Walnut Creek, California
January 18, 2008
 A
preliminary assembly and annotation of the soybean genome,
Glycine max, has been made available by the
U.S. Department of Energy Joint
Genome Institute (DOE JGI), to the greater scientific
community to enable bioenergy research.
The announcement was made by Eddy Rubin, DOE JGI Director,
during his keynote remarks Jan. 15 at the Plant and Animal
Genome XVI Conference in San Diego,CA. The preliminary data can
be accessed at
http://www.phytozome.net/soybean.
The soybean genome project was initiated through the DOE JGI
Community Sequencing Program (CSP) by a consortium led by DOE
JGI’s Dan Rokhsar, Stanford’s Jeremy Schmutz, Gary Stacey of the
University of Missouri-Columbia, Randy Shoemaker of Iowa State
University, and Scott Jackson of Purdue University, with support
from the U.S. Department of Agriculture and the National Science
Foundation.
The large-scale shotgun DNA sequencing project began in the
middle of 2006 and will be completed in 2008. A total of about
13 million shotgun reads have been produced and deposited in the
National Center for Biotechnology Information (NCBI) Trace
Archive in accordance with the consortium’s commitment to early
access and consistent with the Fort Lauderdale genome data
release policy.
The current assembly (representing 7.23x coverage), gene, set,
and browser are collectively referred to as "Glyma0". Glyma0 is
a preliminary release, based on a partial dataset. This is
expected to be replaced with an improved, chromosome-scale
"Glyma1" version by the end of 2008. Early users of this data
are encouraged to track their favorite genes by saving local
copies of the DNA sequences of these loci, and not by identifier
or sequence coordinate, as these will change in future versions.
DOE JGI’s interest in sequencing the soybean stems from its role
as a principal source of biodiesel, a renewable, alternative
fuel with the highest energy content of any alternative fuel.
Detailed knowledge of the soybean genetic code will enable crop
improvements for more effective application of this plant for
clean bioenergy generation. Knowing which genes control specific
traits, researchers are able to change the type, quantity,
and/or location of oil produced by the crop. Through utilization
of the sequence information generated by DOE JGI, it may be
possible to develop a customized biomass production platform for
combining oil seed production for biodiesel with enhanced
vegetative growth for ethanol conversion--doubling the energy
output of the crop. In 2004, over 3.1 billion bushels of
soybeans were grown on nearly 75 million acres in the US, with
an estimated annual value exceeding $17 billio--second only to
corn, and about twice that of wheat.
Several other individuals, projects, grants, and agencies have
made this monumental project possible. These included the four
major projects: Public Expressed Sequence Tags (ESTs), SoyMap
(which includes BAC libraries, modern physical mapping, and
clone-based sequencing), and the Genetic Map with funding from
USDA, NSF, United Soybean Board (USB), and the North Central
Soybean Research Program (NCSRP).
The Public EST Project, supported by USB and NCSRP, was led by
Lila Vodkin of the University of Illinois at Urbana-Champaign;
Randy Shoemaker of the USDA-ARS, Ames, Iowa; and P. Steven Keim
of Northern Arizona University.
The original physical map development, funded by USB, was
conducted by Jan Dvorak, from the University of California,
Davis, along with the Washington University Genome Center in St.
Louis, Missouri, and David Grant, USDA-ARS, Ames, Iowa.
The NSF SoyMap team, comprising principal investigator Scott
Jackson, Gary Stacey and Henry Nguyen, Jeff Doyle of Cornell
University, William Beavis of the National Center for Genome
Resources (NCGR) in Santa Fe, New Mexico, and Iowa State,
Gregory May (NCGR), Will Nelson and Rod Wing of the University
of Arizona, with Randy Shoemaker, anchored the map and conducted
quality control.
The team devoted to genetic mapping and physical map anchoring,
yielding several thousand sequence-based markers, included
USDA-Agricultural Research Service (ARS) investigators,
including Perry Cregan and Dave Hyten of Beltsville, Maryland,
Randy Shoemaker, David Grant, and Steven Cannon of Ames, Iowa,
along with James Specht of the University of Nebraska, Lincoln.
The annotation of the soybean genome was carried out by a team
of researchers from the DOE JGI and the University of California
Berkeley’s Center for Integrative Genomics, with support from
the DOE, USDA, NSF, and the Gordon and Betty Moore Foundation.
The U.S. Department of Energy Joint Genome Institute,
supported by the DOE Office of Science, unites the expertise of
five national laboratories -- Lawrence Berkeley, Lawrence
Livermore, Los Alamos, Oak Ridge, and Pacific Northwest -- along
with the Stanford Human Genome Center to advance genomics in
support of the DOE missions related to clean energy generation
and environmental characterization and cleanup. DOE JGI’s Walnut
Creek, CA, Production Genomics Facility provides integrated
high-throughput sequencing and computational analysis that
enable systems-based scientific approaches to these challenges. |
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