The U.S. Department of Energy Joint Genome Institute (DOE JGI) has released
a complete draft assembly of the soybean (Glycine max) genetic code, making
it widely available to the research community to advance new breeding
strategies for one of the world?s most valuable plant commodities. Soybean
not only accounts for 70 percent of the world?s edible protein, but also is
an emerging feedstock for biodiesel production. Soybean is second only to
corn as an agricultural commodity and is the leading U.S. agricultural
export.


DOE JGI?s interest in sequencing the soybean centers on its use for
biodiesel, a renewable, alternative fuel with the highest energy content of
any alternative fuel. According to 2007 U.S. Census data, soybean is
estimated to be responsible for more than 80 percent of biodiesel
production.

?The genome sequence is the direct result of a memorandum of understanding
between DOE and USDA to increase interagency collaboration in plant
genomics,? said DOE Under Secretary for Science Dr. Raymond L. Orbach. ?We
are proud to support this major scientific breakthrough that will not only
advance our knowledge of a key agricultural commodity but also lead to new
insights into biodiesel production.?

?Soybeans have been an important food plant providing essential protein to
people for hundreds of years,? said USDA Chief Scientist and Under Secretary
for Research, Education, and Economics Dr. Gale A. Buchanan. ?Now, with the
new knowledge available through this joint DOE/USDA genome sequencing
project, researchers everywhere will be able to further enhance important
traits that make the soybean such a valuable plant. It?s a great day for
agriculture and people everywhere.?

This effort was led by Dan Rokhsar and Jeremy Schmutz of the DOE JGI, Gary
Stacey of the University of Missouri-Columbia, Randy Shoemaker of the U.S.
Department of Agriculture (USDA)-Agricultural Research Service (USDA-ARS),
Scott Jackson of Purdue University, with support from the DOE, the USDA, and
the National Science Foundation (NSF). In addition, the United Soybean
Board, the North Central Soybean Research Program, and the Gordon and Betty
Moore Foundation, have supported the soybean genome effort.

?Soybean is the one of the largest and most complex plant genomes sequenced
by the whole genome shotgun strategy,? noted Rokhsar. The process entails
shearing the DNA into small fragments enabling the order of the nucleotides
to be read and interpreted. Steven Cannon of the USDA-ARS collaborated with
the DOE team to ensure the accuracy of the assembly.

Preliminary scientific details emerging from the sequence analysis will be
presented by Schmutz at the International Conference on Legume Genomics and
Genetics in Puerto Vallarta, Mexico, December 8, 2008. The soybean genome
sequence information can be browsed at [www.phytozome.net].

Schmutz and colleagues have begun to analyze the soybean genome, which at
one billion nucleotides is roughly one-third the size of the human genome.
Preliminary studies suggest as many as 66,000 genes?more than twice the
number identified in the human genome sequence, and nearly half-again as
many as the poplar genome, sequenced by DOE JGI and published in the journal
Science in 2006.

?We have ordered and localized about 5,500 genetic markers on the sequence,
which promise to be of particular importance to those researchers seeking to
optimize certain qualities in soybean,? said Schmutz. Thousands of these
markers were developed by Perry Cregan and colleagues of the USDA-ARS with
support of the United Soybean Board. A genetic marker represents a known
location on a chromosome that can be associated with a particular gene or
trait. Prospective genome pathways of interest are those that directly
influence yield, oil and protein content, as well as drought tolerance and
resistance to nematodes and diseases such as the water mold Phytophthora
sojae, previously sequenced by DOE JGI, which causes stem and root rot of
soybean.

In 2007, soybean accounted for 56 percent of the world?s oilseed production.
James Specht, Professor at the University of Nebraska, said that this
nitrogen-fixing legume crop offers the dual benefit of a seed high in
protein and oil?with room for improvement. ?With the advent of low-cost
re-sequencing technologies, soybean scientists now have the means to
identify sequence differences responsible for yield potential?the most
desired of all crop traits, but to date the most intractable.?

?The soybean genome sequence will be a valuable resource for the basic
researcher and soybean breeder alike,? said Jim Collins, Assistant Director
for the Biology Directorate at the NSF. Collins and Judith St. John of USDA
Agricultural Research Service co-chair the Interagency Working Group on
Plant Genomes, which oversees the National Plant Genome Initiative. ?The
close coordination between the DOE sequencing project and the NSF SoyMap
project facilitated through the National Plant Genome Initiative has added
value to the sequence and physical map resources for this important crop,?
Collins said.

The soybean genome project is already making its mark out in the field.

?It?s tremendous that the soybean genome is out in the public?s hands.? Said
Rick Stern, a New Jersey soybean farmer and chair of the Production Research
program for the United Soybean Board (USB). ?Now every breeder can go into
this valuable library for the information that will help speed up the
breeding process. It should cut traditional breeding time by half from the
typical 15 years.?

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 HudsonAlpha Institute for Biotechnology -- 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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