Walnut Creek, California
December 9, 2008
Data released to advance
biofuel, food, & feed research
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
http://www.phytozome.net/soybean.
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 DOE 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, Calif., Production Genomics Facility
provides integrated high-throughput sequencing and computational
analysis that enable systems-based scientific approaches to
these challenges. Additional information about DOE JGI can be
found at:
http://www.jgi.doe.gov/.
Source:
ArgenBio
Completan la secuencia del genoma de la
soja
El Instituto de Genómica del Departamento de Energía de Estados
Unidos (DOE-JGI) acaba de hacer público el borrador completo del
genoma de la soja (Glycine max). Esta información, permitirá
acelerar los programas de mejoramiento de uno de los cultivos
más importantes del mundo.
La soja no sólo constituye el 70% de la proteína comestible del
mundo, sino que también es una de las materias primas más
promisorias para la producción de biodiesel. Justamente por eso
el DOE JGI se propuso secuenciar el genoma de este cultivo. “La
secuenciación del genoma de la soja es el resultado directo de
un memorando de entendimiento entre los Departamentos de Energía
(DOE) y de Agricultura (USDA) de Estados Unidos para aumentar la
colaboración entre estas agencias en genómica de plantas”,
señaló el Subsecretario para Ciencias del DOE, Raymond L.
Orbach. "Estamos orgullosos de apoyar este adelanto científico
que no sólo es un avance para nuestro conocimiento sino también
una herramienta clave para la agricultura y para la producción
de biodiesel”, agregó. Según el Subsecretario para la
Investigación, Educación y Economía de la USDA, Gale A.
Buchanan, “con estos nuevos conocimientos, los científicos de
todo el mundo podrán trabajar en el mejoramiento de
características importantes para la soja". Los investigadores
involucrados en el proyecto comenzaron a analizar el genoma de
la soja, que tiene aproximadamente mil millones de nucleótidos
(un tercio del genoma humano). Los estudios preliminares
sugieren que contiene 66.000 genes, más del doble de los que hay
en el genoma humano, y casi un 50% más que el número de genes
del álamo, secuenciado por el DOE JGI y publicado en la revista
Science en 2006. Para los productores de soja es muy importante
que esta información esté disponible para todo el mundo. Rick
Stern, productor de New Jersey y Director del Programa de
Investigación para la Producción del United Soybean Board (USB),
agregó: “Ahora cada fitomejorador podrá buscar información en
esta valiosísima biblioteca para acelerar los procesos de
mejoramiento. Es probable que con estas herramientas se acorten
los tiempos a la mitad”.
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