Real Time deployment of pathogen resistance genes in rice

Lead Research Organisation: Rothamsted Research
Department Name: Biointeractions and Crop Protection

Abstract

Bacterial blight and rice blast are two key pathogens reducing rice productivity worldwide. Varietal resistance is an effective, reliable and environmentally friendly way of protecting rice against these pathogens. The development and use of modern molecular breeding techniques has shortened the generation of elite rice lines for varietal release from 8-10 years to 2-3 years. This means that real-time deployment of resistant varieties with various combinations of resistance genes can be customized through gene rotation or mixture in a single genetic background.

New varieties resulting from current breeding projects will be released in two to three years. This makes a range of varieties each with a unique combination of resistance genes available to growers. A key question, then, is: Where should these varieties be deployed? Each variety should be deployed where the matching virulence is not present, or is at an extremely low frequency, in the pathogen population. This ensures that the resistant variety remains effective for the maximum possible time. We thus need a method to ascertain the absence, or possible presence in extremely small frequency, of pathogen virulence in the field.

We therefore aim to develop and apply a combined modelling and field monitoring approach to determine areas where a novel resistance gene can safely be deployed because virulence is at a sufficiently low frequency in the pathogen population. The method:
-1- Will quantify the number of infections in observational plots of a susceptible variety. A similar plot with the novel resistant variety will show no infections (ideally). Using a statistical method we will then be able to estimate the maximum expected frequency of virulence in a field pathogen population. If this frequency is small enough (e.g. 10-10) we can decide that the new resistant variety be released.
-2- Will be scaled-up from the field level to a regional level. This will enable us to make decisions about variety release at larger spatial scales. The model will be parameterised from field monitoring of an aggressive bacterial blast strain currently expanding in the north of Thailand.
-3- Will be made available, with the necessary training, for future use to the rice research community.
-4- Will start to be used alongside its development to help solve the emerging problem posed by the new expanding aggressive bacterial blast strain that threatens northern Thailand's rice production.

The outputs of the project will be a set of methods to establish where in the Philippines and Thailand novel resistant varieties can be released to maximise the durability of varietal resistance. This will be of clear benefit to growers as they will suffer less from virulent strains breaking the novel resistance. This in turn will improve the income of poor growers. The project will also train staff in statistical methods, epidemiological modelling and the use of the methods developed in the project. The project will also help breeders to establish breeding targets by providing them with information on the presence of pathogen virulence in the field.

Planned Impact

The outputs of the project will be a set of methods to establish where in the Philippines and Thailand novel resistant varieties can be released to maximise the durability of the resistance. This will be of clear benefit to growers as they will suffer less from virulent strains breaking the novel varietal resistance. This in its turn will improve the income of poor growers. The project will also benefit breeders with information on virulence present in pathogen field populations, helping to establish breeding targets. Furthermore researchers from Rothamsted Research will train researchers from PhilRice, Kasetsart University and IRRI in statistics, data analysis and epidemiology. A workshop will be dedicated to the transfer of models to PhilRice, Kasetsart and IRRI.

This project is designed around impact. In the work in Objective 1 and 2 (see also section 8. Proposed Scientific Research and Activities) we will develop strategies for the deployment of rice varieties resistant to bacterial blight and rice blast. The insight developed during the project will be disseminated, applied and exploited through existing mechanisms of communication with the industry by IRRI, PhilRice and Kasetsart University. Moreover the varieties used in the experimental work are at this moment leading to varieties to be released in two or three years. Information on areas in the Philippines where these varieties can be deployed is a direct impact of the project.

The new emerging aggressive bacterial blight strain in the North of Thailand poses a threat to the entire region. A breeding line from the Kasetsart University breeding program seems to be resistant to the new bacterial blight strain. This breeding line will be tested in the field during the project and will be the first direct application of the methods developed in the proposal. We hope to have solved the emerging problem within the lifetime of the project.

Communication and engagement with the wider public: The insight gained and advice developed through the project will also be presented to the wider public and grower groups. IRRI, Kasetsrat University and PhilRice maintain active communication with the rice sector. Most of this interaction is throughout webpage, online magazines (e.g. RiceToday, IRRI, Ag-Bio Newsletter, Thailand) blogs, and other forms of social media. Events are organised where growers are informed about new developments. For example, IRRI engages in direct interaction with farmers using participatory events and PhilRice is present at the Rice Summit organized by the different Regional Units of the Department of Agriculture of the Philippines.

These pathways to impact have been developed and have proven to be successful. They are being used in on-going work on bacterial blight and rice blast management.

Transfer of the mathematical methods to IRRI, PhilRice and Kasetsart University: In the development of this proposal we identified the need for capacity building through statistics and modelling training, as well as training in epidemiology, for the PDRAs and the Co-Is in the project. At Rothamsted Research there is a series of short duration courses aimed at research assistants and researchers that introduces a range of statistical methods and introduces the use of statistical computer packages. The courses are
1. Basic Statistics
2. Design and Analysis of Simple Experiments
3. Introduction to Regression
This will enable to researchers involved to engage fully with the development of the models and statistical methods. Additionally we will develop a workshop specifically aimed at transferring the methods developed in this project to all researchers involved in the project. Epidemiology training will be done by FB through a course to be given at Kasetsart University.

