Knowing poplar's DNA is expected to yield biofuel advances and more

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The genetic makeup of the poplar or black cottonwood tree is spelled out with 480 million letters arranged in 7.5 million groups.

And what it spells is "biofuel."

David Gilbert, Department of Energy Joint Genome Institute
Researchers studied the Populus genome, which is shared by these hybrid poplars in Washington State.
Click photo for larger image.

The U.S. Department of Energy's Joint Genome Institute in Walnut Creek, Calif., has succeeded in sequencing the genome -- the hereditary information encoded in an organism's DNA -- with help from a West Virginia University biologist.

DOE undertook the project to complete the first sequence of a tree genome with the goal of enhancing the production of biofuels. The project involved 108 co-authors from 34 institutions in eight countries.

Stephen DiFazio, a WVU assistant professor of biology, said sequencing of the poplar tree brings insight into the makeup of the broad-leaf hardwood and a better understanding of all trees.

With the sequencing project completed, it's now time to watch the results branch out.

David Gilbert, JGI's manager of public affairs, said the project will help optimize ethanol production from cellulose that makes up the tree cells and lead to domestic growth of trees as an efficient means of producing ethanol.

"Within five years, you will see more emphasis on the plantation approach for development of woody crops for ethanol," Mr. Gilbert said.

The genome also will make it possible to genetically engineer trees to produce more cellulose and less lignin -- the glue that holds cellulose together.

Such engineered trees, Dr. DiFazio predicted, might look something like "a Dr. Seuss tree" with a short, stout trunk and a green tufts of leaves on top. These fast-growing trees would be grown on plantations, with an effort to keep them apart from wild trees.

"I think this is nothing short of revolutionary," Dr. DiFazio said. "We now have the entire complement of genes ready for the taking. People have the tools in hand to look for different functions and to tailor trees for different purposes.

"This is an opportunity for new discoveries in trees," he said. "In fact, we are able to do things now we couldn't do before the gene sequence became available."

Maud Hinchee, chief scientist at Arborgen, a Summerville, S.C., company that does research, development and commercialization of genetic technology to help sustain forests, said the genome project has even wider application.

"The sequencing of the [poplar tree] enables researchers to better understand how to grow trees for all applications including pulp and paper, wood products and the biofuels industry," she said.

Ms. Hinchee said wood products grown as "a dedicated energy crop" will help to support DOE's goal to have biofuels represent 30 percent of U.S. transportation fuels by 2030.

The DOE chose the poplar because of its compact genome that's one-sixth the size of the human genome and one-fortieth that of the pine genome, said Dr. DiFazio, who served as a staff scientist at DOE's Oak Ridge National Laboratory in Tennessee before taking the position at WVU.

He spent two years working almost full time on the project and is listed as second co-author. He said the project was worth the effort.

"This was the biggest and most complex genome project the DOE has ever tackled," he said. "We learned a lot of lessons that can be applied to other genome projects."

Mr. Gilbert said the DOE will turn attention to sequencing the genome of other biofuel plants including switch grass, sorghum, casaba and soybeans.

Sequencing a genome is tedious work. The DNA is cut into small segments then entered into sequencing equipment that identifies their makeup, letter by letter. Once the groups of letters are determined, the process becomes one of building "a gigantic puzzle with 7.5 million pieces," Dr. DiFazio said.

Those pieces then were assembled to determine the makeup of the tree's 45,000 genes, which in turn were put in proper order to reflect the architecture of the tree's 19 chromosomes.

Now researchers can focus on figuring the function of each of the 45,000 genes.

"Genes related to cellulose synthesis already are identified -- we have the genes and the sequencing -- but we don't yet know how all the genes work together to produce cellulose," Dr. DiFazio said.

Genetically engineered trees must be grown on farms or plantations. But Dr. DiFazio said the tree crop will mimic the corn crop -- plants that no longer resemble the original version of the plant.

Trees, like corn, would be developed to maximize their value to humans.

For now, it is not economical to raise trees as a crop. But if trees produced abundant cellulose quickly, they could become a crop. But care must be taken to analyze the impact of genetic-engineered trees and keep them isolated to protect forests, Dr. DiFazio said.

Once the role of each gene is determined, Dr. DiFazio said, trees can be developed to function in ways important to people and the environment.

He said trees can be engineered to remove carbon from the atmosphere and store it in a binding form in roots and soil. Such trees could be used in reducing the greenhouse effect and global warming.

Trees also can be engineered to help clean up the environment by removing heavy metals and other contaminants from soil and groundwater at places including abandoned mine sites.

With the genome in hand, scientists also can develop trees requiring fewer herbicides and insecticides. Such projects have been underway, but the genome sequencing should expedite that research, Dr. DiFazio said.

He received his master's degree in ecology and doctoral degree in forest genetics at Oregon State University.

Dr. DiFazio's role involved processing the genome and figuring out how it fit together, then matching the sequence to determine the makeup of the tree's 19 chromosomes.

One of the major findings during the sequencing process was the similarity in the genome of trees and smaller weedy plants. Dr. DiFazio said subsequent projects could include the sequencing the genome of the eucalyptus or peach tree.

"The toughest part of this project was completing the catalog of genes," Dr. DiFazio said. "Now we can figure out their functions.

"People will be working on this for the foreseeable future."

Dr. Stephen DiFazio: "This is nothing short of revolutionary."
Click photo for larger image.

David Templeton can be reached at dtempleton@post-gazette.com or 412-263-1578.


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