Exploiting next generation sequencing technologies to understand pathogenicity and resistance in Fusarium oxysporum

洋葱是世界上每个农业国家都种植的重要园艺作物，也是仅次于番茄的世界第二大蔬菜作物。洋葱在许多国家是一种主要农作物，对健康有一系列好处，包括抗癌、抗血栓和抗生素作用。尽管洋葱很有价值，但由于洋葱多样性集、纯育种系和基因组信息等资源有限，对洋葱育种和遗传改良的研究有限。病害是制约洋葱生产的主要因素之一，其中最重要的是由土传植物病原菌尖孢镰刀菌引起的。该真菌种类繁多，有许多不同的亚种(Formae Speciales，f.spp.)它们会攻击各种农作物。在洋葱中，尖孢镰刀菌(F.oxporum f.sp.)洋葱(FOC)可以在任何时期侵染植物，在幼苗上引起‘倒伏’症状，在更成熟的植物和鳞茎上引起基腐病。这导致了收获前和/或收获后的严重损失，估计每年给英国农民造成的损失约为1100万英镑。由于FOC是一种土壤传播的病原体，会产生可存活多年的长寿命孢子，因此控制方法很困难，以前依赖于土壤消毒/巴氏杀菌、用杀菌剂浸泡或种子处理。这种方法在很大程度上是不成功的，对环境造成了不良影响，并受到了限制杀虫剂使用的立法的威胁。在缺乏有效的防治措施的情况下，鉴定洋葱对枯萎病的抗性是非常可取的，但到目前为止还相对不成功。然而，在我们开发的利用洋葱幼苗进行的快速筛选试验中，使用一种高致病性的FOC分离物，我们已经鉴定出具有比当前商业品种更高水平的基础腐烂水平的洋葱品系。在华威大学、East Mling Research和国际蔬菜育种公司Nickerson-Zwaan的一个合作项目中，我们提议提供信息、工具和资源，主要通过培育抗FOC洋葱品系来更有效和可持续地控制镰刀菌基础腐烂。这将使广泛的利益相关者受益，包括育种者、种植者和其他研究人员。该项目的主要成果将是1)鉴定FOC致病力/效应基因，这些基因可作为区分该病原菌与其他尖孢镰刀菌的标记。2)鉴定洋葱中的FOC抗性基因座和相关的遗传标记，以用于未来的育种计划；3)产生新的洋葱种群，分离出抗FOC的洋葱品系，并预育洋葱品系，以便为工业开发抗基础腐烂洋葱品种。种植者和工业显然将从这项研究中受益，因为抗病品种的部署将使他们在未来的洋葱基础腐烂防治方面有一个更可持续和更有吸引力的选择。此外，与控制FOC致病性的基因相关的DNA标记也应该为开发土壤、洋葱种子、种子和鳞茎中病原体的诊断和定量测试提供一个平台，这将帮助农民对疾病风险做出决定，并制定管理方案。总体而言，这意味着公众将受益于用更少的杀虫剂投入种植的质量更好的洋葱。

Onion is an important horticultural crop which is cultivated by every agricultural nation in the world and is also the second most valuable vegetable crop in the world behind tomato. Onions are a staple crop in many countries and deliver a range of health benefits including anticarcinogenic, antithrombotic and antibiotic effects. Despite the value of the crop, research into breeding and genetic improvement is limited as few resources such as onion diversity sets, pure breeding lines and genomic information are available.Diseases are one of the major constraints to onion production and one of the most important is caused by the soilborne plant pathogen Fusarium oxysporum. This fungus is diverse and has many different sub-species (formae speciales, f.spp.) which attack various crop plants. In onion, F. oxysporum f.sp. cepae (FOC) can infect plants at any stage causing a 'damping-off' symptom on seedlings and a basal rot on more mature plants and bulbs. This results in severe pre- and/or post-harvest losses and has been estimated to cost farmers in the UK in the region of £11M per annum. As FOC is a soilborne pathogen which produces long-lived spores that survive for many years, control approaches are difficult and have previously relied on the use of soil sterilisation / pasteurisation, drenches with fungicides or seed treatments. This approach has largely been unsuccessful, has undesirable environmental effects and is threatened by legislation governing restrictions in pesticide use. In the absence of effective control measures for Fusarium basal rot, identifying resistance in onion is extremely desirable but so far has been relatively unsuccessful. However, using a highly pathogenic FOC isolate in a rapid screening test we developed using onion seedlings, we have identified onion lines with much higher levels of basal rot resistance than current commercial cultivars.In a collaborative project between the University of Warwick, East Malling Research and the international vegetable breeding company Nickerson-Zwaan, we propose to provide information, tools and resources which will lead to more effective and sustainable control of Fusarium basal rot, primarily through the development of FOC-resistant onion lines. This will benefit a wide range of stakeholders including breeders, growers and other researchers. The main outcomes of the project will be 1) the identification of FOC pathogenicity/effector genes which could be used as markers to distinguish this pathogen from other F. oxysporum f. spp. or non-pathogenic isolates, 2) the identification of FOC resistance loci and associated genetic markers in onion for use in future breeding programmes, 3) the production of new onion populations segregating for FOC resistance and pre-breeding onion lines to enable the development of basal rot resistant onion cultivars for the industry. Growers and the industry will clearly benefit from this research as the deployment of resistant cultivars will give them a more sustainable and attractive option for basal rot control in onion in the future. In addition, DNA markers associated with genes controlling FOC pathogenicity should also provide a platform for developing diagnostic and quantitative tests for the pathogen in soil, onion seed, sets and bulbs which will help farmers make decisions about disease risk and develop management options. Overall this means that the public will benefit from better quality onions grown with reduced pesticide inputs.