A Systems Approach to Disease Resistance Against Necrotrophic Fungal Pathogens

番茄灰霉病菌和菌核病菌寄主范围广，对多种园艺作物危害严重。这两种真菌都会对大田种植和受保护的生菜作物造成重大损失，在英国，这一产业每年价值近2亿英镑。灰霉病是收获后的一个特别问题，而菌核菌在收获前可能导致高达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，喷洒的数量受到限制，时机也很困难。此外，杀菌剂具有中到高的抗药性发展风险。在作物中发展持久的抗性是一个更可持续的解决方案，但对于生菜育种者来说一直是一个顽固的问题。这一建议的目的是证明一种新的抗病原菌育种方法是可能的。我们将在生菜中应用基因组和系统生物学(计算)方法，并将其与定量遗传学研究相结合，以确定提高生菜对灰霉病和菌核病抗性的新基因。这将为在其他园艺作物中开发对这些病原菌的类似抗性提供基础。我们有两个假设要检验。首先，我们可以确定对两种坏死性真菌病原菌--灰霉病和核盘菌都有抗性的基因。对这些真菌的基因组测序表明，它们共享一系列与植物侵染和定植相关的基因，因此寄主对一种病原菌的抗性机制也可能赋予另一种病原菌抗性。第二，我们希望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建立网络模型，研究在拟南芥对灰霉病菌感染的防御反应中，基因是如何相互作用的。我们将大规模的基因表达数据与数学模型相结合来预测关键的抗性基因。在这项工作中，我们将对生菜的防御反应进行网络分析，并测试是否相同的基因参与抗病，和/或网络中的中枢基因是否重要。这是一种全新的作物改良方法，依赖于抵御病原体感染期间的基因-基因相互作用。我们还将在番茄和油菜这两种受病原菌影响的关键作物中寻找抗病基因的保守性。同时，我们将使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菌的抗性的区域。我们将筛选近100份生菜种质和对标准品种抗性最强的杂交种质，以生成作图群体。我们将对已有的作图群体(已知为抗病分离)进行抗病筛选，以确定这些测试的重要基因组区域。最后，我们将整合我们的定量遗传分析和网络分析的结果，以产生用于育种计划的生菜品系和标记。这个项目之所以可能，是因为有可用的生菜基因组序列，以及沃里克创造的广泛的生菜种质和遗传和基因组资源。这项工作将主要通过A.L.Tozer开发出对灰霉病和核盘菌病原菌具有更高抗性的生菜品种。

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.