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By Phil Williams
pwilliam@franklin.uga.edu
The National Science Foundation has awarded $3.4 million to a team led by a UGA botany  professor which will study the role of transposable elements in rice.
The research could lead to new understanding of the world’s number-one crop. More than three billion people around the globe depend on rice as their major staple.
Transposable elements are mobile fragments of DNA that can move from one chromosomal location to another, increasing their contribution to the whole genome until they can account for the majority of the genomic DNA. For years, scientists thought that these elements were “junk” and had no real function in the genomes of plants or animals. That view has dramatically changed in the past few decades, however, and transposable elements are now suspected by many scientists of having major roles in evolution, structure and function.
“Most plants have very large genomes because they contain huge amounts of transposable elements,” says Susan Wessler, Research Professor of Botany and Genetics at UGA and a principal investigator on the NSF grant. “We believe that understanding how these elements function in rice will give us a new perspective on their role in evolution.”
 Co-principal investigators on the five-year project are John McDonald of the UGA genetics department, Susan McCouch from Cornell University and Sean Eddy of the Washington University School of Medicine in St. Louis.
Considerable work has already been done in understanding the rice genome. The Genomics Institute at Clemson University is, in fact, one of the world centers for sequencing and studying the rice genome. Transposable elements make up an estimated 30 percent of the plant’s genome. Geneticists have been making progress understanding transposable elements for some years, but most of the work has been done in plants like maize, where transposable elements were originally discovered.
“What distinguishes transposable elements from the genetic complement of an organism, among other things, is an ability to transpose and amplify,” says Wessler, who is a member of the National Academy of Science. “They shake up an otherwise conservative genome and, in this way, both threaten and enhance genomic potential.”
Rice is a logical next step for scientists studying transposable elements. Although wheat is a more important crop in the United States, the genome of rice is only a fraction the size of wheat’s, making it much easier to study.
The team’s first step will be to identify all the transposable elements in the rice genome. They will then develop them as molecular markers to see if any of them are biologically active and contribute to genome diversity.
Transposable elements may provide a way to diversify the genome in response to environmental changes.
Rice, corn, barley, wheat and sorghum are all grasses, and each species exists in numerous varieties bred over the centuries by farmers and scientists. The mechanisms behind all this genetic diversity are poorly understood, however, and transposable elements may play a major role in many of the plants’ differences, such as size.
“The genomes of the grasses are extremely diverse, due in large part to the activity of transposable elements,” says Wessler. “What we need to know is whether this diversity has functional consequences. If successful, this project will go a long way toward answering that question.”
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