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 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
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
"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
"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.
Patrick Schnable | EurekAlert!
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