Real-time and seasonal forecasting of wheat rust epidemics to inform surveillance and control: Ethiopia as a LMIC test case

Lead Research Organisation: University of Cambridge
Department Name: Plant Sciences


Wheat rusts are fungal diseases that can cause devastating losses to wheat crops. The fungal spores are dispersed by the wind with the potential to cause a rapid spread of a wheat rust outbreak. Whilst fungicides to control the spread of wheat rust are available they need to be applied in a timely manner in order to be effective. Failure to do so can lead to the loss of crops with the added economic costs of wasted fungicide. Wheat rust infects the crop causing the death of the plant and therefore a reduction in the wheat produced in a region; this affects both an individual growers livelihood and on a wider scale the costs incurred as a government imports wheat to supplement in-country wheat produce.

Wheat is a staple food in Ethiopia, as it is in many countries in the world. Ethiopia is also the major wheat producer in sub-Saharan Africa. Thus, outbreaks of wheat rusts have a major impact on the wheat available in the region. The Government of Ethiopia has committed to becoming self-sufficient in wheat by 2020. To meet this policy goal and ensure food security, production losses, such as those due to wheat rusts, must be minimised. The proposed work aims to contribute to this goal by implementing a wheat rust forecasting system in collaboration with the Ethiopian Institute of Agricultural Research (EIAR).

The proposed work will combine expertise on modelling plant diseases at the University of Cambridge, expertise on modelling releases of particles into the atmosphere at the UK Met Office with expertise within Ethiopia at CIMMYT and EIAR to develop a world-leading, wheat rust forecasting service. Information on the location of initial sites of wheat rusts in Ethiopia will be sent to the UK Met Office. This information will be collated from surveillance surveys and from farmer reports using mobile smart-phone technology. The UK Met Office will use forecast data from its state-of-the-art global weather forecast model together with the source information and protocols for spore dispersal developed with the University of Cambridge to forecast the large-scale wind-dispersion of the wheat rust spores. The University of Cambridge's epidemiological model will use the outputs to model the smaller-scale spread of the rusts. This, together with an assessment of the suitability of an area for wheat rust, will be used to produce a forecast risk map (where is the pathogen likely to occur?) and a hazard map (how rapidly will it spread and cause losses once introduced).

The development of products, such as wheat rust forecast risk maps, will be done in consultation with EIAR to ensure that they contain the most useful information for their onward use. EIAR will develop methods to make best use of the forecasts for advising the Ethiopian Government and farmers in order to prepare for potential wheat rust outbreaks and to enable them to take action to prevent the loss of crops. The proposed work includes workshops, exchanges and training to aid capacity building and exploitation of the wheat rust forecasting service. In doing so, strong links between the Ethiopian and UK organisations will provide a basis for further development to support other wind-borne agricultural diseases and demonstrate the value of such a system for other counties.

Technical Summary

Puccinia graminis and P. striiformis, stem and stripe wheat rust, represent the greatest biotic constraint to wheat farmers in Ethiopia, threatening both food security and livelihoods for a large proportion of the 5 million wheat farming households. The Ethiopian Government has made control of wheat rusts a top priority in their ambition for the country to be self-sufficient in wheat by 2020. This proposal will lead to the development of an operational wheat rust forecasting capability to support the role of the Ethiopian Institute of Agricultural Research (EIAR) to help mitigate the impact of wheat rust through timely advice to farmers and the Ethiopian Government.

We propose to develop the wheat rust forecasting capability by combining the modelling strengths of (i) the Numerical Atmospheric-dispersion Modelling Environment (NAME), a Lagrangian model that can forecast the large-scale atmospheric spread of rust disease and (ii) a stochastic, highly-spatially resolved compartmental epidemiological model that can predict the spread of rust disease at field and landscape scales. The modelling will be driven by UK Met Office numerical weather prediction data at 10 km spatial resolution and will produce routine daily forecasts for up to 7 days ahead. Products of wheat rust risk generated by combining the model output with rust suitability maps will be disseminated to EIAR. The source locations of wheat used as inputs NAME will be obtained from surveillance surveys by CIMMYT and the novel use of mobile phone reported outbreak data sent by farmers.

Close collaboration between UK (University of Cambridge, Met Office) and Ethiopian (CIMMYT, EIAR) experts via exchange visits and workshops will result in the development of wheat rust forecast products tailored for in-country use with critical exchange of knowledge between the organisations.

Planned Impact

The pathways to impact extend from core modelling activities (Cambridge and the UK Met Office), through input of data, validation and implementation (via collaborators in CIMMYT and Ethiopian Government Institutes) to direct impacts on wheat-farming families in Ethiopia (via national agencies).

The recently strengthened, Early-Warning Unit within the Ethiopian Institute of Agricultural Research (EIAR), supported by the UK institutions and CIMMYT, will be the critical interface between the model-derived information products and the national agencies responsible for rust control in Ethiopia. The Pathways allow for reciprocal flows of information, linking model forecasts and actual disease status directly with mandated national control agencies. We are confident that the arrangements are carefully designed to result in improved rust control and considerable benefits for wheat farmers in Ethiopia. Both the Epidemiology and Modelling Group at Cambridge and the Atmospheric Dispersion and Air Quality Group in the UK Met Office have experience in using models to inform and solve strategically important practical problems. CIMMYT has a mandate to improve farmers' livelihoods and the group led by Dr D. Hodson has established close contacts with EIAR, the Ministry of Agriculture and Natural Resources (MoANR) and the Agricultural Transformation Agency (ATA).

