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

棒根菌（Plasmodiophora brassicae）是一种土壤传播的芸苔类作物病原体，每年在世界范围内造成重大的作物损失。它是一种专性寄生虫，这意味着它不能在宿主植物外培养，是十字花科植物的一种专门害虫。该科包括蔬菜、油籽、芥菜和块根作物等多种栽培植物。在英国，这包括园艺蔬菜，如花椰菜、西兰花、卷心菜、抱子甘蓝、瑞典菜和大面积作物油菜。2021年，英国芸苔属作物的总种植面积为33.3万公顷，总市场价值为7.71亿英镑。棒根菌感染根部，在那里它繁殖导致宿主细胞增殖，从而在根部形成被称为棒根菌的大虫瘿。这些限制了植物的水分和养分供应，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，需要小心耕种，以防止病原体的进一步传播。可以通过用石灰增加pH值来降低受感染田地的风险严重程度，但这并不能预防感染。轮作也有帮助，更频繁地轮作芸苔属植物，特别是油菜，增加了根茎病感染的风险。没有杀真菌剂不能用于控制俱乐部根。控制这种疾病影响的最重要方法是使用抗性品种，为此进行育种是世界各地育种公司的一项重要活动。已经发现俱乐部群体彼此不同，可以分为不同的群体，这被称为病型或种族。育种者使用的不同抗性基因被发现只赋予对这些病型的一种或一个子集的抗性，目前还没有广泛的抗性。有人试图通过育种将不同的抗性基因组合在一起，但使用传统育种技术通常需要10年以上的时间。一个主要的问题是，因为俱乐部是一个非常可变的病原体，它只是一个时间问题的毒株将出现克服抗性基因。因此，这是一场持续的军备竞赛，在盛衰周期中部署抗性基因，以克服它，并需要新的抗性。一个特别的例子是花椰菜品种Clapton，它花了18年的时间从白菜中培育出一种抗性基因。在沃里克大学，我们一直在研究一种克服这种耐药性的俱乐部分离物，在最初的工作中，我们已经用它来识别来自英国蔬菜基因库的一些样本，这些样本显示出耐药性的证据。在这个项目中，我们将与英国育种公司Elsoms Seeds合作，展示一种新的快速且具有成本效益的筛选策略的概念验证，该策略将结合这些基因库样本的表型分析和基因组测序，以确定它们包含的抗性基因。我们的目标是确定隐性耐药基因，这些基因可能是俱乐部感染所必需的，称为易感因素，可以提供持久的，广谱的耐药，这是病原体难以克服的。隐性的特性也将使这种抗性模式适应于使用新的植物育种生物技术方法更快地在优良作物品种中部署，这将缩短漫长的传统育种过程。该项目还将提供必要的数据，支持后续工作的应用，以进一步表征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.