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Finishing Rice Chromosome Pays Off
Edward R. Winstead

Another rice chromosome has been completely sequenced, this time number ten. It is the third rice chromosome to be published in finished form, with a high degree of accuracy and few gaps. The nine others should be completed by the end of next year, providing scientists and breeders with genetic information that can be used to develop disease-resistant strains and increase yields.

Mt. Tsukuba, Japan, with rice in the foreground.

A finished rice genome will also be valuable to researchers who study related crops. The new findings, published in Science, reveal that many rice genes have counterparts in maize, and they often reside in the same order. This degree of genetic similarity allows researchers to go back and forth between the species and locate specific genes.

Indeed, many plant researchers have utilized the rice chromosome 10 sequence as the raw data have been posted on the Internet over the last three years.

“Throughout the project we’ve heard from researchers working on barley and maize who are using the rice sequence,” says C. Robin Buell of The Institute for Genomic Research (TIGR) in Rockville, Maryland, and a leader of the sequencing team.

The chromosome 10 study is noteworthy for another reason: It illustrates the value of filling in gaps and correcting errors on draft genome sequences.

The finished version of chromosome 10 has twice as many genes as had been reported in two drafts of the rice genome published last year. The actual number is about 3,500 genes; half of these were missed by the shotgun-sequencing method used to create last year’s drafts.

The sequencing of chromosome 10 was co-led by Rod A. Wing of the University of Arizona; Richard McCombie of the Cold Spring Harbor Laboratory in New York; and Joachim Messing of Rutgers University in New Jersey. As part of the International Rice Genome Sequencing Project, the team sequenced the short-grained japonica rice, which is popular in Japan.

Nipponbare is the common germplasm source for the International Rice Genome Sequencing Project.

The size of the rice genome made a large-scale international sequencing project relatively economical. Rice has the smallest genome of plants in the grass family (444 million base pairs). Maize, by comparison, has three billion base pairs—the size of the human genome.

Along with their own sequence data, the publicly funded researchers incorporated data from corporations that produced their own drafts of the rice genome and made them available—Syngenta of San Diego and Monsanto of St. Louis, Missouri.

The rice genome has very much been an example of successful collaborations between public and private researchers, notes Buell.

See related GNN article
»Two Groups Sequence Rice

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The Rice Chromosome 10 Sequencing Consortium. In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300, 1566-1569 (June 6, 2003).

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