Hot Cereal: Rice reveals bumper crop of genes

For about a third of the world’s population, rice equals life. The cereal provides more than half the daily calories that these people consume.

In the April 5 Science, two research groups report that they have independently deciphered almost the complete genetic code, or genome, of rice.

This worldwide staple becomes only the second plant–and the first crop plant–to have its genome unraveled.

The advance could help agricultural scientists produce strains of rice that are hardier, more productive, and less damaging to the environment than current strains are. The rice genome may also provide a boost to the investigation of other cereal crops, such as corn and wheat.

The rice genome “will have a global impact on human health,” Ronald P. Cantrell of the International Rice Research Institute in Manila, Philippines, and Timothy G. Reeves of the International Maize and Wheat Improvement Center in Mexico City contend in an April 5 Science commentary.

One of the teams studying rice, a group of scientists from the Beijing Genomics Institute in China and the University of Washington Genome Center in Seattle, analyzed the subspecies known as indica, the most widely consumed rice in China and India. The second team, led by investigators from the San Diego-based agricultural firm Syngenta, studied a rice subspecies called japonica, which is more commonly grown in Japan and Korea.

Both groups followed a so-called genome shotgun approach, a DNA-sequencing strategy originally developed for microbes and later applied to the human genome (SN: 5/23/98, p. 334). The method tends to leave more gaps than traditional genome-sequencing strategies do, but it’s much cheaper and faster to perform.

The shotgun methods “provide 90 percent of the value for 10 percent of the cost,” says plant geneticist Jeffrey Bennetzen of Purdue University in West Lafayette, Ind.

The two research groups report overlapping estimates of the number of genes in rice. Stephen A. Goff of Syngenta and his colleagues conclude that japonica has 32,000 to 50,000 genes, while the Beijing-Seattle team reports that indica has between 46,022 and 55,615 genes. In either case, that’s many more genes than the 26,000 or so in the small mustard Arabidopsis thaliana, the first plant to have its genome sequenced (SN: 12/16/00, p. 388: First Plant Genome Thrills Biologists).

Indeed, rice may contain more genes than a person does. Some still-controversial estimates suggest that the human genome possesses just 30,000 to 40,000 genes. Using gene number to gauge the complexity of an organism is problematic, however, because many organisms can read individual genes in multiple ways to produce distinct proteins.

“It is entirely possible that humans have many more proteins than rice does, even if they do have fewer genes,” notes Gane Ka-Shu Wong of the University of Washington, who worked on the indica project.

Because rice and A. thaliana represent the two major classes of flowering plants, biologists are eager to compare their genomes. The indica group found that more than 80 percent of A. thaliana genes have counterparts in the rice, but that only about 50 percent of the rice’s genes appear in the mustard’s genome.

“There’s a whole set of novel genes that have never been studied,” says Pamela Ronald of the University of California, Davis.

Some scientists caution that the gene-number estimates for rice are probably too high because they depended on computer scans of raw DNA sequences for certain patterns suggesting a gene’s presence. “I think a lot of the hypothetical genes [the computers turned up] will turn out not to be genes,” says Bennetzen.

Although it’s larger than that of A. thaliana, the rice genome is much smaller than those of other cereals. That’s why crop scientists focused their attention on it first. The wheat genome, for example, has 40 times as much DNA as the rice genome does.

Still, researchers contend that the rice genome provides an excellent foundation for the study of other crops. Goff and his colleagues, for example, found that 98 percent of the known proteins in maize, wheat, and barley have counterparts in rice. Wong says that he and his colleagues now plan to use the shotgun strategy to tackle the genomes of corn and wheat.

With the information in the rice genome, scientists expect to more efficiently breed strains with desired characteristics, such as higher yields, improved disease resistance, or less need of water. “In developing countries, the biggest windfall will be accelerated [rice] breeding programs,” says Robin Buell of the Institute for Genomic Research in Rockville, Md.

The rice genome may also aid a more controversial crop-improvement strategy, the creation of genetically engineered plants. Scientists might, for example, take a rice gene that contributes to disease resistance and add to it to corn.

The International Rice Genome Sequencing Project, a Japan-led public effort to provide a gapfree, even more accurate version of the japonica genome, plans to have its version ready by the end of the year, says Buell, a project member.