A Systems Approach to Disease Resistance Against Necrotrophic Fungal Pathogens

真菌病原菌灰霉病（Botrytis cinerea）和菌核菌（Sclerotinia sclerotiorum）寄主范围广泛，对许多园艺作物造成严重危害。这两种真菌都会对田间种植和受保护的生菜作物造成重大损失，而生菜产业在英国每年价值近2亿英镑。葡萄球菌是收获后的一个特殊问题，而菌核球菌可导致收获前高达50%的作物损失。化学控制是有问题的，因为可用的有效化合物很少，喷雾的次数有限，时间也很困难。此外，杀菌剂具有中等至高度的耐药风险。在作物中发展持久的抗性是一个更可持续的解决方案，但对生菜育种者来说一直是一个难以妥协的问题。本提案的目的是证明一种新的方法来培育病原体抗性是可能的。我们将在莴苣中应用基因组学和系统生物学（计算）方法，并将其与定量遗传学研究相结合，以确定增加生菜对灰绿杆菌和菌核菌抗性的新基因。这将为在其他园艺作物中培养对这些病原体的类似抗性提供基础。我们有两个假设要检验。首先，我们可以鉴定出对两种坏死性真菌病原体灰绿杆菌和菌核菌都具有抗性的基因。这些真菌的基因组测序表明，它们共享一系列与植物感染和定植相关的基因，因此宿主对一种病原体的抗性机制也可能赋予对另一种病原体的抗性。其次，我们想测试将系统生物学研究应用于园艺作物物种的可行性。我们已经使用系统生物学的方法来产生网络模型的基因如何相互作用在防御反应拟南芥由灰孢杆菌感染。我们将大规模基因表达数据与数学模型相结合来预测关键抗性基因。在这项工作中，我们将对生菜防御反应进行网络分析，并测试相同的基因是否参与抗病，以及/或网络中的枢纽基因是否重要。这是一种全新的作物改良方法，依靠防御病原体感染过程中的基因-基因相互作用。我们还将在受这些病原体影响的主要作物番茄和芸苔中寻找抗病基因的保存。与此同时，我们将采用更传统的定量遗传分析来确定生菜基因组中影响对这两种病原体抗性的区域。我们将筛选近100个对标准品种抗性最强的生菜品种和杂交品种，以产生作图群体。将筛选一个预先存在的作图群体（已知对疾病抗性进行分离）对灰孢杆菌和菌丝体的抗病能力，以确定这些性状的重要基因组区域。最后，我们将把我们的定量遗传分析和网络分析结果结合起来，生成生菜品系和标记，用于育种计划。这个项目是可能的，因为生菜基因组序列是可用的，以及广泛的生菜种质和遗传和基因组资源，沃里克已经产生。这项工作将主要通过A.L.Tozer开发莴苣品种，提高对灰绿杆菌和菌核菌真菌病原体的抗性。

The fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum have broad host ranges and cause serious disease on many horticultural crops. Both fungi can cause substantial losses on field-grown and protected lettuce crops, an industry worth almost £200 M annually in the UK. B. cinerea is a particular problem post-harvest, whereas S. sclerotiorum can result in up to 50% crop loss pre-harvest. Chemical control is problematic as few effective compounds are available, the number of sprays is restricted and timing is difficult. Moreover, the fungicides are medium to high risk for development of resistance. Development of durable resistance in the crop is a more sustainable solution, but has been an intransigent problem for lettuce breeders. The objective of this proposal is to demonstrate that a novel approach to breeding for pathogen resistance is possible.We will apply genomic and systems biology (computational) approaches in lettuce, and combine this with quantitative genetics studies to identify novel genes for increasing the resistance of lettuce to both B. cinerea and S. sclerotiorum. This will provide a foundation to develop similar resistance to these pathogens in other horticultural crops.We have two hypotheses we want to test. Firstly, that we can identify genes which confer resistance to both B. cinerea and S. sclerotiorum, two necrotrophic fungal pathogens. Genome sequencing of these fungi has indicated they share a range of genes associated with infection and colonization of plants, hence host resistance mechanisms against one pathogen might also confer resistance to the other.Secondly, we want to test the feasibility of applying systems biology research into horticultural crop species. We have used systems biology approaches to generate network models of how genes interact during the defence response of Arabidopsis to infection by B. cinerea. We combined large-scale gene expression data with mathematical modelling to predict the key resistance genes. In this work, we will carry out network analysis of the lettuce defence response and test whether the same genes are involved in disease resistance, and/or whether the hub genes in the network are important. This is a completely new approach to crop improvement, relying on gene-gene interactions during defence against pathogen infection. We will also look for conservation of disease resistance genes in tomato and Brassica, key crops affected by these pathogens.At the same time we will employ a more traditional quantitative genetic analysis to identify regions of the lettuce genome that influence resistance against both of these pathogens. We will screen nearly 100 lettuce accessions and cross accessions with the greatest resistance to a standard cultivar to generate mapping populations. A pre-existing mapping population (known to be segregating for disease resistance) will be screened for disease resistance to both B. cinerea and S. scerotiorum to identify important genomic regions for these traits.Finally we will integrate our quantitative genetic analysis and results from network analysis to generate lettuce lines and markers for use in breeding programmes. This project is possible because of the lettuce genome sequence that is available, as well as the extensive lettuce germplasm and genetic and genomic resources that Warwick has generated. The work will be exploited primarily through A.L.Tozer to develop lettuce varieties with increased resistance to B. cinerea and S. sclerotiorum fungal pathogens.