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China s Rice Sequencing Project Gets a Much-Needed Boost from SGI Supercomputer

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SGI recently finished installing a 32-processor SGI Origin 800 system in Shanghai at the Chinese Academy of Science’s National Center for Gene Research (NCGR), said to have cost about $400,000.

The deal, in addition to the main 3800 server, includes 10 sets of FP1600W and a 4 TB TP9100 FC RAID. The new system complements an SGI O2 and Octane equipment already in use at the center.

NCGR director Bin Han noted that in shopping around for its new server, the center had competitive offers from Sun Microsystems, Hewlett-Packard, Compaq, and IBM, but went with SGI because of the combination of “the price and services provided to us.”

The new system represents a continuing expansion of the center’s capacity for its study of the Oryza sativa, or rice, genome. Han said the equipment would be dedicated to rice genomic sequence database construction and sequencing analysis.

Through the National Center, China is participating in the four-year 11-nation public project, led by Japan, to sequence the genome for the variety of rice known as nipponbare, or japonica. Much like the international Human Genome Project effort, the countries involved in IRGSP have divvied up the work by chromosome, each country in charge of producing sequence information about a certain region.

In response to the announcement by Syngenta in January that it had completed a sequence of the rice genome — which shocked the project’s members — the China Academy of Sciences met and decided to take measures to double the NCGR’s sequencing capacity. The center also agreed at that time to take on Chromosome 4 in its entirety.

While there is serious international pressure to develop new varieties of rice that can withstand difficult growing conditions and/or provide consumers additional nutritional benefits, the NCGR vehemently denied the claim in a recent SGI press release that the center’s aim “is to create a higher quality of grain that is virus-resistant and at the same time increase the quantity of rice production.” That is “absolutely wrong,” said Han when queried about the project. “We never plan to do that.”

Rather, NCGR will use its capacity for sequencing and bioinformatics to complete work on Chromosome 4 for both the japonica and indica varieties. Han said the center’s goal is to gain a better understanding of the separation and evolution of the two varieties. NCGR researchers are looking forward to publishing a paper on their results in this area soon.

Because it has no fields for growing experimental plants, Han said the center would team up with facilities in Hangzhou and Wuhan for further research. “We are trying to do some transgenic experiments to identify gene function with the collaboration,” he said. While this work is still at an early stage, Han noted that researchers have already raised both indica and japonica varieties for mRNA preparation.

— Sara Harris, Tokyo

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