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December 9, 2008 — 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
"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
"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
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.
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
"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 soybean genome sequence information can be browsed at http://www.phytozome.net/soybean.
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