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May 7, 2000


Rice Genome Gets a Boost


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Rice Genome Gets a Boost; Private sequencing effort yields rough
draft for the public
By Barry A. Palevitz

The Scientist 14[9]:1, May. 1, 2000

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

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

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

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."

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

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.

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

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

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?

Barry A. Palevitz (palevitz@dogwood.botany.uga.edu) is a contributing
editor for The Scientist.


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.