Rice and rice blast: new bases for comparison. (Agriculture).

In a landmark year for agricultural genomics, the sequences of two types of rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, were reported in the 5 April 2002 issue of Science. Then, on 17 July 2002, came the announcement from the National Science Foundation that the complete genome of Magnaporthe grisea, the fungus that causes rice blast disease, had also been sequenced. With the complete genome sequence of both a host and a pathogen, scientists now have the necessary tools to dissect the weapons of the invader along with the defense mechanisms employed by the host crop to withstand attack.

Rice, which feeds half the world's population, was selected for sequencing because it has the shortest genome of the economically important grains. Data gleaned from sequencing the rice genome can be applied to other crops--a boon to companies (such as Monsanto and the Swiss agrochemical company Syngenta) that are interested in developing transgenic crops. Rice blast, which can cause up to 20% loss in grain yield each year, was selected because it is typical of the many fungal pathogens that attack plants; more than 80% of all plant diseases are caused by fungi. "Although these sequences are specific to the rice and rice blast genomes, they will provide a model system for understanding host-pathogen interactions in other cereals and staple food crops," says Ralph Dean, director of the North Carolina State University Fungal Genomics Laboratory and leader of the group that sequenced the M. grisea genome.

A consortium of Chinese scientists led by the Beijing Genomics Institute reported the sequence for indica, the type of rice widely grown in China and southern Asia, while Syngenta carried out the sequencing of japonica, the type grown in Japan and northern Asia. All three groups used the whole-genome shotgun sequencing method, which decodes multiple short fragments of DNA. The many small pieces must then be assembled in proper order and located to their respective chromosomes using bioinformatics computer programs to predict the location of genes on the chromosomes.

But predictions based on computer algorithms are not always accurate, says Daniel Ebbole, an associate professor of plant pathology and microbiology at Texas A&M University. To test the accuracy of the bioinformatics-generated predictions, his lab is sequencing expressed rice and rice blast genes that are known to produce proteins. He is starting with expressed sequences from RNA isolated from the organism, which is translated into the organism's DNA sequence without the intervening unexpressed sequences that are generated in the shotgun sequencing method. Because RNA degrades rapidly, it is not practical to sequence whole genomes using this approach, but it is essential for validating the accuracy of the sequences derived from the shotgun approach.

Whereas the Chinese made the indica sequence freely available to the public (http://rgp.dna.affrc.go.jp/cgi-bin/statusdb/ seqcollab.pl), access to the japonica database is restricted because Syngenta wanted to protect its commercialization exclusivity and patent rights. This has sparked an outcry from scientists in the public sector who feel there should be no restrictions on data that are published in a scientific journal.

However, much of the japonica sequence will be publicly available soon. The International Rice Genome Sequencing Project, a 10-nation consortium, is also sequencing the japonica genome using bacterial artificial chromosome libraries, a more time-consuming but also more accurate approach. These libraries contain DNA pieces from each of the organism's chromosomes and so allow the assignment of sequences to their chromosomes. This, in turn, facilitates proper alignment of the sequence data. Project coordinators hope that by the end of 2002, some 95% of the japonica sequence will be available on the public NIH-administered database GenBank (http://www.ncbi.nlm.nih.gov/Genbank/).

Breakthroughs in genomics could eventually lead to long-term benefits to human health and the environment, including new strategies for reducing the use of fungicides and the creation of new chemicals that are more precise and less toxic. Rice could be bioengineered to augment its defense system for warding off invasion. The genomic data could also enhance marker-assisted selection for conventional breeding and spark genetic engineering strategies to address otherwise intractable problems.

In the meantime, there are several safe and effective alternatives for fighting rice blast, including planting early in the growing season, use of resistant rice varieties, avoiding excessive nitrogen fertilizer use, and proper flooding of rice paddies. A project sponsored by the Manila, Philippines-based International Rice Research Institute and begun in 1997 involved planting mixtures of glutinous and nonglutinous rice in the same fields, which virtually eliminated rice blast in Yunnan province and other parts of China.