Durable rice blast resistance through genomic analysis of the host-pathogen interaction

Rice provides 23% of calories consumed by mankind, and this figure is even higher in many developing countries. In fact, rice is the primary dietary staple for at least 70% of the world's poorest people. In Sub-Saharan Africa, most countries have adopted rice as a strategic crop in their food security policies in order to meet the needs of their growing urban populations. One of the biggest constraints on rice production in Sub-Saharan Africa is a devastating disease called rice blast. This disease can cause losses of up to 50% of the rice harvest in these regions, causing severe economic problems for farmers and leading to rice shortages and a greater need for importation of rice at high prices. This project aims to characterise populations of the pathogen that causes rice blast using genome sequencing, in order to determine its variability and capacity to cause disease on the most widely grown rice varieties. We then aim to use this knowledge to identify novel sources of resistance from world-wide rice stocks and, in particular, rice varieties especially bred to thrive in African growing conditions. We will then use modern, marker-assisted plant breeding approaches to create durably resistant rice varieties for use by growers in Sub-Saharan Africa. During the course of the project we will carry out training of four post-doctoral research fellows, who will spend significant amounts of time working in the region, and who will disseminate skills in molecular genetics, genomics and bioinformatics. We will also train two PhD students from Sub-Saharan Africa who will work in each member laboratory and receive training in modern genetic and genomic techniques applied to controlling one of the world's most devastating plant diseases.

The aim of this project is to use a combination of next generation DNA sequencing and genome wide association studies to carry out genotypic and phenotypic diversity studies of the rice blast pathogen, Magnaporthe oryzae, in Africa. This information will be used to identify novel sources of rice blast resistance that will be deployed through marker-assisted rice breeding programmes to produce high yielding, locally-adapted rice cultivars with durable disease resistance. Specifically, the target countries will include Kenya, Uganda, and Burkina Faso where rice blast remains a major disease constraint that significantly impacts grain yields. The overall goal of this project is to develop a strategic and efficient method to breed for improved disease resistance based on pathogen diversity and availability of host resistance genes. The project will bring together leading international scientists from the rice blast research community with complementary expertise in pathogen biology and genomics (Talbot, Mitchell), rice blast resistance genetics and breeding (Correll, Wang) and local expertise in rice blast resistance deployment and rice breeding (Wasilwa, Okori, Harvey, Ibrahima). This international team is well-equipped to carry out the fundamental science proposed, but also to translate the findings into durable resistance that will impact directly on farmers' ability to grow rice successfully in resource-poor regions of Africa. The overall objective of the project is to gain a thorough understanding of the phenotypic and genotypic diversity of the regional rice blast pathogen population in order to guide introgression of multiple sources of resistance into New Rice for Africa (NERICA) rice lines and other high performance rice cultivars using marker assisted breeding.

Immediate outputs of this research will be in the form of technologies, training, knowledge and processes. The research will involve leading research laboratories from
the UK and USA, coupled with resources and knowledge from global rice research centres (WARDA and IRRI). Key training will be provided to students and researchers from three African countries; Kenya, Uganda and Burkina Faso. National institutions (KARI, Makerere University) will anchor research to the local research and development uptake pathways. The BecA-ILRI hub in Kenya will support regional up-and-outscaling of the project outputs, including the repository, disease management strategies arising, and newly developed rice cultivars. The project associate partners will include stakeholders not primarily involved in the research, but necessary for product development and uptake. These will include national level farmer organizations, extension agencies, and the Association for Strengthening Agricultural Research in Eastern and Central Africa (ASARECA) The programme will disseminate information through a communications strategy that provides access to knowledge and technology via publication, bulletins, and extension agencies. In the median to long-term, the output of this project will reach the farming community through engagement of national institutions with their associate partners.