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Chinese Team Makes Public Novel Rice Genome Sequence

SAN DIEGO, Jan. 16 – Marking a milestone for plant-genomics research, scientists in China have made public a sequence of a widely grown rice strain that has never before been sequenced.

The results of the indica strain sequence, presented to a genomic conference here by the Beijing Genomic Institute, marks the end of an effort whose novelty, humility, and speed surprised many researchers.

 

“Two months ago I had not heard of the initiative,” Mike Gale, associate research director at the John Innes Centre in the UK, said during the 10th annual Plant, Animal & Microbe Genomes conference held here. “No one knew about it. They got the money from the Chinese Academy, put their heads down, and did the job.

 

“This is a fantastic thing,” he said.

Quiet toil

 

The Oryza sativa indica strain, which accounts for the majority of rice grown in China, has never before been sequenced. Preliminary results of the BGI project, begun in May 2000 and completed in October 2001, was published in the Chinese Science Bulletin when its draft was complete.

 

However, the extent of the work remained virtually unknown outside a cadre of Chinese genomics researchers until the team presented their findings here on Sunday.

 

BGI researchers sequenced the indica strain using a whole genome shotgun approach, according to Jun Yu, a member of the team. The effort yielded 386 million base pairs in a six-fold coverage, and an initial analysis by BGI researchers showed that the genome contains approximately 60,000 to 65,000 genes.

 

The effort, which independent researchers are only now beginning to analyze, is the first rice genome to be released to the public. Last January, Syngenta and Myriad Genetics announced the draft sequencing of the japonica strain, but the companies have yet to release those data.

 

An international public consortium, the International Rice Genome Sequencing Project, is set to finish its own sequence of the japonica genome by the end of 2002, according to scientists close to the project. The IRGSP, which includes the United States, Japan, and China, is performing the sequence using the BAC by BAC approach which when compared with whole-genome shotgun sequencing is more time-intensive.

 

The Chinese sequencing data are under review for publication in the journal Science, researchers familiar with the Chinese work said. Sources also indicated that Syngenta, of Basel, Switzerland, may have submitted its data to the same journal and that both papers would be published in the same issue, perhaps in May. This information could not be immediately confirmed.

 

“This is huge,” Rod Wing, director of the Clemson University Genomics Institute and the former US representative to the IRGSP, said of the indica sequence. “Rice is the rosetta stone for cereals. The [world] population will double in 50 years. We have to know everything we can about the most important food crop in the world.

 

“Knowing this [sequence] now will accelerate everything,” he said.

 

What’s more, understanding indica together with the anticipated public release of japonica will allow research not possible with only one genome alone.

 

“Rice is a model for all cereal plants,” said Ed Kaleikau, director of the plants division at the US Department of Agriculture. “[Its sequencing] will lead to the identification of genes not only important in rice but in other cereals. Eventually it will lead to a better understanding of rice and all cereal crops” including wheat, barely, and corn.

 

“For ag-important plants, this could be compared to the [sequencing of] the human genome,” said Kaleikau. ”A better understanding of plant biology is now available for the second largest [plant] kingdom.”

 

Researchers are now beginning to analyze the sequence data, which can be accessed at http://btn.genomics.org.cn/rice or http://210.83.138.53/rice/download.php.

 

“It appears the Chinese have put it into the public domain with no strings attached,” said Gale.

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