Investigating Gene Function in the Rice Blast Fungus by Next Generation DNA Sequencing.

This project aims to learn about the biology of rice blast disease, one of the world's most serious crop diseases, which each year destroys enough rice to feed more than 60 million people. There is an urgent need for new strategies to control plant diseases in order to ensure global food security in the future. It is estimated that the rice harvest needs to increase by almost 40% by 2030 to feed the planet's growing population. Understanding and controlling plant diseases is therefore an important challenge. In this study, we propose to use 'next generation DNA sequencing' to provide a rapid new method for carrying out genetic analysis in the rice blast fungus. Next generation sequencers allow scientists to determine sequences at least a hundred times more quickly than has previously been possible. We aim to carry out genetic analysis of the rice blast fungus by mapping molecular markers and using them to pinpoint the location of mutations that affect the ability of the fungus to cause disease. In this way we will be able to identify new genes which condition the ability of a fungus to invade and cause disease in a host plant. By gaining new insight into the biology of the fungus we hope to be able to identify new targets for durable disease control. The project will be carried out with an industrial partner, Syngenta, where scientists are attempting to develop new fungicides, which are safe, have less environmental impact and work more effectively than current treatments. This project will provide a new method for determining the mode of action of new potential fungicides, enabling researchers at Syngenta to develop the most promising chemicals and learn more about how they work. When considered together the project therefore promises to provide fundamental new information about this disease, which will be important for its long term control, while also providing a novel method which is of immediate value to the agricultural biotechnology industry in the UK

This is an industrial partnership project that will develop a new method for carrying out classical genetic analysis in a plant pathogenic fungus. Using the Illumina Genome Analyser, we have sequenced the genomes of two isolates of the rice blast fungus Magnaporthe oryzae of opposite mating type (Mat1-1 and Mat1-2) and identified 16,401 single nucleotide polymorphisms (SNPs) with an average density of 1 SNPs per 2.53kb across the M. oryzae genome. We aim to use these SNPs as molecular markers in bulked segregant analysis experiments to identify the positions of specific mutations. M. oryzae is a haploid fungus and therefore all genetic markers that are unlinked to the region of interest will segregate with a 1:1 ratio, while genetic markers close to a specific mutation will show significant linkage disequilibrium, departing from this expected ratio. We aim to carry out bulked segregant genome analysis in which Illumina genome sequencing will be used to sequence a bulked DNA sample of segregating progeny from a M. oryzae genetic cross. In this way we will identify a mutation of interest by screening for its presence within a group of SNPs that show significant linkage disequilibrium. We will first test the technique on a defined auxotrophic mutant and optimize its efficiency. We will then use the procedure to clone the SMO locus of M. oryzae, which is a novel pathogenicity gene that is necessary for infection-related development and invasive growth in rice tissue. In collaboration with Syngenta, we will utilize the new method in fungicide mode-of-action studies to define new targets for disease control.

The major aim of this research project is to use next generation DNA sequencing to provide a rapid new method for carrying out forward genetic analysis in the plant pathogenic fungus Magnaporthe oryzae. The project will develop new methods, superior to conventional approaches, which are of immediate utility to the fungicide discovery industry. 1. Track record. The Talbot Laboratory has a strong industrial partnership track record. During the last 16 years, the PI's laboratory has carried out projects with industrial partners which have lead to new proprietary information and repeat contracts. The PI also spent a year on sabbatical with Paradigm Genetics, gaining first-hand experience of the functional genomics and agricultural biotechnology industry. Most recently, a novel disease control strategy for plant pathogenic fungi has been patented. Professor Talbot also leads the School of Bioscience's participation in the BBSRC 'Excellence with Impact' competition. 2. Exploitation and application. This industrial partnership will develop new methods that will be of immediate utility for fungicide discovery. From an established relationship with Syngenta we intend to build a platform to bring products to the marketplace. We will integrate the following activities into our study: - At the start of the project, the PI and Syngenta staff will meet Research & Knowledge Transfer's IP & Commercialisation unit in order to agree a strategy to protect and manage intellectual property and develop potential commercialisation opportunities. - We will agree technical and commercialisation milestones, which will trigger further actions in order to ensure that IP management and exploitation issues will be considered throughout the grant lifecycle and beyond; - During each meeting we will determine: a) whether the work is sufficiently advanced in order to efficiently time IP protection and b) how to optimise the strength of the IP underpinning the work, both technically and commercially. 3. Communications and Engagement. The PI is a significant opinion-former in fungal genetics and plant pathology and has interpreted work in this field in invited commentaries for Nature, Science, Nature Biotechnology and Current Biology. In addition to our standard communication activities we intend to conduct the following activities: i. Promotion of careers in the Biosciences. During September 2009, postdoctoral staff from the Talbot Laboratory presented posters during a careers event at our 'Britain needs Bioscientists' one day conference. We intend to participate in this event again and also continue other outreach activities. ii. Public Understanding of Science. The School of Biosciences is committed to the public understanding of science. We will prepare and submit articles to popular science magazines in order to develop public interest and awareness of this exciting topic. We will, with support from our press office, ensure that results will be disseminated from our work. 4. Capability. The PI will have overall responsibility for ensuring the delivery of this impact plan. The appointed PDRA will be expected to contribute substantially to these activities and will be given training. The Talbot Laboratory has an extensive track record of industrial collaboration and the PDRA will spend substantial time working directly with Syngenta researchers. We will ensure that the PDRA selected is provided with the opportunity to develop their awareness of, and skills in, knowledge transfer. We will: - Provide knowledge-exchange mentors; - Organise a secondment for the PDRA to work with Research & Knowledge Transfer; - Encourage the PDRA to engage in other activities, e.g. Biotechnology YES. - Expect the PDRA to participate in all the IP and commercialization meetings during the project. - Expect the PDRA to author an article for the popular scientific press and conduct school visits.