Pulse-Downy Mildew Pathosystem: deploying disease resistance, pathogenomics and microbial biocontrol

Pulses, in particular peas and broad beans, are important crops both in the UK and worldwide and they are grown as extensive monocultures. Even with long rotations, the crops are vulnerable to major epidemics of economically important pests and diseases, of which downy mildews (caused by the oomycete biotrophic pathogens Peronospora viciae f. sp. pisi (Pvp) and P. viciae f. sp. fabae (Pvf) in peas and beans, respectively) are the most serious. Breeding companies are challenged to produce cultivars with new resistance genes and will benefit from access to crop wild relatives carrying new resistance genes. The disease is managed through deployment of resistant varieties and chemical controls; however a lack of information on prevalent isolates can lead to serious yield losses in crops grown on contaminated sites through uninformed variety selection. Although a differential set of plant cultivars is available to identify the virulence genes in pathotypes of Pvp/Pvf, the test is too time-consuming to be of immediate use to commercial growers and does not allow rapid monitoring of the prevailing isolates. In addition, generating a model for pathogen spread is impossible using current methods. The problem is exacerbated by reports of resistance of oomycete pathogens to pesticides such as metelaxhyl.
Without adequate control regimes, pea and broad bean production will incur greater crop wastage and it is therefore imperative that methods are developed to decrease growers' reliance on pesticides for the control of downy mildew. Deployment of pulse cultivars resistant to prevailing isolates is the most promising approach. Use of appropriate molecular tools will enable breeders, epidemiologists, modellers and growers to: a) identify the prevailing virulent isolate; b) investigate the epidemics of disease; c) monitor pathogen movement and d) deploy the appropriate cultivar(s) resistant to the prevailing isolate rapidly and thus control the disease in an environmentally friendly and sustainable manner. Accurate advice to growers about resistant cultivars requires correct information on the virulence of Pvp/Pvf races within the locality. However, diagnosing the pathogen at the isolate level requires the right tools.
The innovative approach described in this project focuses on the development of molecular tools for accurate identification of Pvp/Pvf isolates as well as for breeding for resistance. We aim to identify new resistance sources to include in breeding programmes and develop molecular markers to enable rapid identification and monitoring of pathogen isolates. We will use next generation sequencing to identify polymorphisms in several isolates. These polymorphisms will then be utilised to generate isolate-specific markers. Once identified, markers will be tested under laboratory conditions and subsequently will also be checked in commercial fields. In addition, we will use biological control agents to control downy mildew disease. These will lead to increased crop productivity, reduced reliance on pesticides and less wastage from diseased plants.

Accessing adequate amounts of nutritious, safe, and culturally appropriate foods in an environmentally sustainable manner is important for a growing population. Producing enough food in the future is possible but care must be taken not to damage the ecosystem and biodiversity. The current recommended approach promotes sustainable intensification: using less water, fertilizer and pesticides to obtain greater yield. Many pesticides may leave residues in or on treated fruits, vegetables, and grains as well as in soil even if they are used according to the manufacturer's instructions.
We hypothesise that identifying new sources of disease resistance, coupled with the identification and proper monitoring of the prevailing pathogen isolate, and selection and use of a beneficial microorganism could in combination control downy mildew on pulses, enabling more effective control of disease while reducing pesticide use.
In current predictive breeding programmes, identifying the prevailing isolates is imperative for the efficient use of gene pools. This project focuses on the identification of new disease resistance sources and development of tools for accurate detection and diagnostics of pea and broad bean downy mildew isolates, Peronospora viciae f. sp. pisi (Pvp) and P. viciae f. sp. fabae (Pvf), respectively. Specifically, we aim to: 1) Characterise the genetic basis of resistance in pea and broad bean to Pvp and Pvf, respectively; 2) Construct annotated genomes of Pvp/Pvf to enable pathogenomics to generate molecular markers for monitoring DM races; 3) Develop isolate-specific diagnostic tools to increase speed/accuracy of detection of Pvp/Pvf and decrease reliance on lengthy differential testing; 4) Identify effectors that differentiate Pvp and Pvf races; and 5) Explore microbial biological control agents to suppress Pvp/Pvf.

The proposed research will impact on one of the most critical global challenges faced today: food security. The growing world population and the current climate changes are placing heavy demands upon our agricultural systems. Microbial diseases and pests cause major constraints to food production and agriculture and have significant economic and social impacts. This was demonstrated recently with the increase in global wheat prices due to the spread of a highly virulent strain of Puccinia graminis tritici, Ug99, as well as the emergence of a new strain (A2-Blue13) of the devastating potato pathogen Phytophthora infestans in the UK. Repeated agrochemical applications are the most common means of controlling such pathogens. Inappropriate use of pesticides, on the other hand, leads to similar problems including: the occurrence of new isolates insensitive to the pesticide used, and residue being left in soils as well as in crops, thus creating environmental pollution. Accurate and robust detection and quantification of pathogenic microorganisms to a strain level is essential for diagnosis, modelling, surveillance and implementing effective disease management strategies. In addition, unculturable and non-sporulating fungi or oomycetes remain a major challenge when studying biotrophic groups.
Pea (Pisum sativum) and faba bean (Vicia faba) are the principal legume crops cultivated in the UK, with areas of 50 K Ha for combining pea (marrowfat and blue), 34 K Ha for vining pea and 170 K Ha for field bean grown reported in 2018. Peas and beans command a price of £240-£350/t depending on quality, variety and purpose, generating revenues in excess of £220 M trade in dried pulse and fresh vegetable sectors, with increasing quantities of the crop now utilised for human consumption. Despite their high value, pulse crops are difficult to grow, compared to cereals, and effective control of diseases can often limit productivity. This is particularly true of downy mildew (DM), caused by Peronospora viciae f. sp. pisi and P. viciae f. sp. fabae, which can cause yield losses of up to 45-75 % in pea and 35-50% in field bean. This project focuses on the identification of new R-genes for breeding purposes, the development of tools for accurate detection and diagnostics of Pvp/Pvf isolates and the evaluation of microbial biological control agents to suppress downy mildew pathogens. Using next generation sequencing technology, isolate-specific molecular markers will be developed and converted into kits so that growers, breeders, epidemiologists and modellers can use them in their investigations.
The knowledge generated from this work has implications beyond this pathosystem to other obligate oomycete crop pathogens, including Peronospora parasitica (brassica downy mildew), Peronospora destructor (onion downy mildew), Bremia lactucae (lettuce downy mildew) and Plasmopara viticola (grapevine downy mildew). Similarly, the research would also benefit other study systems, including obligate fungal pathogens such as rusts and powdery mildews. Ultimately, the results of this research will help design better solutions to tackle plant disease and to improve world agriculture whilst reducing agrochemical inputs.