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Two Groups Sequence Rice
Combining draft sequences may accelerate completion of finished genome
Edward R. Winstead

Featured article.

Two research teams have sequenced related subspecies of rice, the food staple of more than three billion people and a model species for plant researchers. The genomes open the door to improved varieties of rice and the discovery of genes for desirable traits, such as the ability to grow under diverse environmental conditions. The rice data will be used to advance studies of genetically similar crops such as wheat and maize.

Honghe Hani Terraces, a miracle of rice farming, are located in Southwestern China, Yunnan Province, Yuanyang County.

"The draft genome sequences will speed improvements in nutritional quality, crop yield and sustainable agriculture to meet the world's growing needs," Donald Kennedy, Editor-in-Chief of Science, which is publishing the rice genome papers today, is quoted as saying.

"Rice is the world's calorie champion," said Kennedy, who spoke to reporters during a conference call yesterday. "More people depend on—and consume—calories from rice than from any other crop, and when you add in wheat and maize, this really is a major contribution to world health."

The finished genomes will take some of the guesswork out of plant breeding. They certainly should save breeders time because rather than waiting for a seed to develop into a plant in order to assess its usefulness, breeders will be able to determine whether a seed contains a particular gene through genetic analysis.

A complete rice sequence is the basis for comparing genetic differences among strains. The seeds of traditional rice varieties and wild specimens have been stored at places like the International Rice Research Institute Genebank in the Philippines. With the genome, researchers can utilize an enormous amount of information that already exists for many of these strains based on decades of breeding studies. If a gene is known to contribute to trait of interest, variants of this gene can be examined in other varieties.

‘This is plant breeding by design, and this has not been possible before.’

"We can now look and find genes required to produce a desired trait and then cross individual lines to produce a trait that may not exist anywhere in the world," Steven Briggs, head of Genomics at Syngenta and president of the Torrey Mesa Research Institute in San Diego, where the sequencing of one of the strains was done, is quoted as saying. "This is plant breeding by design, and this has not been possible before."

The two research teams—the Swiss-based agricultural biotechnology company Syngenta and a collaboration of publicly funded research institutes—determined the sequences using the whole-genome shotgun method

Stephen A. Goff, of Syngenta in San Diego, and colleagues sequenced the short-grain japonica strain that is popular in Japan. Jun Yu, of the Beijing Genomics Institute (BGI) and the University of Washington in Seattle, and colleagues sequenced the indica strain—the most commonly grown variety in China and many other Asian Pacific regions. Indica is the paternal strain of a 'super-hybrid' variety, called LYP9, which has an increased yield of 20 to 30 percent.

The indica genome contains 466 million base pairs. This is nearly four times larger than the genome of the mustard weed Arabidopsis thaliana, which was sequenced in 2000. The rice genome is six times smaller than that of humans and maize.

Rice belongs to the grass family, which includes other major food crops such as barley, sorghum, millet, and maize. Of the family of grasses, rice has the smallest genome. Genetic maps indicate that all grasses have large regions of their genome in common.

Detail from rice-maize comparative map. View full

Syngenta has lined up maize and rice chromosomes to determine similarities and differences between the species. The discovery of economically important genes in rice should lead to the relatively rapid identification of counterparts in other species. For example, the researchers used a comparative map to investigate a region of the maize genome associated with the ability to germinate in cold, wet soils.

After corn breeders had mapped this trait to a particular region of a maize chromosome, Syngenta researchers identified the genes in the corresponding rice region. "They then went back to maize and confirmed that the genes were involved in germination in cold, wet soils," said Briggs.

Both groups found that rice has a relatively large number of genes, somewhere between 43,000 and 63,000 genes. The number of human genes is estimated to be around 30,000 to 40,000. The different numbers may be related to how each species generates diverse sets of proteins necessary to survive.

Humans have many more proteins than genes, and it appears that portions of genes are mixed and matched to create multiple proteins, a process called alternative splicing. In rice, it appears that the collection of diverse proteins is the result of genes duplicating themselves in the genome. Seventy-five percent of the predicted genes in the japonica genome may be duplicates, according to Goff and colleagues.

The average length of an organism's genes may indicate different strategies for achieving a diverse set of proteins. The indica strain has relatively short genes that are on average about 4,500 base pairs long. The average human gene is about 72,000 base pairs long.

Including the indica and japonica sequencing efforts, there have been four major rice genome projects to date. In 1998, an international consortium began sequencing the japonica (Nipponbare) strain. Led by the Rice Genome Research Program in Tsukuba, Japan, consortium members have been sequencing regions of chromosomes in an incremental process that is slower than shotgun sequencing but potentially more precise. The result is expected to be the most complete rice sequence and the gold standard for future genomic studies of cereals.

Detail from table showing functional classification of rice genes. View full

In 2000, Monsanto of St. Louis, Missouri, generated a draft sequence of the japonica (Nipponbare) strain. The work was done by Leroy Hood's group at the University of Washington in Seattle under contract by Monsanto, and Monsanto made the data available to IRGSP. Writing in today's issue of Science, IRGSP leaders note that the Monsanto collaboration has helped increase the submission of rice sequence to public databases.

Now, Syngenta has proposed a collaboration that aims to combine the published draft sequences and speed the completion of a finished rice genome sequence, Steven Briggs said yesterday. He estimates that the goal is achievable in less than two years, and the collaboration appears to have support from the BGI group.

Gane Ka-Shu Wong, of the University of Washington Genome Center and a member of the BGI project, said yesterday that in the coming months the two groups will develop an integrated map of the two related species. "This will allow us to understand the difference between different rice species," he said.

Wong, a Canadian, said the publication of the indica strain was 'the coming out' for the Beijing Genomics Institute, which now has 600 employees in two locations—in Beijing and near Shanghai. "Two years ago they did not even have a building," he said.

The decision by the editors of Science to publish Syngenta's genome paper was controversial because some researchers argued that the data should be deposited in the publicly funded database called GenBank rather than be available through a company Web site. The controversy was reminiscent of the journal's decision last year to publish the human genome paper by Celera Genomics of Rockville, Maryland.

Winnowing rice, Philippines.

Syngenta allows academic researchers to freely download up to 100 kilobytes of data per week under the condition that the data are not transferred to a third party. Academic researchers may use the data without restrictions and publish findings based on the data. Commercial researchers may also use the data by signing a statement of intent and making arrangements with Syngenta.

"I think over the next ten to twenty years our publishing of the rice genome is going to have a greater impact on global human health than our publishing of the human genome last year," said Kennedy. "We haven't seen anything yet in the way of a direct impact on human health from the human genome," he added, and thinks that plant breeders are likely to see the benefits from this information more quickly.

See related GNN article
» First complete plant genome yields bountiful harvest of genes: Arabidopsis thaliana is sequenced by international collaboration

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Goff, S.A. et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296, 92-100 (April 5, 2002).
Yu, J. et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79-92 (April 5, 2002).
Syngenta to Release its Rice Genome Map. Press release, Syngenta, La Jolla, California (March 29, 2002).
Barry, G.F. The use of the Monsanto draft rice genome sequence in research. Plant Physiol 125, 1164-1165 (March 2001).

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