PANACEA: Pathogenomics for enhancing food security in East Africa

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



Common bean is an essential source of nutrients, vitamins and minerals to approximately 300 million consumers worldwide. Pest and disease, such as angular leaf spot (ALS) caused by Pseudocercospora griseola, can seriously reduce yields and quality, leading to malnutrition and lost incomes. Farmers often rely on growing resistant varieties to combat the effects of disease but unfortunately ALS is genetically diverse, so selecting the best-performing varieties can be problematic. Providing resources for pathotyping fungal pathogens like ALS can help researchers and plant breeders to improve disease management, variety selection and guide the development of new, resistant varieties to help growers to stabilise productivity and to reduce the incidence and severity of disease outbreaks.

The pump-priming project will help to establish new, innovative biological and bioinformatics resources that will provide local experts and researchers with enhanced capability to accurately monitor for differences in ALS races. This will enable new or novel pathotypes to be identified when arise, and if they pose a potential threat to a growing region, allowing for interventions to be made in good time.

The resources will comprise of:
i) An initial pathogen collection of 75-100 P. griseola isolates sampled from across the nine different Ugandan agro-ecologies
ii) Genomic resources developed around the panel providing genotyping information for pathotyping and functional studies
iii) A population diversity screen using the new genomic resource to begin to shed light on ALS pathotypes affecting East African bean crops
iv) Series of meetings, webinars and workshops to optimise the new resources for end-user utility and demonstrate the new resource to stakeholders and local experts.

The new resources will begin to facilitate improved monitoring and surveillance of P. griseola the causal agent of ALS on common bean in order to help prevent future disease outbreaks and to guide variety selection and the breeding of new varieties. This will contribute directly to stabilise yields and productivity, enhancing nutritional intakes and incomes for small-holder farmers and the millions of consumers dependent on common bean as a cheap, nutritious source of food. The resources will also have wider application to scientific researchers with interests in more fundamental aspects of pathogen genomics and epidemiology. The initial framework developed during the project could be applied to other crops/pathogens to support further improvement efforts.

Technical Summary

Angular leaf spot caused by Pseudocercospora griseola is a particularly serious threat to common bean yields in East Africa and effective disease control methodologies can have a strong impact on maintaining yield stability. Growers rely on genetic resistance to mitigate the negative effects caused by ALS on crop yield; unfortunately P. griseola is a genetically diverse, sexual pathogen demonstrating distinct races, making selecting resistant varieties and controlling ALS extremely problematic. Current pathotyping methodologies developed for ALS have had limited impact due to difficulties in maintaining differential varietal sets of South/Mesoamerican origin in East African growing conditions, access to and funding for molecular laboratory facilities, and the infrastructure required to collect a large number of samples from multiple, diverse regions.

Providing improved ALS pathotyping capability would have a profound effect on reducing the negative impacts on yields by facilitating improved monitoring and surveillance to detect changes in pathogen race structure and distribution. The project will provide new, innovative ALS pathotyping resources comprising a unique, extended isolate collection with relevant accession from across all growing regions, enhanced genotyping for identifying SNP variants for conducting assessments into genetic distance and relatedness between isolates, and a draft P. griseola genome for facilitating fundamental research in to ALS. This enhanced suite of resources will enable local plant pathologists to access knowledge, technological capability and scientific expertise in the UK to react effectively to future threats of ALS outbreaks with resources that would be otherwise unobtainable. Reducing the impact of ALS on common bean crops would help to stabilising productivity and food security, whilst contributing effectively to improving nutrition, welfare and incomes.

Planned Impact

The project will initiate the development of a suite biological and bioinformatics resources that shall provide enhanced ALS pathotyping to help reduce the serious effects of the disease on crop yields. Improved resources and capability will facilitate improved disease management across Uganda and East Africa. This will have a profound and direct impact on stabilising crop yields and productivity, whilst contributing to improving nutrition, welfare and economic development.

Direct beneficiaries from the project outputs will include plant pathologists, plant breeders, advisors, thousands of small-holder farmers and larger scale growers, and ultimately millions of consumers dependent on common bean as a vital source of nutrition. The new resources will empower experts at NaCRRI to begin to monitor ALS populations in order to devise improved management strategies; local experts already interact closely with regional grower-collectives and international research agencies to deliver improved common bean varieties, knowledge and advice. These channels will be utilised to disseminate outputs from the pump-priming activities to demonstrate the practical benefits to a wider-user group, in order to stimulate uptake and further investment for expanding pathotyping the resources to meet requirements.

Indirect beneficiaries from the project outputs will include other countries growing common bean such as Colombia, Brazil and India, where ALS can also be problematic. Research organisations and agencies in these regions in will be given to access project outputs in order to exploit maximum value and to support further development of the resources. This will help to contribute to disease management on a wider scale, further stabilising yields and improving socio-economic standards. The new biological resources will also help to support seed certification efforts, providing greater diagnostic capacity, to further reduce the spread and impact of ALS. The project outputs will also provide a mechanism for initiating wider epidemiological studies to investigate the spread and movement of ALS in bean growing regions to help develop longer term disease control strategies. The resources initiated during the project could also be used as a model to develop pathotyping frameworks for tackling disease management challenges in other crops/pathogens.


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Title Genome assembly 
Description We have generated a de novo genome assembly for the common bean pathogen Pseudocercospora griseola to expedite genetic studies in East African Angular Leaf Spot populations 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? No  
Impact The assembly has provided a reference for identifying genetic diversity between P. griseola isolates and is facilitating the development of effective pathogenomics resources for conducting monitoring and surveillance of the pathogen to help reduce negative impacts from disease. 
Title Ugandan Angular Leaf Spot isolate collection 
Description A collection of >100 Angular Leaf spot (Pseudocercospora griseola) collected from across major common bean growing areas in Uganda in 2018-2019 
Type Of Material Biological samples 
Year Produced 2019 
Provided To Others? No  
Impact The collections has provided a core set of isolates for initiating pathogenomics studies in the Angular Leaf Spot pathogen to start to test molecular discrimination strategies for tracking race-types 
Description Poster highlighting project progress 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Poster presented at NIAB Science and Director's days
Year(s) Of Engagement Activity 2019
Description Talk on pathogen genomics at NIAB Science Day 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact The nanopath project was presented in a talk discussing how genomics is being utilized to enhance pathogen surveillance, monitoring and detection. The talk was attended by approx. 80 delegates from NIAB/NIAB-EMR. The talked raised a number of questions from the audience and provided an excellent opportunity to demonstrate how the technology provides accurate and rapid pathotyping capability for crop pathogens such as Septoria.
Year(s) Of Engagement Activity 2017
Description Talk providing overview of the project 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A talk providing an overview of the Panacea project was delivered to post-graduate researchers at NaCRRI in Uganda, highlighting the aims of the project, the new resources that will be generated and the importance of engaging with local researchers and experts to leverage impact from them. The talk generated some fruitful discussions on the relevance of pathogenomics approaches for providing improved motoring of crop diseases and how this type of strategy could be extended to other countries growing phaseolus bean and additional pathogens to create even wider benefits from the technologies.
Year(s) Of Engagement Activity 2018