Walnut Creek, California
January 28, 2009
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The robust growth
habit of sorghum is seen here with rice in the
foreground. Credit: C. Thomas Hash, ICRISAT |
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Scientists at the U.S. Department
of Energy (DOE) Joint Genome
Institute (JGI) and several partner institutions have
published the sequence and analysis of the complete genome of
sorghum, a major food and fodder plant with high potential as a
bioenergy crop. The genome data will aid scientists in
optimizing sorghum and other crops not only for food and fodder
use, but also for biofuels production. The comparative analysis
of the sorghum genome appears in the January 29 edition of the
journal Nature.
Prized for its drought resistance and high productivity, sorghum
is currently the second most prevalent biofuels crop in the
United States, behind corn. Grain sorghum produces the same
amount of ethanol per bushel as corn while utilizing one-third
less water. As the technology for producing "cellulosic" (whole
plant fiber-based) biofuels matures, sorghum's rapid
growth--rising from eight to 15 feet tall in one season--is
likely to make it desirable as a cellulosic biofuels
"feedstock."
"This is an important step on the road to the development of
cost-effective biofuels made from nonfood plant fiber," said
Anna C. Palmisano, DOE Associate Director of Science for
Biological and Environmental Research. "Sorghum is an excellent
candidate for biofuels production, with its ability to withstand
drought and prosper on more marginal land. The fully sequenced
genome will be an indispensable tool for researchers seeking to
develop plant variants that maximize these benefits."
Plant DNA is often notoriously difficult to analyze because of
large sections of repetitive sequence and sorghum was no
different. Jeremy Schmutz of the DOE JGI partner HudsonAlpha
Institute for Biotechnology (formerly the Stanford Human Genome
Center) and John Bowers of the University of Georgia pointed to
these complex repetitive regions as accounting for the
significant size difference between the rice and sorghum
genomes, while also suggesting a common overall genome structure
for grasses.
"Sorghum will serve as a template genome to which the code of
the other important biofuel feedstock grass
genomes--switchgrass, Miscanthus, and sugarcane--will be
compared," said Andrew Paterson, the publication's first author
and Director of the Plant Genome Mapping Laboratory, University
of Georgia.
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The robust growth
habit of sorghum is seen here with rice in the
foreground. Credit: C. Thomas Hash, ICRISAT |
|
Scientists and industry officials
say that completion of the sorghum genome will aid with
sequencing of numerous other related plants, including other key
potential bioenergy crops.
"I expect our improved understanding of the sorghum genome to
have a major impact on the development of improved bioenergy
crops for the emerging biofuels and renewable power industries,"
said Neal Gutterson, President and Chief Executive Officer of
Mendel Biotechnology.
Sorghum's is only the second grass genome to be completely
sequenced to date, after rice. With approximately 730 million
nucleotides, sorghum's genome is nearly 75 percent larger than
the size of rice.
Researchers used the whole genome "shotgun" method of sequencing
first pioneered in the Human Genome Project. In this method,
short random DNA fragments are partially sequenced and then
analyzed by powerful supercomputers to reconstruct the original
genome sequence. The repetitive sections and the length of the
sorghum genome made assembling this "puzzle" a highly
challenging computational problem.
By comparing sorghum's assembled code with rice's, the
scientists were able to provide a "reality check" for rice's
previously published estimate of protein coding genes.
"We found that over 10,000 proposed rice genes are actually just
fragments," said DOE JGI's Dan Rokhsar, the publication's
co-corresponding author. "We are confident now that rice's gene
count is similar to sorghum's at 30,000, typical of grasses."
Other major contributions to the sorghum project were made by
the research groups of Joachim Messing of Rutgers University,
Therese Mitros of the University of California, Berkeley, and
Klaus Mayer of the Helmholtz Center in Munich.
The sorghum sequencing project was initiated in 2005 under the
auspices of DOE JGI's Community Sequencing Program (CSP), funded
by the Office of Biological and Environmental Research within
the DOE Office of Science. The CSP was launched in 2004 to
provide the scientific community at large with access to
high-throughput sequencing at the DOE JGI Production Genomics
Facility for larger projects of relevance to DOE missions.
Sequencing project selection is based on scientific
merit--judged through independent peer review--and relevance to
issues in alternative energy production, global carbon cycling,
and biogeochemistry. Information about the CSP's latest call for
proposals can be found at:
http://www.jgi.doe.gov/CSP/user_guide/index.html
This and other DOE JGI projects will be highlighted at the
Institute's upcoming Fourth Annual User Meeting, March 25-27 (http://www.jgi.doe.gov/meetings/usermtg09/index.html).
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/.
New Brunswick, New Jersey
January 28, 2009
Sequencing of sorghum genome completed
Drought-resistant food, feed and biofuel source sequenced by
international team
Source:
Rutgers University
In a paper published in the journal Nature
this week, Rutgers researchers Joachim Messing, Rémy Bruggmann,
and a team of international collaborators have described the
genome of sorghum, a drought-tolerant African grass. The
findings could one day help researchers to produce better food
crops for arid regions with rapidly expanding human populations,
such as West Africa.
Messing, director of the Waksman Institute of Microbiology at
Rutgers, The State University of New Jersey, has been deeply
involved in both the rice genome and maize (corn) genome
sequencing projects. In 1982, he developed the modified shotgun
sequencing approach used in the sorghum sequencing that
represents a significant advance in methodology.
This approach takes into account the highly repetitive nature of
large genomes including many plant species and the human genome.
By using paired sequence reads instead of single sequence reads,
the scientists can jump over repeat sequences, constituting
about 62% in sorghum, and produce an accurate and contiguous
picture of the entire sorghum genome.
"I was very pleased that our earlier DNA sequencing concept has
worked so well with an important genome like sorghum," Messing
said. "The efficiency and utility of this method will make it
faster and far less expensive to sequence other complex genomes
in the future."
The investigators chose sorghum, which is in the same family
(grasses) as maize, rice and wheat, because of its importance
for civilization. "We are interested in it for food and animal
feed, and more recently as the basis of a biofuel," Messing
said.
In the United States, sorghum is mainly used as feed and it is
grown in the south because it tolerates drought. One variety,
known as grain sorghum, is a food staple in places such as
Africa and India. According to Daniel G. Peterson, another of
the paper's senior authors, sorghum is higher in protein and
lower in fat content than maize and is close to maize in
nutritional content. Its resistance to heat and water stress
allow it to be grown in regions where corn or other grain crops
cannot compete.
Another variety – sweet sorghum – has a sweet stem and is thus
similar to sugar cane. The Food and Agriculture Organization of
the United Nations has introduced sweet sorghum in China because
of the country's interest in having a biofuel crop and its
ability to grow in areas where corn would not. Brazil's
extensive biofuel economy is based on sugar cane and is regarded
as the most productive biofuel crop in the world. Sweet sorghum
rivals sugar cane for this application and sorghum is superior
to corn as a biofuel since the entire plant may be used, not
just the grain – the kernels of corn.
"We now will have a better idea of how many properties of the
grasses, such as drought resistance, sugar in the stem, or grain
productivity are encrypted in their genes," Messing said.
"Knowing this may enable us to laterally move these genes around
among these crop species, to customize them based on the needs
of geographic location and climate."
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