Ames, Iowa
February 25, 2008
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Iowa
State University's Patrick Schnable, left, and Srinivas
Aluru contributed their expertise in corn genetics and
supercomputing to a $32 million, three-year project to
assemble the corn genome sequence. They discovered
several hundred new corn genes not found in other plants
and identified almost 100 genes which have nearly
identical copies in the genome. Photo by Bob Elbert. |
Iowa State University researchers helped write the first
draft of the corn genome sequence that will be announced
Thursday, Feb. 28, at the 50th Annual Maize Genetics Conference
in Washington, D.C.
Patrick Schnable, a Baker Professor of Agronomy and director of
the Center for Plant Genomics and the Center for Carbon
Capturing Crops, and Srinivas Aluru, a Stanley Chair in
Interdisciplinary Engineering and a Professor of Electrical and
Computer Engineering, led the work at Iowa State and provided
the project with expertise in corn genomics and supercomputing.
(Iowa State researchers and their U.S. Department of Agriculture
collaborators also developed the B73 inbred corn line that was
sequenced by the genome project. Developed decades ago, the B73
line is noted for the high grain yields it contributes to
hybrids. Derivatives of B73 are still widely used to produce
many commercial hybrids.)
"We are proud that Iowa State University researchers have
contributed to this draft sequence of the corn genome," said
Gregory Geoffroy, Iowa State's president. "Understanding the
corn genome will accelerate efforts to develop crops that can
meet society's growing needs for food, feed, fiber and fuel.
This project is also a wonderful example of how Iowa State
researchers are able to work across disciplines to solve
problems important to Iowa and the world."
The announcement
The overall genome project is led by Richard Wilson, the
director of the Genome Sequencing Center at the Washington
University School of Medicine in St. Louis. He will make a brief
announcement about the sequencing project and researchers will
take questions during a news conference at 12:30 p.m. Thursday,
Feb. 28, in the Hoover Room of the Marriott Wardman Park Hotel
in downtown Washington. Wilson will also make remarks about the
draft genome during a reception from 6:30-8 p.m. Thursday at the
Smithsonian Institution's National Museum of Natural History on
the National Mall. And Wilson will present a scientific talk
about the draft genome at 8:35 p.m. Friday, Feb. 29, back at the
Marriott Wardman Park Hotel. Wilson's talk will describe the
draft corn genome, explain the work needed to produce it and
look ahead to the research that needs to be done to improve it.
The genome project also includes researchers at the University
of Arizona in Tucson and the Cold Spring Harbor Laboratory in
New York. The $32 million, three-year research project is
supported by the National Science Foundation, the U.S.
Department of Agriculture and the U.S. Department of Energy.
The Iowa State science
Schnable and Aluru led Iowa State's work to refine assemblies of
the genomic sequences generated by researchers at Washington
University. In addition, they identified almost 100 genes which
have nearly identical copies in the genome. Schnable said these
nearly identical paralogs may have played important roles during
the evolution and domestication of corn and may have contributed
to the ability of breeders to mold this important crop species
to meet human needs. The Schnable and Aluru teams also
discovered several hundred new corn genes that are not present
in other plants. Some of these genes may be responsible for
unique attributes of corn.
The corn genome is an especially difficult jigsaw puzzle to put
together, Schnable said. There are some 2.5 billion base pairs
that make up the double helix of corn DNA. The corn genome also
has long lines of repetitive code. And corn has 50,000 to 60,000
genes to identify and characterize. That's about twice the
number of genes in humans. Plus, 50 percent or more of the corn
genome is made up of transposons or jumping genes. Those are
pieces of DNA that can move around the genome and change the
function of genes.
Solving all those assembly challenges took a lot of computing
power and some new software technology. Aluru and his research
team developed software called "PaCE" and "LTR_par" that runs on
parallel computers -- including CyBlue, Iowa State's IBM Blue
Gene/L supercomputer capable of 5.7 trillion calculations per
second. PaCE can generate draft genome assemblies in hours or
days instead of months. LTR_par identifies retrotransposons,
another mobile genetic element that can cause genome changes
such as mutations, gene duplications and chromosome
rearrangements.
The implications
Schnable said the resulting draft of the corn genome provides
plant scientists with a lot of data to work with. He said it's a
lot like the collection of maps, diary entries, dried plants and
animal specimens brought back by the Lewis and Clark expedition
to the Pacific. The explorers gathered and assembled a great
deal of basic information about the Louisiana Purchase that
required years of subsequent analysis and study.
"This will enable so much exciting corn research," Schnable
said. "This will raise questions about the biology of corn and
provide great tools to answer them."
Those answers could help scientists modify and improve corn
plants, Schnable said. The genome, for example, could help
scientists:
- develop crops that can
withstand global climate change
- add nutritional value to grain
- sequester more atmospheric carbon in agricultural soils
- or boost yields so crops can meet growing demands for
food, feed, fiber and fuel.
"In addition, what we learn from
the corn genome will allow us to better understand other
grasses," Schnable said.
The genome of corn is very similar to the genomes of rice,
wheat, sorghum, prairie grasses and turf grasses. Therefore,
Schnable said the draft of the corn genome can help researchers
improve the other cereals and grasses.
In addition to advancing our understanding of corn, the genome
project has helped Iowa State launch several academic careers.
As graduate students, Scott Emrich, Ananth Kalyanaraman and
Sang-Duck Seo worked on the corn genome project. Emrich is now
an assistant professor of computer science and engineering at
the University of Notre Dame in Notre Dame, Ind.; Kalyanaraman
is an assistant professor of electrical engineering and computer
science at Washington State University in Pullman; and Seo is an
assistant professor of art at the University of Nevada, Las
Vegas.
And so, Schnable said, the corn genome project has already been
very useful. As researchers turn the first draft into new
chapters describing their discoveries, he said it will be even
more important to researchers and society. |
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