This statement is a formal announcement of our intention to obtain the full genome sequence of the fungus responsible for the most serious disease of cultivated rice- the blast fungus Magnaporthe grisea. An international consortium has been formed in order to carry out this ambitious task under the directorship of Dr. Ralph Dean. The founders of the consortium include groups from the USA, UK, France, South Korea and Japan.

1. Background

There are a number of compelling reasons for obtaining the full genome sequence from Magnaporthe grisea which have acted as the impetus for this initiative.

1.1 Rice Blast Disease - A significant threat to global food supply

Rice is the staple food for one half of the world’s population and so diseases of this crop are of special concern. One of the most widespread and devastating diseases is rice blast which causes significant crop losses throughout South East Asia and South America. Major epidemics covering vast areas occur on a regular basis causing severe food shortages to entire nations.

1.2 Rice Blast Disease - The economic problem

Rice blast causes between 11% and 30% crop losses annually. This represents a loss of 157 million tonnes of rice. Rice blast is controlled using resistant cultivars or by application of fungicides, although problems are associated with both forms of management. Where blast is prevalent, resistant cultivars have an expected field life of only 2 -3 growing seasons due to the generation of newly virulent forms of the fungus. Fungicide resistance is also of concern and there is a considerable need for environmentally compatible, novel fungicides offering durable management of rice blast. This disease represents the world’s largest fungicide market and is one of the only agricultural markets where fungicide development costs can be justified for a single-disease stand-alone product.

1.3 Rice Blast Disease - The scientific model

The rice blast fungus Magnaporthe grisea has emerged as a model system for understanding fungal-plant interactions. Through the efforts of researchers worldwide, the Magnaporthe grisea is being analysed at the genetic, cellular, and molecular level and studies have already revealed fundamental aspects of its biology. The mechanism of plant infection by M. grisea is arguably better understood than in any other cereal disease. Scientific reports of these studies have appeared in the most highly cited journals in the natural sciences including Nature, Science, Genes and Development, The Plant Cell and The EMBO Journal. Reciprocal genetic and molecular studies of rice have allowed a holistic view of the interaction to emerge, encompassing infection-related development, disease symptom production, host metabolic responses and host resistance.

2. The Scientific Case for a Genome Study

Researchers studying the rice blast fungus met recently at the 2nd International Rice Blast Conference in Montpellier, France. It was clear from discussions that three main experimental aims are paramount at this time

• To determine the molecular basis of rice blast disease
• To determine how resistant rice cultivars are able to perceive and respond to the rice blast fungus
• To understand the genetic mechanisms leading to generation of newly virulent forms of the fungus

In order to achieve these aims in full it is necessary to obtain the complete genome sequence of Magnaporthe grisea. Definition of the 9-10,000 genes in the rice blast genome will allow systematic identification of pathogen-specific genes and determination of their respective role in disease. Moreover, determination of the entire accurate genome sequence will reveal genome organisation permitting investigation into the evolutionary history of the rice blast fungus and identification of the mechanisms of genetic change that influence its virulence. We will also be able to identify the likely reservoir of specific determinants of avirulence, or plant recognition. This will allow systematic definition of novel resistant rice cultivars using the genetic resource of the pathogen.

3. The Rice Blast Genome Project

3.1 Genomic Resources

Genomic analysis of the rice blast fungus is well underway in publicly-funded institutions throughout the world and in the Agricultural Biotechnology Industry. A number of key genomic resources are already in place that will allow rapid progress to be made.

• Integration of linkage maps to generate a saturated RFLP genetic map
• Production of BAC libraries by two consortium members.
• Clemson BAC library consists of 9216 clones offering 25-fold genome coverage
• Sequence ready-framework of one chromosome using BAC clones complete
• BAC-end sequencing and DNA fingerprinting to create sequence ready-framework of entire genome in progress
• At least 1000 non-redundant ESTs generated and released to public domain.
• At least 2945 non-redundant ESTs generated by private sector members of consortium
• Complementary genome efforts on rice are well-established, 30,000 ESTs have already been generated

3.2 Organisation

To sequence the rice blast genome will require a large international effort and co-operation between public and private sector institutions. The project will be directed from Clemson Univerisity Genomics Institute who will act to collate and administer data generated by consortium members. The project will be led by Dr. Ralph Dean co-director of Clemson Univerisity Genomics Institute.