Publications

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Bourhis Y (2019) Sampling for disease absence-deriving informed monitoring from epidemic traits. in Journal of theoretical biology

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Bourhis Y (2019) Translating surveillance data into incidence estimates. in Philosophical transactions of the Royal Society of London. Series B, Biological sciences

 
Description We have developed a method to calculate the maximum proportion of a virulence gene in a pathogen population when no virulent genotypes are detected during monitoring rounds. We have developed a methodology to quantify the risk of virulence even when none is observed. This method can also be used to advise on the size of monitoring plots.

We have tested four breeding lines for their resistance to the aggressive bacterial blight strain in the north of Thailand. In box experiments these lines performed very well compared with susceptible lines. Field studied were less clear because of low disease levels.

In Thailand, the distribution and spread of the new aggressive strain of bacterial blight that has broken the xa5 resistant gene was mapped across the Chiang Rai province between 2016-2018. In 2016 the breaking strain was found in 3.6% of samples by 2018 this number had increase to 29%. This must be interpreted with some caution due to more purposive sampling in later years.

Analysis of data of bacterial blight from 5 seasons and 4 sites in the Philippines has revealed new insights into the mechanisms of this serious epidemic. Disease incidence was generally larger in the susceptible variety compared to the resistant variety grown in the same site-season. However, we found no evidence to suggest that primary infection efficiency in resistant varieties was less than that for susceptible varieties. There was little evidence to suggest that the source of primary infection decayed over the season. Our findings suggest that environmental and management factors had greater effect on the disease than climate. Primary infection was characterised by apparently spatially-random observations of disease incidence at the start of the epidemic. As the season progressed, we observed an emerging short-range (1.6 m - 4 m) spatial structure in the disease incidence at many of the sites, suggesting secondary spread was predominantly short-range.
Exploitation Route This finding will be used to develop monitoring systems to ascertain the absence of virulence before a new cultivar is released. We have ahope to find a breeding line that is resistant or tolerant to the new aggressive bacterial blight strain.
Sectors Agriculture, Food and Drink

 
Description The methods we develop in this project will be used by IRRI, PhilRice and Kasetsart University in their breeding and cultivar release program.
First Year Of Impact 2017
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description Epidemiology of pathogens Phillipines 
Organisation Philippine Rice Research Institute
Country Philippines 
Sector Public 
PI Contribution In collaboration the Rothamsted team develops models that are applied to the data gathered by the collaborators. The collaborators provide expertise on the bacteria and local environmental conditions
Collaborator Contribution The collaborators plan the field work which involves regular assessment of disease incidence
Impact The collaboration is multi-disciplinary. Rothamsted provide expertise on epidemiological modelling and PhilRice on plant-microbe interactions
Start Year 2017
 
Description epidemiology of pathogens of rice 
Organisation International Rice Research Institute
Country Philippines 
Sector Charity/Non Profit 
PI Contribution In this collaboration the Rothamsted team develops models and methods that then are applied to the data gathered by the collaborators. Further the Rothamsted team helps guide the monitoring efforts of the collaborators.
Collaborator Contribution The collaborators do field work, monitoring and experiments in rice crops. They have (I) monitored the emergence and spread of a new virulent bacterial blight strain, (ii) done epidemic detailed assessments in rice fields of the development of bacterial blight epidemics, (iii) tested out new resistant lines.
Impact So far 3 publications.
Start Year 2016
 
Description epidemiology of pathogens of rice 
Organisation Kasetsart University
Country Thailand 
Sector Academic/University 
PI Contribution In this collaboration the Rothamsted team develops models and methods that then are applied to the data gathered by the collaborators. Further the Rothamsted team helps guide the monitoring efforts of the collaborators.
Collaborator Contribution The collaborators do field work, monitoring and experiments in rice crops. They have (I) monitored the emergence and spread of a new virulent bacterial blight strain, (ii) done epidemic detailed assessments in rice fields of the development of bacterial blight epidemics, (iii) tested out new resistant lines.
Impact So far 3 publications.
Start Year 2016
 
Title Disease Incidence Estimation App 
Description The app allows the user to calculate a sample size from a population given that they wish to be sure that the incidence is below a given threshold 
Type Of Technology Webtool/Application 
Year Produced 2018 
Impact We have not measured how widely the app has been used but the associated paper was only published in January 2019 
URL https://yo-b.shinyapps.io/incidence-estimation/
 
Description Training course on Mathematical Models 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact A training course on "Mathematical Models: Tools for Incorporation of Multi Functionality in Agriculture under Climate Change" was held at King Mongkut's University of Technology Thonburi, Bangkok, Thailand. Dr Frank van den Bosch and Prof. Sujin Patarapuwadol were invited to instruct courses at this event. Following this a student from the University visited Rothamsted to learn more about modelling. She is currently writing up the results from her visit into a paper.
Year(s) Of Engagement Activity 2016
URL http://www.biotec.or.th/en/images/stories/News/2016/Training_MathematicalModels/MultifunctionalityWK...
 
Description Workshop on monitoring and management of invasive pests 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact The Thai Phytopathological Society, Kasetsart University, Rothamsted Research and Food and Agriculture Organization (FAO) organized a workshop on Monitoring and Management of Invasive Plant Pathogens in Bangkok. This workshop was intended to introduce and discuss the concepts of monitoring and management of invasive plant pathogens. The workshop included (i) the development of multiple pest survey techniques, (ii) methods to develop surveys such that a pathogen is detected at an early stage, (iii) monitoring to ascertain pathogen absence, (iv) some aspects of control of invasive pathogens. The objective of the course is to provide participants with concepts and tools that will enable them to develop and use methods for monitoring, detection and control of invasive plant pathogens. Kasetsart University have expressed an interest in organising similar training events.
Year(s) Of Engagement Activity 2016