Real Time deployment of pathogen resistance genes in rice

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.

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.