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.

The proposed research is a Newton-Bhabha development programme. The overall aim is to transfer and optimize UK expertise in genomics, which is the scientific approach involving analysis in parallel of the complete set of genes of an organism, for improvement of both economic and environmental sustainability of mustard rape (Brassica juncea) in India. The crop characteristics (traits) that are the focus of the research were defined by the Indian partners in the proposal as the most important challenges faced by the crop in India. There are tolerances to the range of environmental challenges (stresses): diseases and infestations from fungi (causing white rust, stem rot, black spot), viruses (Turnip mosaic virus), pests (aphids and butterflies) and root parasites (broomrape) and conditions of high temperatures, drought and salinity. Of particular importance is that multiple stresses are often encountered simultaneously and interactions and trade-offs between tolerance mechanisms can be expected, necessitating an integrated approach across this broad range of challenges. Included in a broad correlation analysis between the traits will be an assessment of associations with variation in classes of chemicals produced by the plants that are recognised as playing roles in tolerance to environmental stresses. To enable this programme to be undertaken thoroughly and successfully, we have assembled a consortium comprising 39 co-applicant scientists representing 17 institutions. The approach is to establish a toolkit of technologies to help understand the basis of naturally-occurring tolerances and to enable future work to enhance them. These include the establishment of a platform enabling the association of trait variation in panels of genetically diverse mustard rape varieties with variation of both gene sequences and gene activity (expression) to enable the development of molecular markers to accelerate breeding and identify candidate causative genes for further investigation. Non-GM approaches for improvement beyond the range of existing natural variation will be established for mustard rape, including modernised resources for the traditional approaches of radiation breeding and wide crossing with related species, and the emerging technology of genome editing. Underpinning the programme is the experience gained in developing the Brassica juncea genomic platform currently used by the University of York and University of Delhi South Campus as part of their current Crop Genomics and Technologies (CGAT) project "Broadening the genetic diversity underpinning seed quality and yield related traits in mustard rape and oilseed rape" will be updated to incorporate emerging genome sequences from B. juncea and its progenitor species. The platform will be used to support the trait-focussed activities of the consortium, modelled on the University of York-led "BBSRC Renewable Industrial Products from rapeseed (RIPR) programme". A particular feature will be the highly integrated nature of the research with expertise contributed by world-leaders in the respective components being shared. UK expertise will be transferred to partners in India for application in mustard rape. The benefits of scientific understanding and ability to improve traits in mustard rape accrue primarily to the Indian members of the consortium. However, they will also be of use for improving the corresponding traits in oilseed rape for cultivation in the UK.

