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的园艺作物，也是世界上仅次于番茄的第二大蔬菜作物。洋葱是许多国家的主要作物，具有一系列的健康益处，包括抗癌、抗血栓和抗生素作用。尽管这种作物很有价值，但育种和遗传改良的研究受到限制，因为诸如洋葱多样性集、纯育种品系和基因组信息等资源很少。洋葱病害是制约洋葱生产的主要病害之一，其中最重要的病害是由土传植物病原菌尖孢镰刀菌引起的。这种真菌是多种多样的，有许多不同的亚种（formae speciales, f.spp.），它们攻击各种作物。在洋葱中，尖孢菌。cepae （FOC）可以在任何阶段感染植物，导致幼苗“受潮”症状，并在更成熟的植物和鳞茎上引起基腐病。这导致了严重的收获前和/或收获后损失，据估计，英国农民每年损失1100万英镑。由于FOC是一种土壤传播的病原体，其产生的长寿命孢子可存活多年，因此控制方法很困难，以前依赖于使用土壤消毒/巴氏消毒、杀菌剂浸泡或种子处理。这种方法基本上是不成功的，有不良的环境影响，并受到限制农药使用的立法的威胁。在没有有效防治措施的情况下，鉴定洋葱的抗性是非常必要的，但迄今为止还相对不成功。然而，我们利用洋葱幼苗开发的高致病性FOC分离物进行快速筛选试验，发现洋葱品系比目前的商业品种具有更高的基础腐病抗性。在华威大学、East Malling Research和国际蔬菜育种公司Nickerson-Zwaan的合作项目中，我们建议提供信息、工具和资源，主要通过开发抗枯萎病的洋葱品系，从而更有效和可持续地控制基腐病。这将使包括育种者、种植者和其他研究人员在内的广泛利益相关者受益。该项目的主要成果将是：1)鉴定FOC致病性/效应基因，作为区分该病原菌与其他尖孢镰刀菌或非致病性菌株的标记；2)鉴定洋葱中FOC抗性位点和相关遗传标记，用于未来的育种计划。3)生产抗FOC的新洋葱群体和预育种洋葱株系，以便为工业开发基础抗腐病洋葱品种。种植者和产业显然将从这项研究中受益，因为抗性品种的部署将使他们在未来更可持续和更有吸引力的选择来控制洋葱的基腐病。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、洋葱套和洋葱鳞茎中的病原体诊断和定量测试提供平台，这将有助于农民做出疾病风险决策并制定管理方案。总的来说，这意味着公众将受益于在减少农药投入的情况下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.