Rice's Genetic Map May Help Build a Better Cereal

By ROBERT LEE HOTZ, TIMES STAFF WRITER

LA Times

April 5, 2002

Science: Researchers hope to boost yield and make the grain more nutritious

Competing public and private research groups released remarkably complete drafts of the genetic sequence of rice Thursday, unlocking hereditary secrets of the plant that feeds half the world.

The findings by a corporate biotechnology laboratory in San Diego and an international academic team led by scientists in Beijing promise to almost immediately accelerate the search for more productive and nutritious strains of rice.

Researchers also are eager to use rice--the first crop to yield most of its genetic code--as a key to decipher the more complicated genetics of wheat, corn and other major cereal crops. Already, the genetics of rice have scientists rethinking the nature of complexity.

Rice has the smallest genetic sequence of all the cereal crops, yet it grows from a genome--an organism's complete DNA code--that contains more genes than required to make a human being, the scientists discovered. It has as many as 55,000 genes--thousands more than does a person--even though it is one-sixth the size of the human genome.

"It is surprising," said one project's co-leader, Yang Huanming, senior geneticist at the Beijing Genomics Institute and the Chinese Academy of Sciences.

These strands of rice DNA ensnarled the researchers in a controversy over commercial secrecy and public access. It echoed the rivalries that racked the effort to decipher the human genome.

The detailed drafts of the rice genome were created by two independent teams, each using similar gene-sequencing techniques on a different strain of rice. The research is published today in the journal Science.

An academic consortium of Chinese and American researchers documented the genetic information in a strain of rice called Indica, which is the most widely grown variety of rice in China and most Southeast Asian countries.

The project, led by Yang and Jun Yu at the Beijing Genomics Institute, is said to be the most ambitious genome research ever undertaken in China. In all, 11 groups in China collaborated with the University of Washington in Seattle to complete the draft sequence.

"The importance of the rice genome sequence to agriculture is as great as that of the human genome sequence to health," Yang said.

San Diego Team Studied 2nd Strain

A corporate research team led by Stephen A. Goff at the Torrey Mesa Research Institute in San Diego completed a detailed genetic draft of a second rice strain called Japonica, the most popular variety of rice in Japan.

The Torrey Mesa group is owned by Swiss agrochemical company Syngenta International, which spent about $30 million on its sequencing project.

Global production of rice, the world's most important staple crop, has risen threefold over the last three decades.

But crop yields are fast approaching the plant's natural limit on its ability to turn the energy of sunlight into carbohydrates.

Researchers hope that they can identify key rice genes to boost its yield and make the plant more nutritious by increasing its vitamin content. They also hope to make rice easier to grow, by breeding strains better able to withstand disease, drought and poor soils.

"We believe the future of agriculture will be navigated using the rice genome map," Goff said.

Rice shares many of the same genes as wheat and other cereal crops. Those genes also appear to fall in much the same order in all of them. So, to understand how a gene works in rice is to understand how it functions in all grains, the researchers said.

"Rice may turn out to be the Rosetta Stone of all genome sequences, although it was entirely unexpected," said Gane Ka-Shu Wong at the University of Washington.

Already, plant breeders at Syngenta have used the rice genome to create "virtual" maps of corn and wheat to identify potentially useful genes.

Syngenta found that about 98% of the known corn, wheat and barley genes are present in rice. Once the gene for a beneficial trait can be identified and mapped, it can be moved into any crop relatively quickly.

"This is plant breeding by design and this has never been possible before," said Steven Briggs, president of the Torrey Mesa Research Institute.

Both sequences still are incomplete, however, with as many as 11,000 gaps still to be filled in.

Limits on Access to Data Criticized

In their work, the two teams used preliminary genome research conducted by the International Rice Genome Sequencing Project and the agricultural biotechnology company Monsanto.

By pooling all the drafts, the finished rice sequence may be complete in 18 months, experts said.

Efforts to retain corporate control of the rice sequence information threatens the openness on which scientific progress often depends, several scientists said.

In a move that drew sharp criticism from geneticists around the world, Syngenta executives decided to keep the company's rice genetic sequence in a proprietary company database, placing restrictions on its use. Monsanto has also limited access to its rice data.

Normally, making such genetic data freely available is a strict condition of publication in major peer-reviewed journals.

Attempting to accommodate Syngenta's commercial interests, the journal Science, published by the American Assn. for the Advancement of Science, relaxed its rules and agreed to let Syngenta control the Japonica genetic database.

It is a compromise, Briggs said.

The company is offering its genetic information freely only to researchers who promise not to use it commercially. But it will not prevent those academic scientists from patenting their findings or demand review of research before it is published.

"We think the public benefit of bringing this [rice genome] out of trade-secret status outweighs whatever the precedent of letting [Syngenta] deposit it on their own Web site creates," Science editor Donald Kennedy said.

By contrast, the Chinese-led team deposited its data in an independent online forum called Genbank where the genetic information is freely available to all researchers, with no commercial restrictions on its use.

It is the second time that Science has allowed a company to limit access to genetic-sequence data. In 2000, the journal published with considerable fanfare a human genome prepared by the Celera Genomics Group without requiring the company to deposit its data in Genbank.

UC Davis rice geneticist Pamela Ronald called the rice genome sequence "significant," but was disappointed in how the information is being handled.

Syngenta's efforts to limit access to its database could easily slow research, Ronald said. "What happens with these company collaborations is that they get bogged down in legal paperwork. It is very frustrating," she said.

Added crop genetics expert Jeff Bennetzen at Purdue University: "It would be best if the information were released . . . for all to use without any strings attached. These sequences identify virtually all the genes in rice."

Times staff writer Aaron Zitner contributed to this report.