July 29, 2002 The sequencing of the rice genome this spring represented a major milestone in the search for higher-yield, more disease-resistant rice crops.
Now, another major step has been taken. The genome of one of the world's worst plant blights - rice blast disease, which each year destroys enough rice to feed 60 million people worldwide - has also been sequenced.
The genome of Magnaporthe grisea - the fungus that causes rice blast - is now available online at http://www-genome.wi.mit.edu/annotation/fungi/magnaporthe/. According to Dr. Ralph Dean, professor of plant pathology, director of North Carolina State University's Center for Integrated Fungal Research, and principal investigator of the $1.8 million grant that led to the sequencing of rice blast, it is the first time that the genomic structure of a significant plant pathogen has been made publicly available.
Joint funding from the U.S. Department of Agriculture-National Science Foundation Microbial Genome Sequencing Program spearheaded the research. Dean said this project was the only one jointly funded by these two organizations.
"We now have the genome of the most important cereal and the most important pathogen," Dean said. "Having the genome of both rice and rice blast gives us the greatest opportunities to dissect, understand and manage plant disease."
Dean's lab at NC State worked with researchers at the Whitehead Institute/MIT Center for Genome Research in Cambridge, Mass. The sequencing is expected to cover about 95 percent of the genome, Dean says.
Researchers decided to put the data online so other scientists can also work to solve the problems caused by rice blast. When half of the world's population depends on rice for a majority of their caloric intake, finding these solutions faster is imperative, Dean says.
NC State's lab provided the framework for the sequencing, Dean explains. He and his colleagues broke the rice blast genome - which is approximately 40 million base pairs long - into libraries of smaller fragments of DNA called BACs, or bacterial artificial chromosomes. They then identified sequence tag connectors, or small tags of DNA, that showed how the fragments fit together, as in a jigsaw puzzle. This "fingerprinting" technique gave researchers a snapshot of all the genes in the rice blast genome.
Whitehead Institute researchers then worked to do the shotgun sequencing - or determining the exact order of DNA's four chemical bases - of the genome, and achieved 6x coverage. This means that the location of every base, or DNA letter, in the rice blast genome was determined an average of six times, ensuring a relatively high degree of accuracy.
Dean says NC State researchers are now working to tie the shotgun assembly to the framework, and then annotate, or predict the location of, the genes. He says NC State and Whitehead Institute will publish a paper after this assembly and annotation are completed, probably by early fall.
Dean already has $5.9 million in funding over four years from the NSF to use functional genomics to put the sequencing information for both rice and rice blast to good use.
Dean says the goal is to "identify all genes in the pathogen and the host that are functionally responsible for controlling interactions of whether you have disease or whether you don't have disease." To accomplish this Dean and his lab will look at gene expression profiles, which entails finding which genes are being turned on or off when the pathogen attacks the host. They will also work to systematically eliminate each gene pathogen one by one to see what effect it has on the disease process.
"Essentially, we'll study how genes differ in a disease-causing interaction versus a non-disease-causing interaction," Dean says.
Visit the Web at http://www.riceblast.org for more information on rice blast and the International Rice Blast Genome Consortium, a group of scientists who hope to develop strategies to manage the disease.
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