Published online 5 April 2002 | Nature | doi:10.1038/news020402-6


Rice genome unveiled

Draft DNA sequences of the world's most important crop announced.

Rice feeds two-thirds of the worldRice feeds two-thirds of the world© Getty Images

Two research groups today publish draft sequences of the rice genome.

Rice (Oryza sativa), the first crop to have its genome sequenced, is the staple food of two-thirds of the world's people. It is also the model scientists use to study the other cereals, which together provide about 90% of our calories.

The information in the genome could help food production keep pace with the planet's growing population and declining arable land area. "The world's poor need the best that technology has to offer," says Ronald Cantrell, director general of the International Rice Research Institute in Manila, the Philippines.

Across the world, researchers are already trying to create cereal varieties with traits such as drought and salt tolerance, pest resistance, higher yield and improved vitamin content.

Biotechnologists hope to locate useful genes among 10,000 varieties of rice and engineer them into new varieties. And conventional plant breeders can now work out whether a hybrid carries a desired gene without having to wait for the plant to mature and then carrying out laborious tests.

The vast majority of rice genes will also have close or identical relations in the other cereals. "We can use the rice genome to help improve wheat and corn right now. The genes are interchangeable," says a member of the commercial sequencing team, Stephen Goff of the Torrey Mesa Research Institute, San Diego.

Team effort

One team, based at the Beijing Genomics Institute (BGI), China, has sequenced the strain grown most widely in China and Southeast Asia1, a variety called indica. Another, a US-based group working for the biotech company Syngenta, has sequenced japonica, the strain that grows in the cooler, drier areas such as Japan and Europe2.

Both groups believe they have sequenced more than 90% of rice's total DNA. Syngenta have worked out 390 million of japonica's estimated 420 million DNA letters. The Beijing group put the indica genome at about 466 million letters.

“The International Rice Genome Sequence Project is set to deliver a complete sequence in 2004”

Both groups used 'whole shotgun' sequencing to blast the genome into around 100,000 smaller, more manageable pieces. Computers then reassembled the sequenced shards.

The publicly funded International Rice Genome Sequence Project, is set to deliver a complete sequence based on a slower, more expensive, but more complete, technique in 2004.

"This will be gold standard", says plant biologist Michael Bevan of the John Innes Institute, Norwich, UK. "These papers are landmarks, but they're only part of the story."

Rooting around

On the evidence so far, Syngenta reckon rice has about 40,000 genes. The BGI group plump for around 50,000. "I was surprised at how similar they came out," says Goff.

That means rice probably has more genes than we do, despite having only one-seventh as much DNA.

One reason for this difference is that plants' genes seem to be on average much shorter than mammals'. A rice gene is usually about 4,500 DNA letters long. The average human gene probably stretches to over 30,000 letters.

Plants are also prone to copying genes, chromosomes, and sometimes their entire genome. This might be a way for them to generate genetic diversity. Mammals can rearrange individual genes to make several different sorts of protein. Plants show much less of this, seeming to rely on a larger number of shorter genes.

“Rice probably has more genes than we do”

Rice is the second plant genome to be completed. The first was thale cress, Arabidopsis thaliana. This weed is beloved of researchers, but an agricultural nonentity. The ancestors of rice and thale cress diverged about 150 million years ago, and went on to form the two major groups of flowering plants.

The rice genome contains versions of 85% of the genes found in Arabidopsis. Comparisons between the species should aid the search for agriculturally useful genes.

In contrast, only about half of the genes in rice seem to be also present in Arabidopsis. The other half of the genome has chemical peculiarities that are "unrecognizable in any other organism", says Gane Wong, a member of the Beijing team.

Wong speculates that rice doubled its genome after the split with Arabidopsis. Now it seems to be in the process of modifying the duplicate in some way, perhaps switching off many of the copies. "We may have caught evolution red handed," he says.

Rice has more than twice as much DNA as Arabidopsis, but is a genetic pigmy compared to other cereals. Wheat, for example, has six copies of every chromosome and 16 billion letters of DNA. Most of this extra genetic material does not encode proteins; wheat probably has only a few genes that rice doesn't.

Data access

Controversy erupted last month around rumours that the journal publishing the genomes, Science, would do so without requiring Syngenta to make its data fully accessible. Some researchers argue that all published DNA sequences should also be placed on a public database called GenBank.

In the end, Syngenta has made its sequence freely available, through its own website, to non-profit institutions. Commercial researchers can access the data to check or challenge the genome, but must pay to exploit the information.

Bevan is sanguine about this arrangement. "Syngenta put a lot of resources into the project, and they need to see returns," he says. "Hopefully they will have extracted all the juice they want from the genome in a year or so and will make it fully accessible." The presence of the other, fully accessible sequence nullifies Syngenta's advantage, Wong adds. 

  • References

    1. Yu, al. A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 296, 79 - 92 (2002). | Article | ISI |
    2. Goff, S. A. et al. A draft sequence of the rice genome (Oryza sativa L. ssp japonica). . Science 296, 92 - 100 (2002). | Article | ISI |