Management and execution of the project will proceed by allocation of BAC clones to consortium members. Our aim is to generate a complete genome sequence. BAC-end sequencing and DNA fingerprinting data is being used to create a sequence ready framework of the genome in order to define a minimal route for efficient sequencing. Seed BAC clones across the genome will be fragmented, cloned into M13 and pUC and shotgun sequenced using principally dye-terminator cycle sequencing chemistry. Sequences will then be built into contiguous sequences using appropriate software. Sequencing will proceed by selecting adjacent minimally overlapping BAC clones. EST sequencing projects using cDNA libraries derived from M. grisea at alternate developmental stages or under various environmental stresses will also continue. Genome sequencing will be carried out at national genome centres or in individual consortium members’ laboratories. Milestones will be set by the directorate and progress assessed and reported in an International Rice Blast Genome Project report published on a quarterly basis.

In the first instance the consortium will solicit funding for a public project from national and international agencies, foundations and companies.

3.3 Funding

3.3.1 Public Sector Support

Current rice blast genome work is funded by the National Science Foundation of the USA (NSF) and through the Japanese Science Ministry. The European Union fund a Training and Mobility of Researchers Project on Cereal Pathogens which includes a substantial programme of rice blast research. Rice blast research is funded in the USA through the United States Department of Agriculture (USDA), NSF and the Rockefeller Foundation, in the UK by the Biotechnology and Biological Sciences Research Council (BBSRC), the Nuffield Foundation and The Overseas Development Agency, and in France by the Centre National Recherches Scientifique (CNRS) and the Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD). These agencies will form the core public funds to which bids for support will be made.

3.3.2 Private Sector Support

Rice blast research is being carried out in many of the world’s most successful agrochemical and biotechnology corporations. Significant support for genome research on rice blast has been already been provided by Novartis. Novartis has provided funds to the Clemson University Genomics Institute for the BAC-end sequencing and DNA fingerprinting. The data is being made publically available to provide a foundation for a whole genome sequencing initiative. Researchers at the DuPont Company have pioneered many aspects of rice blast research including a very significant genomics initiative. Other companies with interests in rice blast research include Monsanto/American Cyanamid, Zeneca, AgrEvo, Rhone-Poulenc, Bayer and BASF. Associated biotechnology subsidiaries and smaller start-up companies also have substantial interests in rice blast research. Applications for support will be made to individual companies and consortia of the above.

3.3.3 The Case for Funding an International Genome Project

3.3.3.1 Public Sector

We believe there is an overwhelming case for a concerted, co-operative effort to sequence the rice blast genome. Generating an accurate genome sequence will provide an enormous resource for molecular plant pathology researchers worldwide. The rice blast fungus genome will become the template against which all cereal pathogens are compared in terms of gene identities and gene organisation. Rapid gene functional analysis will be carried out and genome-wide expression profiles determined in a series of isogenic strains carrying mutations in key regulatory genes controlling pathogenicity and development. Very significant advances in understanding plant disease establishment by fungi will be possible given this resource.

3.3.3.2 Private Sector

Company investment in this initiative offers the chance of exploiting functional genomics for identification, validation and mode of action studies on new compounds and for screening chemical libraries. Identification of novel target sites for chemical inhibition can proceed rapidly given a freely accessible database of genome information. This is likely to be of greater value to a company than small numbers of ESTs generated in individual laboratories. Generating expression profiles and individual validated targets will also offer the greatest chance of filing robust patents. Generating a complete genome sequence will prove invaluable in the long term due to the likely low level expression of a significant proportion of important genes and for comparative genomic approaches in other target organisms. Importantly, the generation of a full genome sequence is also prohibitively expensive for any single company to embark upon. Pooling resources across the public and private sectors in an international effort will provide very significant added-value to any company investment.

4. Ethical, Social, Economic and Ecological Impacts

Defining the genome sequence of a cereal pathogen of global significance represents an exciting and timely venture to embark upon. Knowledge gained from this project is likely to impact the long term disease management programmes for rice and many of the other important cereal crops. This has enormous implications for the economic well-being of the Agrochemical and Agbiotech industry as a whole and will have wider consequences in ensuring growth of the food supply for the next millenium. This project may seem ambitious at this time, but in the longer term will be seen as a vital step towards the understanding of plant disease for its effective management.

Founder Members of the IRBG Consortium