Wild Grass Genome Sequenced

While scientists and engineers around the world continue to work on complex technological solutions to the food and energy crises, like solar panels and drought management, one team of researchers has turned back to the basics of plant biology.

The International Brachypodium Initiative, based at Oregon State University, recently completed the DNA sequence for the wild grass Bracypodium distachyon. The new data, published in the February 11 issue of Nature, is expected to serve as an important aid in developing better biofuels from wild grasses and improving food crops from the wheat family. Of the three major food crops, wheat is the only one that has yet to be sequenced; the maize and rice genomes were completed in the past two years.

With the completion of the DNA sequence, Brachypodium can now serve as a “model system” for wheat and other grasses. Biologists use model systems to study similar organisms that are too complex or difficult to work with directly. By using Brachypodium, researchers will be able to more efficiently sequence other plant genomes, including wheat. Once they know the full genome sequence, they can more easily manipulate specific genes to make the plants grow more favorably for energy and food production.

The plant genus Arabidopsis, which is related to broccoli and canola, has served as a primary model system for plant biologists for the past few years.* Yet it’s not useful for studying cereal and grass crops, like wheat and switchgrass, due to genetic dissimilarities. Brachypodium, on the other hand, has key genetic similarities with these types of plants, making it a strong candidate for a model system. The Brachypodium genomic information is now available to researchers across the globe in a database titled “BrachyBase” (www.brachybase.org).

“Brachypodium is going public with a genomic quality and knowledge of its genes that is unprecedented in other plants,” said Todd Mockler, a principal investigator of the study and a botanist at Oregon State University. “It is a hypothesis-generating tool that will facilitate researchers taking the next step.”

Mockler and his colleagues targeted Brachypodium because of its small size and genomic simplicity. Standing at around eight inches tall at maturity, Brachypodium is much more suited for study in the lab than wild grasses like switchgrass, which can grow up to ten feet tall. Its genome is also relatively small and simple, consisting of only 270 million base pairs. The wheat genome, by comparison, contains 16 billion base pairs, 59 times more than the Brachypodium genome, and five times more than the human genome. So while Brachypodium holds little agricultural significance or economic value, it makes for a viable aid for studying plants that do hold such value.

While Mockler focused on sequencing the Brachypodium genome, other members of the initiative have worked on applications for the new findings. David Garvin, a U.S. Department of Agriculture research geneticist based at the University of Minnesota who also was a principal investigator in the study, is using the grass genome to study characteristics of food crops, primarily disease resistance in wheat. In 2007, a new strain of stem rust, a deadly plant disease, spread throughout the Middle East. Garvin plans to use the Brachypodium sequence to figure out which genes in wheat can be manipulated to resist stem rust, in hopes of protecting these food crops for the millions of people who depend on them.

Brachypodium is also important in studying alternative energy sources because of its genetic similarity to switchgrass, a promising fuel crop, according to John Vogel, a molecular biologist at the U.S. Department of Agriculture Research, who was also involved with the sequencing study.

With its large size and ability to grow in various soil and climate conditions, switchgrass has strong potential as a biofuel feedstock crop. For example, it could be used to make cellulosic ethanol, a potential alternative to gasoline. This can be accomplished by breaking down cellulose-rich cell walls in the plant—a process that Vogel hopes to speed up by using the Brachypodium genome to pinpoint genes that, when manipulated, will weaken those cell walls.

As research into food and energy production continues, the newly completed Brachypodium sequence will serve as a guide to manipulate crops and optimize their potential. Sharlene Weatherwax, director of the Biological Systems Science Division at the U.S. Department of Energy, which funded part of the study, explained that that the key to accomplishing that goal is to understand the biology of the plants of interest.

“You want a pilot to lead this type of search,” she said. “Brachypodium serves as a pilot for looking further into wild grasses and cereals.”

*Correction (April 26, 2010): This sentence originally read “The plant genus Arabidopsis, which includes broccoli and canola…” Arabidopsis does not include broccoli and canola, it is related to both plants under the plant family, Brassicaceae.