Flowering time in crop plants is agronomically important because it impacts on quality, yield and scheduling of production. Research into the molecular pathways controlling flowering time in the model plant Arabidopsis has progressed rapidly over the past 20 years and has led to a much greater understanding of the genetic regulation of flowering. However, to date there has been little translation of this huge investment in Arabodopsis research into real benefits in crop plants. Premature bolting (flowering) of rocket before it is harvested is a major problem for growers, as secondary metabolites are produced in the leaves which give the plant a bitter and unpleasant taste and render the crop unsaleable. Delayed bolting is a desirable trait in commercial rocket varieties as it preserves the quality of rocket leaves sold for consumption in leafy salads, and increases sustainability by reducing wastage caused by premature bolting of crops in the field. Several genes have been identified which, if mutated, result in delayed flowering in Arabidopsis. These include genes involved in the photoperiodic pathway, the vernalisation pathway, the autonomous pathway, and genes responsible for integrating the floral pathways. Many of these genes have been cloned from Arabidopsis and homologues of some of these genes have been identified in a diverse range of species, including monocots, where they have been shown to have similar, or conserved roles in regulating flowering time. This project will exploit the knowledge of molecular pathways controlling flowering gained from model plants such as Arabidopsis, and also from the knowledge gained about genes controlling bolting in lettuce (which is part of a current BBSRC funded project in the Supervisors lab), to identify novel alleles of flowering time genes that have either been induced through mutagenesis, or have arisen naturally, that can be used to delay bolting in rocket. This will be done through the following approaches; a). An EMS mutagenised population will be screened for late bolting lines that have been created as a result of the mutagenesis treatment. b). Flowering time genes will be identified and isolated from Rocket, this will be done through homology to known flowering time genes in Arabidopsis which is a close relative of Rocket. c). A Rocket diversity set will be screened for natural variation affecting bolting time. d). Sequences of flowering time genes in the late bolting Rocket lines that have been isolated from a). and c). will be analysed to identify polymorphisms that may be the cause of the late bolting phenotype. This may be done through comparing the transcriptome sequence of the late bolting lines with WT lines, and/or PCR-based cloning and sequencing of the target genes. e). Polymorphisms in flowering time genes will be followed through a back-crossing programme to see if they co-segregate with the late bolting phenotype and thus could be causing the late bolting. f). Late bolting Rocket lines will be grown in commercially managed field trials to test the robustness of the late bolting in different field conditions. g). The effect of delayed bolting on senescence in rocket will be investigated through the analysis of the expression of senescence-associated genes in the late bolting lines. The principle objectives/outputs of this research project are; i). The identification of Rocket genes controlling bolting time. ii). The creation of late bolting lines in a commercially relevant Rocket cultivar which can readily be incorporated into breeding programmes to generate new varieties with delayed bolting. iii). The identification of naturally occurring alleles of known flowering time genes that have a robust effect on bolting time in different genetic backgrounds. iv). To examine the advantages conferred by delayed bolting in terms of reduced crop losses and possibly also through effects on leaf senescence.

In order to keep pace with the world's expanding population, global crop yields are required to double by 2050 and this requirement is made even more challenging by the rising global temperatures and emerging erratic weather patterns caused by climate change. To meet this challenge with minimal environmental impact, it is imperative that the productivity of agricultural land is increased through strategic and technological advances. Seed-borne pathogens attack developing seedlings, compromising germination and plant establishment and ultimately reducing crop yield. As a result, seeds need to be disinfected and this is typically achieved by washing seeds with or without chemical additives, coating the seeds with fungicide, or soaking germinating seedlings in fungicide drenches. Such approaches have limited applicability as they can affect the germination of the seed and they are not effective in treating all diseases. In addition, due to stricter regulatory controls on the use of chemical agents, seed companies are in need of alternative means of disinfecting seeds without negatively affecting their viability. PlasSeed proposes the use of gas plasma technology as a novel and potentially revolutionary means of disinfecting seeds. Gas plasma has been shown to have a broad range of antimicrobial properties and the technology offers a chemical-free, dry, low-energy alternative to existing seed disinfection techniques.

Flowering is a key component of plant adaptation, affecting geographical distribution and suitability for farming practices. It is highly relevant to yield, quality and environmental considerations as flowering at the appropriate time ensures best use of the available growing season, promoting sustainability and reducing the need for inputs. The genus Brassica includes species with many morphological forms that are cultivated for use as vegetables, oils, fodder and condiments, and much of this morphological diversity can be attributed to variation in flowering time. Biennial cultivars require a period of cold treatment (vernalization) to induce flowering. This flowering behaviour is critical for the production of some vegetable forms and for adaptation to certain agricultural practices, such as planting of overwintering cauliflower varieties. Annual Brassica cultivars do not require cold treatment to flower, although some annuals can respond to vernalization by flowering earlier and more uniformly. How different varieties respond to vernalization has a big effect on when and how they mature. Many vegetables are harvested and eaten at the vegetative stage, prior to flowering. Successfully predicting the timing and length of the vegetative phase has a big influence on the quality and commercial return from the crop. For other vegetables it is the timing of the floral transition that is critical. In this project we will identify genes which can exert greater or lesser control on the vernalization process with the aim of using this information to produce parent lines and hybrids which have a more predictable harvest period. We will relate variation at these loci to performance under present and historical weather patterns to associate specific allelic combinations with maturity under different climatic conditions. Knowledge of key Brassica vernalization genes and how they vary in different vegetable Brassicas will allow us to address key questions about the impact of climate patterns on the availability of UK-produced quality Brassica vegetables.