Direct Project Impacts: Core project modelling activities are seen as the drivers of the impact pathway. The feasibility of developing short-term, rust spore dispersal forecasts in Ethiopia has already been demonstrated. This project will rely on cutting-edge modelling and forecasting technologies from leading UK research Institutes to enhance and improve information products which Ethiopian partners can utilise to achieve impact on rust control. Work under Obj. 1 will result in two critical products (i) the coupling of spore dispersal with climatic suitability to develop accurate short-term forecast maps for risk of rust outbreaks (ii) development of an epidemiological model to predict likely spread of disease and a platform to assess the effectiveness of different control strategies. Initial risk maps will be developed and tested in Ethiopia during the first main cropping season (Aug-Dec 2017), then refined for the second cropping season (Aug-Dec 2018). Functional epidemiological models will be tested after 1 year and refined in the second year. Critical to achieving long-term impact from the project is developing the capacity and operationalising the rust early warning unit within EIAR (Obj. 2). Capacity building will be achieved through a series of workshops, in-country training courses and scientist exchange visits. These will take place in year 1 and the first half of year 2. Field survey and rust phone survey data will be critical inputs used to validate the forecast model outputs (Objective 3). The epidemiological models (developed in Obj. 1) will be used as a platform to test optimal control strategies using what-if scenarios in year 2.

Top-level Impact: The overall top-level impacts from the proposed work are improved and earlier rust control for wheat farmers in Ethiopia, leading to improved food security and income generation for wheat farming families. It is envisaged that direct impacts on farmers would be realised by the end of foundation project. Successful realisation requires, several factors outside of the direct influence of the project that include the procurement and efficient deployment of fungicides and capacity of the farmers to act on the improved information flows.

Long-term sustainability: Given the high political priority for rust control in Ethiopia, a functional national early warning unit with the capacity to improve rust control, optimise resources and enhance wheat productivity is likely to be institutionalised and attract continued national support.
Description We have successfully completed a further year of adapting the meteorologically-driven dispersal model for wheat rusts in Ethiopia, extending the model from wheat stem rust to include wheat stripe rust also, which in 2017, provided to be the commoner of the two pathogens. More generally, we completed the development of a major summary of countries at risk in Southern and East Africa, the Middle East and South Asia from aerial dispersal of wheat stem rust, and important pre-cursor to testing the real-time forecasting scheme which now receives weather forecast data from the new UK Met Office super-computer.
We have completed another successful year during which we have continued to produce daily forecasts of wheat strip rust and wheat stem rust for the whole of Ethiopia. We have extended the reach of the forecasts, which enable growers to have a three week window in which to deploy fungicides, through cascading 'wheat rust advisories' through the Ministry of Agriculture and via SMS phone technology organised by the Ethiopian Agricultural Transformation Agency. Feedback from both these agencies indicate that the forecasts are reaching hundreds of thousands of smallholder farmers as well as extension staff. The modellers now routinely incorporate meteorological conditions for infection. We have also adapted the protocols to take account of field observations from trained observers which are then used to inform new sources from which we run the Lagrangian dispersion models. Considerable work is being undertaken to validate the models using both historical and data for the current year. There are still challenges to overcome in training individuals at the Ethiopian Institutes in epidemiology. Repeated attempts to arrange training visits have been frustrated by changes in personnel at Ethiopia, lack of firm availability of Ethiopian scientists to attend sessions at Cambridge and the Met Office and ultimately to difficulties in achieving visas for the visitors.
Exploitation Route The forecasting system and the operational protocols that we are building between Cambridge, Met Office, CIMMYT and the Ethiopian Institutes is seen by both the Gates Foundation and DfID as a successful exemplar of what can be achieved in real-time forecasting for major diseases. We are in discussion with the Gates Foundation and DfID about gaining support to continue this work beyond the current project. We have also been encouraged to consider extension of the methods to South Asia, initially Bangladesh and Nepal for wheat rusts with the possibility of adapting the methods for wheat blast which is another major threat to wheat production. An exploratory analysis to transfer the methods from Ethiopia to Nepal and Bangladesh is underway funded by DfID. Further development of the model for Ethiopia is also being supported by DfID and the Gates Foundation.

The methods including the underlying models and the early warning system have now been extended to Nepal and Bangladesh where they are being further tested and already showing promising results, uptake and attention by in-country partners.
Sectors Agriculture, Food and Drink

Description We are continuing to work with the Ethiopian Institute of Agricultural Research to advise on an early warning unit for wheat stem and leaf rust in Ethiopia. We have also extended the collaboration (unfunded by this grant) to work with the Ethiopian Agricultural Transformation Agency which is developing a scheme for accessing very large numbers of smallholder farmers using SMS text messaging with the options of also receiving inputs by return from growers. This is an area of active investigation for future development. We report elsewhere in this submission about approaches from the Gates Foundation and DfID to continue with the work and to extend its reach. The methods have now been extended to Nepal and Bangladesh under funding from FCDO, which is enabling us to introduce, and further test, the wheat rust early warning system now for three wheat rust diseases with significant engagement from in-country partners in both countries.
Sector Agriculture, Food and Drink
Impact Types Economic,Policy & public services

Description The work developed in the project has led to advice on disease outbreaks in the UK, US and multiple countries in Africa
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a national consultation
Impact Provided UK Government with outputs for predictive models to assess when, where and how it is appropriate to deploy resources to manage emerging epidemics of plant disease and plant pests in the natural and semi-natural environments. Work has informed Government policy. Also provided warning systems for spread of wheat rust diseases in East African countries and risks to Middle East and South Asia