International Research Team Announces Finished Rice Genome

TIGR Scientists Say First Complete Crop Genome Will Improve Agriculture

August 10, 2005

Rockville, MD--Every year, the world consumes over 880 billion pounds of rice, which feeds half the population. Those tiny grains add up. So maybe it's no surprise that this important food crop turns out to have more genes than humans.

It's certainly not to researchers at The Institute for Genomic Research (TIGR), who have been sequencing the first food crop genome as part of an international consortium for the last six years. The completed sequence, published in the August 11 issue of Nature, unveils a genome consisting of roughly 400 million DNA bases holding 37,544 genes on rice's 12 chromosomes.

"Rice is a critically important crop, and this finished sequence represents a major milestone," said Robin Buell, lead investigator for TIGR's portion of the project. "We know the scientific community can use these data to develop new varieties of rice that deliver increased yields and grow in harsher conditions."

Over the next 20 years, world rice production must increase by a projected 30% to feed the earth's growing population. This finished sequence will provide an indispensable roadmap to agricultural researchers using both biotechnology and conventional breeding to develop hardier rice varieties. The genetic map will greatly speed their hunt for genes that increase yield, protect against disease and pests, or provide drought-resistance in rice and other cereal crops. Rice is genetically similar to maize, wheat, barley, rye, sorghum, and sugarcane.

"Rice is the Rosetta Stone for crop genomes," Buell says. "We can use the rice genome as a base for genomic studies of cereals." She adds that rice has a considerably smaller genome than maize and wheat, making it a better candidate for sequencing. Luckily, though, the rice genome is largely co-linear with other cereal genomes. In other words, similar genes in the other plant species should pop up in roughly the same spots as their rice counterparts. With the finished sequence, rice researchers gain a kind of genetic GPS, while other cereal researchers inherit a hand-drawn map with some important landmarks.

TIGR researchers sequenced more than 10% of the genome of the temperate subspecies of rice, Oryza sativa subspecies japonica, which is cultivated mainly in Japan, Korea, and the U.S. Their effort was part of the International Rice Genome Sequencing Project (IRGSP), which began in 1998 and pooled the resources of groups from ten nations, including Japan, China, India, Thailand, Taiwan, Brazil, France, Canada, the United Kingdom, and the United States. Japan leads the IRGSP.

The newly complete rice genome builds upon earlier draft sequences published by private companies Monsanto and Syngenta. In what Buell calls a "nice model of a public-private partnership," these companies donated their genome sequences to the IRGSP, saving the public consortium both time and money.

"Much as the Human Genome Project has revolutionized biology, the rice genome promises to inspire new cereal crop research," remarks TIGR President Claire Fraser. "This is a major step forward for agriculture."

Already, in fact, the finished rice genome is accelerating discovery. Scientists have used the finished sequence to identify genes that control fundamental processes, such as flowering. Rice's similarity to barley also has helped researchers identify genes responsible for resistance to barley powdery mildew and stem rust, two major crop diseases.

In the current study, researchers compared rice to the only other fully sequenced plant genome: Arabidopsis thaliana, a leafy plant that is a popular laboratory model. While 90% of Arabidopsis proteins also occur in rice, only 71% of rice's proteins also occur in Arabidopsis. That, says Buell, suggests that rice may hold many rice-specific or cereal-specific genes.

Along with TIGR, other U.S. groups involved in sequencing the genome included Cold Spring Harbor Laboratory, the University of Arizona, Rutgers University, Washington University in St. Louis, and the University of Wisconsin-Madison. Major funding for TIGR's portion of the project came from the U.S. Department of Energy, the National Science Foundation, and the U.S. Department of Agriculture's Cooperative State Research, Education, and Extension Service.

The rice project is an important part of TIGR's plant genomics program, which includes other major research projects involving maize, potato, and Arabidopsis. TIGR is also conducting research involving pine, barley, banana, and plant pathogens. Work on rice at TIGR continues with a four-year project to annotate the genome-identifying its features, assigning known information to each gene, and creating comparative line-ups with other plant species. The finished rice genome is available at www.tigr.org/tdb/e2k1/osa1/.