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

Lead Research Organisation: National Institute of Agricultural Botany
Department Name: Centre for Research

Abstract

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Technical Summary

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.

Planned Impact

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.

Publications

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Tör M (2023) Recent developments in plant-downy mildew interactions. in Seminars in cell & developmental biology

 
Description New sources of Peronospora viciae f sp fabae resistance identified in Vicia faba lines
Exploitation Route Novel sources of genetic resistance shared with UK plant breeders for developing improved varieties
Sectors Agriculture

Food and Drink

Environment

 
Title Pathotyped P. viciae isolate panel 
Description A panel of 35 single spore P. viciae isolates has been created from collections from various field sites across the UK 
Type Of Material Biological samples 
Year Produced 2022 
Provided To Others? No  
Impact Pathotyped P. viciae isolates for developing a novel pathogenomics platform 
 
Title Peronopora viciae f sp fabae assembly 
Description Draft short read genome assembly for Peronospora viciae f sp fabae 
Type Of Material Technology assay or reagent 
Year Produced 2021 
Provided To Others? No  
Impact Provision of a reference for conducting variant analysis in pathogen populations 
 
Title Peronospora viciae f sp pisi genome assembly 
Description We have developed a short-read genome assembly for Pisum downy mildew derived from a single spore isolate obtained from a UK P. viciae culture. This will provide a reference genome for conducting subsequent SNP calling and effector discovery for ongoing work in the pulse downy mildew pathosystem project. 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? No  
Impact New capability to conduct novel comparative genomics studies in pisum and closely related faba bean downy mildew species. 
 
Title Re-sequenced genomes 
Description 15 x re-sequenced P. viciae genomes (10-20 x coverage, 150 bp PE reads) 
Type Of Material Biological samples 
Year Produced 2023 
Provided To Others? No  
Impact Sequencing of pathotyped P. viciae isolates for providing genomic information for designing molecular diagnostic assays 
 
Description Presentation at the second UK Legume Research Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A key note presentation including key outputs from the project was delivered at the second UK legume research conference in University of Reading, February 2024.
Year(s) Of Engagement Activity 2024
URL https://www.niab.com/research/agricultural-crop-research/research-projects-agriculture/characterisin...