、管理知识产权，并促进行业合作伙伴采用技术。

Crop protection is of crucial importance to the global food supply chain. Despite the major technological advances since the green revolution, plant diseases continue to pose a threat to food security. Aggravated by legislative restrictions on the use of pesticides and GM crops, there is an urgent need to develop alternative crop protection methods. This objective has become a key priority of the sustainable intensification agenda in the UK. Quantitative disease resistance is an attractive concept for crop protection. Unlike qualitative resistance, which relies on single resistance genes, quantitative resistance depends on a multitude of interacting genes and mechanisms. Accordingly, it is more resilient against co-evolution by pathogens and offers broad-spectrum protection against multiple pathogen isolates and species. Despite these advantages, however, quantitative resistance has not been exploited to its full potential, because of its complex regulation and sometimes variable effectiveness compared to conventional protection strategies. For instance, while quantitative resistance slows down disease progression, it is often too weak to prevent infection by virulent pathogens completely.Induced resistance (IR) is an adaptive immune response that allows plants to boost their innate level of quantitative resistance. IR typically develops after recovery from biotic stress and is based on a form of immune memory called priming, which enables a faster and/or stronger defence induction against future pathogen attack. We have previously shown that long-lasting IR in the model plant Arabidopsis has an epigenetic basis, involving genome-wide reductions in DNA methylation, which can be transmitted to subsequent generations. While epigenetic IR (epi-IR) after exposure to disease stress can be variable, we found that direct manipulation of the Arabidopsis epigenome can yield near complete levels of protection against downy mildew disease. The epigenetic loci controlling this artificial epi-IR response are stable over multiple generations and are not associated with major reductions in plant growth, making it attractive for exploitation in crop protection. However, crops have larger genomes than Arabidopsis, rendering them more vulnerable to genome-wide reductions in DNA methylation. Thus, to advance this research, we propose to develop a more precise and adjustable method to introduce epigenetic variation in plant genomes. This would not only be of high translational value to crop protection and breeding, but also represent a valuable research tool to explore the complex mechanisms by which epigenetically altered DNA loci prime defence genes.Based on preliminary proof-of-concept results, our project will develop a novel tool for adjustable introduction of epigenetic variation in plant genomes, taking advantage of the expertise and resources in our labs. This adjustable epi-mutagenesis will be optimised for epi-IR against downy mildew disease in both Arabidopsis and lettuce. We will then use the method to screen Arabidopsis mutants impaired in epigenetic gene regulation for their ability to develop and retain epi-IR, followed by next-generation sequencing analyses to reveal the underpinning mechanisms on a genome-wide scale. In parallel, we will exploit our method by selecting for epigenetically modified lettuce lines with high levels of epi-IR against downy mildew disease. These lines will be characterised for commercially relevant traits and used to generate epigenetic recombinant inbred lines, in order to separate epi-IR from potentially undesirable effects on growth and seed set. The project will be conducted in partnership with ENZA, a global crop breeding company covering >50% of the lettuce seed market in the UK. This partnership will be supervised by a business development manager to ensure efficient knowledge exchange, manage intellectual property, and facilitate adoption of the technology by the industry partner.