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

油菜根腐病是油菜类作物的一种土传病原菌，每年在世界范围内造成严重的作物损失。它是一种专性寄生虫，这意味着它不能在宿主植物之外培养，是十字花科植物的一种专门害虫。这个家族包括广泛的栽培植物，从蔬菜、油籽、芥菜和根茎作物。在英国，这包括花椰菜、花椰菜、卷心菜、球芽甘蓝和瑞典菜等园艺蔬菜，以及大面积的作物油菜。2021年，英国的Brassica作物种植面积为33.3万公顷，总市值为771m GB。Clubroot在繁殖的地方感染根部，导致宿主细胞增殖，导致根部产生巨大的虫卵，被称为球茎。这些限制了植物的水分和养分供应，导致生长减慢和产量损失。棒状根腐烂很容易向土壤中释放数以百万计的病原体孢子。休眠的孢子非常稳定，这意味着农田可能会被感染15年或更长时间，需要仔细耕种，以防止病原体的进一步传播。用石灰提高pH值可以降低受污染田地的危险程度，但这并不能防止感染。轮作也有帮助，轮作中更频繁地包括油菜，特别是油菜，会增加根瘤病感染的风险。防治丛枝病最重要的方法是利用抗性品种和育种，因为这是世界各地育种公司的一项重要活动。已发现根瘤病种群彼此不同，可分为不同的类群，称为致病类型或小种。育种者使用的不同抗性基因被发现只对这些病型中的一个或一个子集产生抗性，目前还没有广谱抗性可用。人们试图通过育种将不同的抗性基因组合在一起，但使用传统的育种技术通常需要十多年的时间。一个主要的问题是，因为根瘤病是一种非常易变的病原体，出现克服抗性基因的毒力菌株只是个时间问题。因此，有一个持续的军备竞赛的盛衰周期，部署一个抗性基因被克服，并需要新的抗性。特别是花椰菜品种克拉普顿，它花了18年的时间从大白菜的抗性基因育种。在华威，我们一直在研究一种克服这种抗药性的棒状病毒分离物，在最初的工作中，我们已经使用它来鉴定来自英国蔬菜基因库的一些样本，这些样本显示出抗药性的证据。在这个项目中，我们将与英国育种公司Elsom 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中的三个样本的表型和基因组测序，以确定它们包含的抗性基因。我们的目标是确定潜在的根瘤病所需的隐性抗性基因，称为敏感因子，可以提供持久的、广谱的抗性，而这种抗性是病原菌难以克服的。这种隐性的性质也将使这种抗性模式易于在使用新的植物育种生物技术方法的优秀作物品种中更快地部署，这些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，以进一步确定我们识别的抗性基因的特征。

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.