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

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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.