Rice Genome Gets a Boost

Courtesy of MonsantoRice, the most widely consumed staple food grain, is harvested on about 10 percent of the world's arable land. Researchers are cranking out genomes faster than many scientists can digest them. Just 10 days after publication of Drosophila's sequence (see page 10), Monsanto Co. announced it will soon release a rough draft of the rice genome containing 400 million bases of DNA. Rice is the world's most important food crop. The International Rice Research Institute in the Philippines estimates that by 2020, four billion people will depend on it. That's one of the reasons plant geneticists want to sequence its genome--finding unknown genes and gene combinations could be a passport to better rice quality, yield, and pest protection. According to Benjamin Burr of Brookhaven National Laboratory on Long Island, N.Y., "This is the ultimate tool for conventional plant breeding. In the future, breeders can identify genes by looking at the database." Rice's nuclear blueprint is around seven times smaller than corn's (or human's, for that matter) but three times larger than that of the tiny mustard plant Arabidopsis, whose sequence is due later this year. St. Louis-based Monsanto didn't actually do the rough draft; the company contracted the work to genomics guru Leroy Hood of the University of Washington in Seattle. Hood, who recently resigned from the university to head a new nonprofit Institute for Systems Biology next door, used the shotgun technology he pioneered for the Human Genome Project in which pieces of DNA are incorporated into BACs--bacterial artificial chromosomes--for sequencing. According to Hood, he approached Monsanto CEO Robert Shapiro a few years ago about joint projects. After doing some initial BAC sequences, he decided to finish the job. Hood said it was "incredibly inexpensive" to decipher rice, but he wouldn't reveal how much it actually cost. Monsanto was equally mum, claiming the information is proprietary. Hood gave full credit to Monsanto, which recently became a wholly owned subsidiary of Pharmacia Corp., for the decision to make the rice draft public. According to Monsanto spokesman Gary Barton, "We realized this was valuable information that could speed up the process .... The decision reflected the desires of the entire company." Still, Monsanto stands to profit from the release in several ways. The company is already invested in rice--it could have a herbicide-resistant (Roundup Ready) variety to market as early as 2003. Burr thinks "they will learn a lot more about the rice genome by putting the information in the public's hands a lot sooner." Rice also shares sequence similarity, including higher-order clustering of genes or synteny, with other grasses. Says Barton, "Rice is important for rice ..., but also broadly as a model for other grasses like corn and wheat, which are major interests for Monsanto." If the rice sequence spurs new, economically important discoveries, the decision to release the data will pay off. Burr agrees that "everyone wins." Courtesy of MonsantoThe rough draft contains about 85 percent of the rice genome. A Model of Cooperation? Monsanto's announcement was good news to the International Rice Genome Sequencing Project, or IRGSP, a 10-country consortium led by Japan that has already deposited about seven million bases in GenBank.1 The group planned to finish the job by 2008, but IRSGP member Burr thinks the additional data will cut five years from the project. "Around 50 percent of the effort is picking the next BAC. That's off the table now." Adds Burr, "This is a great gift--everybody is delighted." Monsanto and Hood even chose the same rice variety--Nipponbare--that IRGSP chose. Consortium leader Takuji Sasaki of the Rice Genome Research Program in Tsukuba, Japan, has been working with it for years. Burr sees other long-term dividends from the rough draft: It should improve the atmosphere in plant genetics, where academic researchers tend to view industry counterparts as secretive. Monsanto's action could be a precedent for cooperation and trust--hopefully the field will become more collegial, the way it was years ago. What's Next? Monsanto will deliver the rough draft to the Japanese Ministry of Agriculture, Forestry and Fisheries by June, which will then make it available to IRGSP members. The company will also set up its own server for other researchers. While Monsanto will provide the data free of charge, users must sign a registration agreement giving the company first crack at potential commercial applications, though the licenses will be nonexclusive. Courtesy of MonsantoA Monsanto scientist places DNA samples into a thermocycler in the company's sequencing lab. Hood thinks the rough draft contains about 85 percent of the rice genome, so why will it take three more years to finish? For one thing, all of the BAC sequences will have to be assembled according to international standards. Also, "There will be gaps among the BACs that will have to be filled in," notes Burr. Finally, all genes must be assigned positions along rice's 12 chromosomes. The problem is, nobody really knows how large the rice genome is. It could be just 400 million bases, but Burr guesses it will be more. Rice sequencers will get a better idea when they merge the Monsanto data with a physical map of the genome. To complicate matters, the final sequence probably won't include DNA in centromeres, chromosomal regions that spindle fibers attach to during mitosis. Centromeres are difficult to decipher because they contain highly repetitive sequences. But an international team led by Daphne Preuss of the University of Chicago says "green" centromeres contain some genes, at least in Arabidopsis.2 Regardless of the final tally, Burr is elated: "We're going to know rather soon where all the rice genes are. The next step is a concerted effort to find out the function of all those genes." That kind of functional genomics calls for even more collaboration--and a group at the Philippines' International Rice Research Institute is ready to pitch in. As for Hood, his association with Monsanto ended with the rough draft, which "is really too bad for us." But rice left an impression: Hood's institute will probably hire people to work on plant genomics. Seattle, anyone?S Barry A. Palevitz (palevitz@dogwood.botany.uga.edu) is a contributing editor for The Scientist. References 1. T. Sasaki and B. Burr, "International Rice Genome Sequencing Project: the effort to completely sequence the rice genome," Current Opinion in Plant Biology, 3:138-41, April 2000. 2. G.P. Copenhaver et al., "Genetic definition and sequence analysis of Arabidopsis centromeres," Science, 286:2468-74, Dec. 24, 1999.

Rice Genome Gets a Boost

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