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Plant Physiol, March 2001, Vol. 125, pp. 1164-1165
The Use of the Monsanto Draft Rice Genome Sequence in
Research
Gerard F.
Barry*
Genomics, Monsanto, 800 North Lindbergh Boulevard, St. Louis,
Missouri 63167
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ARTICLE |
Monsanto recently produced a draft
of a rice (Oryza sativa) genome in support of its ongoing
internal research programs in genomics and crop improvement. The
sequence data were produced primarily in the laboratories of Dr. Leroy
Hood (University of Washington, Seattle) under contract for Monsanto.
In addition to being one of the most important world food crops, rice
serves as a useful research model. The syntenic relation between the rice genome and those of other cereal grasses has been widely recognized and the availability of detailed information about the rice
genome will likely advance global efforts to improve other major food
crops in the grass family, including corn (maize), wheat, barley,
sorghum, millet, and others. The increased research in rice may
be expected to have many direct and indirect benefits for this critical
crop and its relatives, and ultimately may contribute to an improvement
in food production in many world areas. The International Rice Research
Institute (Los Banos, The Philippines) estimates that 1 billion
new rice consumers will be added in Asia by 2020. By that date, 4 billion people more than one-half the world's populationwill depend
on rice as a staple of their diet.
The Monsanto draft rice genome sequence was produced from rice cv
Nipponbare, a japonica variety that has been used widely in genetic
studies in ricethe same cultivar used by the International Rice
Genome Sequencing Project (IRGSP;
http://rgp.dna.affrc.go.jp/Seqcollab.html). Formally launched in
February 1998 to complete and publish the entire genome sequence of
rice, IRGSP members have agreed to use a single germplasm, to share
materials and information, to immediately make public completed
portions of the genome, to achieve certain accuracy standards, and to
coordinate their work.
In early 2000, Monsanto decided to share the draft sequence data with
the IRGSP to benefit this 11-member consortium in reaching its primary
objective soonerthe production of a complete and finished sequence of
the genome of rice cv Nipponbare. Monsanto's sequence data and
supporting materials have been made available to the IRGSP through the
Japanese Ministry of Agriculture, Forestry, and Fisheries, the lead
agency in the IRGSP, which distributes the company's data to members
according to their assigned chromosome. The work of the IRGSP is
expected to continue, incorporating data from Monsanto's draft
sequence, until the entire rice genome sequence has been completed. As
each segment (in units of P1 artificial chromosomes or bacterial
artificial chromosomes [BACs]) of the sequence is completed,
it will be placed in public databases, in accordance with existing
IRGSP policy. The availability of the draft sequence and the related
materials is expected to reduce both time and cost for the IRGSP.
Monsanto has established a website, http://www.rice-research.org,
that provides registered researchers around the world access to the
company's rice genome sequence data. The Monsanto Rice Genome
Sequencing project produced approximately 399 Mb of sequence from 3,391 BACs. Small amounts of contaminating sequence were removed from this
"initial" dataset and redundant sequences were assembled into
longer contigs. This process produced the "draft" dataset totaling
259 Mb of assembled sequence data. Some redundancy may remain, for
example, where sequence quality at the ends of contigs was not high
enough to determine if overlaps were present. Both the "initial"
dataset and the "draft" dataset are available for performing BLAST
searches. The "initial" dataset consists of the original contigs of
the BAC sequencing project that have not been assembled; therefore, the
contig lengths are shorter than in the "draft" dataset. In
addition, the "initial" dataset still contains redundancy and contaminants.
The data are provided at no charge. To access the
http://www.rice-research.org database, principal investigators and
their institutions complete a Database Registration Agreement
(available on http://www.rice-research.org). User names and passwords
are assigned for use by principal investigators and their lab members. Because Monsanto supports global agricultural research to improve rice
and other important food crops and such advances are aided by the
dissemination and exchange of information, Monsanto encourages the
publication of results derived from the use of this rice genome sequence database and research results obtained from the use of http://www.rice-research.org, including information obtained from a
search of the database. These results may be published in scientific publications or presented in open public forums. There are more than
300 registered users and the site has around 1,000 visits per day.
Monsanto recently completed an analysis of its rice genome
sequence and produced a file containing all of the di-, tri-, and tetranucleotide simple sequence repeats of 24 bp (or greater) in the
draft sequence. These simple sequence repeats are the parts of the
genome predicted to be most immediately useful in rice breeding. All of
these potential molecular breeding tools (around 6,650 in number and
flanked by 100 bp of unique sequences on each side) have been
included in this file and may be freely downloaded from
http://www.rice-research.org. These sequences have also been deposited
in GenBank. These new data are expected to help expand knowledge of
rice genetics and accelerate breeding research in rice in research labs
around the world. It is hoped that these data will benefit efforts in
marker discovery and mapping in rice.
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ACKNOWLEDGMENTS |
I wish to acknowledge the contributions of the large number of
Monsanto and University of Washington (Seattle) scientists who have
contributed to the Monsanto Rice Genome Project and of these and many
other Monsanto staff who have worked to make this scientific
achievement a valuable resource for the public research community.
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FOOTNOTES |
*
E-mail gerard.f.barry{at}monsanto.com; fax
314-694-1671.
© 2001 American Society of Plant Physiologists
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