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

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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 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 resistant 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 faba 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 faba 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.