Horticulture: Development of novel durable resistance for clubroot in C genome brassicas

根肿病（Plasmodiophora brassicae）是芸苔属（Brassica）作物的土传病原体，每年在世界范围内导致显著的作物损失。它是一种专性寄生物，这意味着它不能在其宿主植物外培养，并且是菊科植物的专业害虫。这个科包括从蔬菜、油籽、芥菜和根作物的广泛栽培植物。在英国，这包括园艺蔬菜，如花椰菜、花椰菜、卷心菜、布鲁塞尔芽甘蓝和瑞典菜，以及大面积作物油菜。2021年，英国的芸苔属作物种植面积为33.3万公顷，总市值为7.71亿英镑。根肿病会感染根部，在根部繁殖，导致宿主细胞增殖，导致根部产生大的虫瘿，称为根棒。这些限制了对植物的水和营养供应，导致生长减少和产量损失。棒状的根很容易腐烂，释放出数百万的病原体孢子到土壤中。休眠的孢子非常稳定，这意味着田地可以被感染15年或更长时间，需要小心养殖以防止病原体的进一步传播。受感染田地的风险严重程度可以通过用石灰增加pH值来降低，但这并不能防止感染。作物轮作也可以帮助和更频繁的包括油菜，特别是油菜，在轮换增加根肿病感染的风险。没有杀菌剂不能控制根肿病。控制这种疾病的影响的最重要方法是通过使用抗性品种和育种，这是世界各地育种公司的重要活动。已发现根肿病种群彼此不同，并且可以被分类为称为致病型或小种的不同组。发现育种者使用的不同抗性基因仅赋予对这些致病型中的一种或一个子集的抗性，并且目前没有可用的广谱抗性。有人试图通过育种将不同的抗性基因联合收割机组合在一起，但使用常规育种技术通常需要十多年的时间。一个主要的问题是，由于根肿病是一种非常多变的病原体，出现一种克服抗性基因的强毒株只是时间问题。因此，利用抗病基因来克服它，需要新的抗性，这是一个持续的繁荣-萧条周期的军备竞赛，一个特别的例子是花椰菜品种克莱普顿，它花了18年的时间才从中国白菜中培育出抗病基因。在沃里克，我们一直在研究一种能克服这种抗性的根肿病分离株，在最初的工作中，我们用它来鉴定来自英国蔬菜基因库的一些样品，这些样品显示出抗性的证据。在这个项目中，我们将与英国育种公司Ellingseeds合作，展示一种新的快速和具有成本效益的筛选策略的概念验证，该策略将联合收割机表型分析和基因组测序结合起来，以确定其中三个基因库样本所包含的抗性基因。我们的目标是确定隐性抗性基因，有可能是根肿病感染所需的，称为易感因素，可以提供持久的，广谱的抗性，是很难克服的病原体。隐性的性质也将使这种抗性模式适合于使用新的植物育种生物技术方法更快地部署在优良作物品种中，这种方法将缩短漫长的传统育种过程。该项目还将提供必要的数据，以支持后续工作的应用，以进一步验证我们发现的抗性基因。

Clubroot (Plasmodiophora brassicae) is a soil-borne pathogen of Brassica crops that leads to significant crop losses worldwide each year. It is an obligate parasite, meaning that it cannot be cultured outside its host plant, and is a specialist pest of plants in the Brassicaceae family. This family includes a wide range of cultivated plants from vegetables, oilseeds, mustards and root crops. In the UK this includes horticultural vegetables like cauliflower, broccoli, cabbage, Brussels sprouts and swedes and the broadacre crop oilseed rape. In combination the UK Brassica crops were grown on 333,000 ha in 2021 with a total market value of £771m.Clubroot infects roots where it multiplies leading to host cell proliferation that results in large galls on the roots that are known as clubs. These restrict water and nutrient supply to the plant leading to reduced growth and yield loss. The clubbed roots rot readily releasing millions more pathogen spores into the soil. The resting spores are very stable meaning that fields can be infected for 15 years or more and need to be farmed carefully to prevent further spread of the pathogen. The severity of risk from infected fields can be reduced by increasing the pH with lime but this does not prevent infection. Crop rotation can also help and more frequent inclusion of Brassicas, especially oilseed rape, in rotations increases the risk of clubroot infection. There are no fungicides not available to control clubroot.The most important way to control the impact of this disease is through the use of resistant varieties and breeding for this is an important activity of breeding companies around the world. Clubroot populations have been found to differ from each other and can be classified into different groups which are referred to as pathotypes or races. The different resistance genes used by breeders are found to confer resistance to only one or a subset of these pathotypes and there is currently no broad spectrum resistance available. There are attempts to combine different resistance genes together by breeding, but this typically takes more than a decade to do using conventional breeding techniques. A major problem is that, because clubroot is a very variable pathogen, it is only a matter of time before a virulent strain will emerge that overcomes the resistance genes. There is thus a continuous arms race of boom-bust cycles of deploying a resistance gene to it being overcome and new resistance is required.A particular example is the cauliflower variety Clapton which took 18 years to breed in a resistance gene from Chinese cabbage. At Warwick we have been working on a clubroot isolate that overcomes this resistance and, in initial work, we have used it to identify a number of samples from the UK Vegetable Genebank that show evidence of resistance. In this project we will partner with the UK breeding company Elsoms Seeds to demonstrate proof-of-concept for a new rapid and cost effective screening strategy that will combine phenotyping and genome sequencing of three of these genebank samples to identify the resistance genes they contain. We are aiming to identify recessive resistance genes that have the potential to be required for clubroot infection, termed susceptibility factors, that could provide durable, broad spectrum resistance that is difficult for the pathogen to overcome. The recessive nature would also make this mode of resistance amenable to faster deployment in elite crop varieties using new plant breeding biotechnology methods that would short-cut the lengthy conventional breeding process. The project will also provide essential data to support the application of follow-up work to further characterise the resistance genes we identify.