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ENERGY DEPARTMENT Joint Genome Institute director Eddy Rubin (left) and public affairs manager David Gilbert plant a poplar sapling on the front lawn of the Institute Thursday. (JOSE CARLOSFAJARDO - MediaNews)
For the first time, scientists have decrypted the DNA for a tree — a black cottonwood on the banks of a Pacific Northwest salmon river — and discovered a genetic richness useful for squeezing more woody growth out of all trees, and possibly more gallons of fuel for cars and trucks.

Researchers from seven nations revealed the draft genetic recipe of the first tree in Thursday's edition of the journal Science and said genes for its basic functions supply the ingredients for life, not only in cottonwoods, aspens and poplars, but also in all other trees.

In celebration, scientists planted a poplar sapling Thursday at the Joint Genome Institute in Walnut Creek, where banks of DNA sequencers and computers broke the tree's genetic code. Gerald Tuskan, a leading poplar researcher at Oak Ridge National Laboratory, said poplar holds clues to the essential biology of trees, such as making woody fibers preserved over hundreds of millions of years of evolution.

By breeding or modifying genes for growth or different cell makeup, timber species could produce more and straighter boards. Trees for paper could produce longer fibers, and plantations of energy trees could turn out more gallons of ethanol fuel per acre.

"We're pretty sure the information we get from poplar can be transferred to other trees," said University of British Colombia botany professor Carl Douglas.


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The cottonwood, a member of the large poplar genus, was chosen because poplars have a smaller amount of DNA than most trees, can easily sprout clones — bury a cut stem and a clone will grow — and grow fairly quickly, ideal for tree genetics studies.

"It's a very nice sort of guinea pig for researchers," said University of Florida plant biologist John Davis. "It's very nice to have the same tree and use it year after year after year."

The same factors have made poplar a choice feedstock for producing ethanol fuel, and the only such bioenergy crop so far targeted for the Pacific Northwest and Central Valley in California.

What scientists had not expected to find was such great genetic diversity among individual trees. Two poplars arching over an avenue might look almost identical, but if not grown from the same parent they would be more genetically different than two human beings living across the same street, Tuskan said, lead author on the study of the poplar genome.

"There's a lot of variation from individual to individual and even within individuals," he said.

Poplars are 60 million years old and so have had a lot of time for mutations to build up, far more than Homo sapiens. The trees have a sixth as much DNA as humans but twice as many genes, about 45,000.

For now, an acre of wild poplars grows about two tons of dried plant mass each year. Poplar plantations that supply pulp and paper to industry can get 8 to 10 tons. The U.S. Department of Energy's goal for Tuskan and colleagues is to double that biomass production within 10 to 15 years.

"Now we have a handle on the genes that control those traits," said Davis. "This is a parts list, and now we're looking at hundreds, not tens of thousands" of genes keying for the desired traits.

Scientists can raise or lower the expression of those genes by the dozens and see what happens to the plant to hone in on genes for selective breeding or modification. "Instead of just crossing that good-looking tree with this good-looking tree and hoping for the right seedlings, you can know ahead of time that if you cross this tree and that tree, you can get the genes you're after," Davis said.

But with one proposal already for a United Nations ban on commercial growth of transgenic energy plants and trees, scientists are debating what kinds of genetic modifications pose a risk to the wild and the effectiveness of methods for gene containment, such as by sterilizing the tree or harvesting it before the tree flowers.

Altering genes for the type or amount of lignin in a plant so that it breaks down more easily probably would be an evolutionary disadvantage for the plant, so the risks of spreading such modified genes in the wild are expected to be low. But other changes could pose greater risks, said Douglas at the University of British Columbia, who worked on the poplar genome study.

"It could be that a tree that grows much faster would have the ability to crowd out other trees and reproduce more successfully," he said.

Sterilization and other strategies for gene containment can minimize those risks, but "no one can be able to claim that their containment is 100 percent."

Scientists know the approximate functions for about half of those genes because similar genetic code exists in the DNA of plants and animals already sequenced. Computer analysis suggests the other half possess very gene-like characteristics but their function is unknown.

For reasons as yet unclear, poplars and their evolutionary ancestors are full of gene duplications, as if a child kept copies of all parental genes, three times over. One duplication, dated roughly 120 million years ago, is still evident in almost 60 percent of the cottonwood's genes, the scientists reported.

"So it doubled, doubled again and then doubled a third time, so for any one gene you may have eight copies," Tuskan said. "But in fact natural selection has operated in that period, and some genes have disappeared, some have degenerated into non-coding sequence and some have taken on new functions, usually associated with differences in tissue and developmental expression."

These doublings are fairly common in plants — wheat has multiple copies of genes — and are thought to provide the raw material for evolution.

Poplars have seen a recent explosion in genes for resisting disease and insect attack, something that scientists believe is tied to evolutionary pressure in the last few tens of thousands of years from rapidly mutating germs and bugs on a tree with a long life.

Poplars also have about eight times as many genes as a common weed for making lignin, a substance that stiffens plant cell walls and resists degradation.

"It was a pleasant and positive surprise, the level of diversity in this genome," said the University of Florida's Davis. "What it does is create this tool kit where we can go in and create even greater levels of genetic diversity for genes that matter" in the production of ethanol.

Leading targets are genes that enhance stem growth and disease resistance, while making lignin either easier to break down or reducing its content in the trees' cell walls, where it interferes with converting plant materials into sugars that can be fermented into ethanol.

"Both of those approaches look very promising," said Tuskan. "We will be able to change cell wall chemistry, and we will be able to change harvestable yield."