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

洋葱是世界各农业国普遍栽培的重要园艺作物，也是仅次于番茄的世界第二大蔬菜作物。洋葱是许多国家的主要作物，并提供一系列健康益处，包括抗癌，抗血栓形成和抗生素作用。尽管洋葱具有很高的价值，但育种和遗传改良方面的研究仍然有限，因为洋葱多样性集、纯育种系和基因组信息等资源很少。病害是洋葱生产的主要制约因素之一，其中最重要的一种是由土传植物病原体尖孢镰刀菌（Fusarium oxysporum）引起的。这种真菌是多样的，并有许多不同的亚种（formae speciales，f. spp.）它们攻击各种农作物。在洋葱中，F.尖孢头孢专化型（FOC）可在任何阶段感染植物，在幼苗上引起“猝倒”症状，在更成熟的植物和鳞茎上引起基部腐烂。这导致严重的收获前和/或收获后损失，据估计，英国农民每年损失约1100万英镑。由于FOC是一种土传病原体，可产生存活多年的长寿孢子，因此控制方法很困难，以前依赖于使用土壤消毒/巴氏灭菌，用杀真菌剂浸泡或种子处理。这种方法基本上不成功，对环境有不良影响，并受到限制农药使用的立法的威胁。在缺乏有效的防治措施的情况下，确定洋葱的抗性是非常必要的，但迄今为止一直相对不成功。然而，在我们使用洋葱幼苗开发的快速筛选试验中使用高致病性FOC分离物，我们已经鉴定出比当前商业栽培品种具有更高水平的基腐抗性的洋葱品系。在沃里克大学、东马岭研究所和国际蔬菜育种公司尼克森-茨旺之间的合作项目中，我们提议提供信息，工具和资源，这将导致更有效和可持续的控制镰刀菌基腐病，主要是通过发展抗FOC洋葱线。这将使包括育种者、种植者和其他研究人员在内的广泛的利益相关者受益。本项目的主要成果是：1）鉴定FOC致病性/效应基因，作为区分FOC与其他F. oxysporum F. spp.或非致病性分离物，2）鉴定洋葱中的FOC抗性基因座和相关遗传标记以用于未来的育种计划，3）产生分离FOC抗性的新洋葱群体和预育种洋葱品系以使得能够开发用于工业的抗基部腐烂的洋葱栽培品种。种植者和行业显然将从这项研究中受益，因为抗性品种的部署将为他们提供一个更可持续和更有吸引力的选择，用于未来的洋葱基腐病控制。此外，与控制FOC致病性的基因相关的DNA标记还应提供一个平台，用于开发土壤、洋葱种子、洋葱套和洋葱鳞茎中病原体的诊断和定量测试，这将有助于农民做出有关疾病风险的决定，并制定管理方案。总的来说，这意味着公众将受益于减少农药投入而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.