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New genome sequence will aid study of important food, fuel crops

11.02.2010
A global initiative that includes key scientists from Oregon State University has successfully sequenced the genome of the wild grass Brachypodium distachyon, which will serve as a model to speed research on improved varieties of wheat, oats and barley, as well as switchgrass, a crop of major interest for biofuel production.

The advance was announced today in the journal Nature.

The primary international repository for the Brachypodium genome sequence data, called “BrachyBase,” is situated at OSU, and helps scientists around the world make important advances for human nutrition and new energy sources.

Brachypodium is actually a wild annual grass plant, native to the Mediterranean and Middle East, with little agricultural importance and is of no major economic value itself. But it allows researchers to obtain genetic information for grasses much more easily than some of its related, but larger and more complex counterparts with much larger genomes – plants which are hugely important in world nutrition.

“Some plants are a geneticist’s nightmare,” said Todd Mockler, a principal investigator on this project and assistant professor in the Department of Botany and Plant Pathology. “Wheat, for instance, is an important crop, but it has an enormous and complex genome five times larger than a human.

“Brachypodium is just the opposite of that,” added Mockler, who is a member of OSU’s Center for Genome Research and Biocomputing. “It has one of the smallest known genomes among grasses, it’s easy to work with and it is physically small. We can grow 50,000 plants in a normal-sized laboratory and do larger experiments. The plants are easy to grow, easy to genetically manipulate, easy to study and have a short lifecycle.

“And what we learn from Brachypodium will be of critical value in work with other plants of agronomic importance.”

A team of 12 OSU researchers led the transcriptome and small RNA sequencing on this project, which involved scientists from around the world, in work supported by the Joint Genome Institute of the U.S. Department of Energy. Other parts of the initiative were supported by the U.S. Department of Agriculture, and the work conducted at OSU was also funded in part by the OSU Computational and Genome Biology Initiative and the Oregon State Agricultural Research Foundation.

“We are launching Brachypodium with one of the most comprehensive genome annotations of any species, ever,” Mockler said. “This is a point that took us a decade or more to reach with other plant species, and that’s a reflection of some extraordinary new DNA sequencing technology available at OSU and elsewhere. It gives scientists a chance to move quickly ahead with genetic advances.”

Development of new genomic technologies for plants like Brachypodium has been a major focus of scientists at OSU.

“What this work provides is a highly informative roadmap to explore and improve plants of great agricultural value, like wheat,” said James Carrington, director of the Center for Genome Research and Biocomputing, and a co-author of the study. “The quality of science that can be done with plants like Brachypodium is really exceptional.”

Much of the early funding support was from the Department of Energy, Mockler said, which wants to develop better feedstocks for production of cellulosic ethanol – essentially, fuel from non-food plant material, as opposed to food crops such as corn. It’s widely believed that a grass plant called switchgrass may work well for this, but it’s never been domesticated – the evolution of switchgrass as a crop is now at the stage that corn, for instance, was about 10,000 years ago, before generations of selective breeding produced improved crops. Genetic modification may be able to produce switchgrass that could grow taller, faster, and have cell walls that are easier to break down, or lead to plants that better resist drought or disease.

“Beyond that, however, there may also be opportunities to improve food crops,” Mockler said. “This is the first sequenced plant genome that is closely related to temperate cereals such as wheat and oats, which are important food crops around the world.”

The “cool season” cereal, forage and turf grasses, of which Brachypodium is a member, are part of the Pooideae subfamily, and the last of three important subfamilies of grasses to have one of their genomes sequenced. The other important grass groups that, combined, provide the bulk of human nutrition are Ehrhartoideae, which includes rice; and Panicoideae, with includes corn, sorghum, sugarcane and other grass crops. With more than 3,000 species, the Pooideae is the largest grass subfamily. Some early work has already been done, now that the Brachypodium genome has been sequenced, to compare the traits of these three major grass subfamilies.

Brachypodium seeds have been shared with more than 300 laboratories in 25 countries, and the genome information is now freely available to any researcher in the world.

The similarities in gene content and gene family structure between Brachypodium, rice and sorghum supports the value of Brachypodium as a functional genomics model for all grasses,” the researchers wrote in their study. “The Brachypodium genome sequence analysis reported here is therefore an important advance towards securing sustainable supplies of food, feed and fuel from new generations of grass crops.”

About the OSU College of Science: As one of the largest academic units at OSU, the College of Science has 14 departments and programs, 13 pre-professional programs, and provides the basic science courses essential to the education of every OSU student. Its faculty are international leaders in scientific research.

Todd Mockler | EurekAlert!
Further information:
http://www.oregonstate.edu

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