The Language of the Trees

By Jerry W. Kram
Gerald Tuskan, a lead researcher at Oak Ridge National Laboratory, is teaching people how to "speak to the trees." He, along with hundreds of other researchers, is doing so by using the complete genome of Populus, also known as black cottonwood or poplar. Tuskan helped to lead a consortium of more than 250 scientists in 34 countries to publish the Populus genome in September 2006. In the little more than a year since the genome was published in Science, the poplar has been talking, and scientists have been listening.

One of the most basic questions that scientists have been trying to answer is: What makes a tree a tree? "We are learning a lot of things that make woody plants woody and perennial plants perennial," Tuskan says. "What we learn in poplar is the basics of cell wall development, which is really the basis for biomass power or liquid fuels for transportation. We can study these things directly in poplar, and then take that information and apply it to other species like eucalyptus, switchgrass or miscanthus."

A genome gives scientists a road map to the valuable and interesting traits in an organism. "The genome allows us access to the genes that control development and function of the organism," Tuskan says. "So if you have a phenotype or a trait you are interested in-whether it is hemicellulose in the cell wall, or its growth rate or disease resistance-you used to have to isolate the part of the genome where that trait was controlled. Then you would have to spend time trying to sequence the gene involved. Both of those processes would take years."

Once the genes are identified, researchers can then inhibit or "overexpress" them to see what impact that has on trees. Several of these studies could have profound impacts on the use of poplar in the biomass industry. Using a tool called a microarray, researchers can examine how thousands of genes are turned on and off as the poplar grows and experiences changes in the environment, Tuskan says. "So, instead of studying one gene or one enzyme, we are studying the entire organism," he says.

Some interesting discoveries have already been made. One ORNL research team led by Tongming Yin discovered the genes that determine whether a tree is male or female. This is important because male trees accumulate more biomass under stressed conditions, Tuskan says. "We could never isolate the biological mechanism that controls gender," he says. "We've been able to determine that chromosome 19 has a region that controls gender. Just from a biological point of view, this is a wonderful discovery, but from an applied point of view, it allows breeders and geneticists to select male and female genotypes when the seeds germinate."

Another ORNL study, led by Udaya Kalluri, has been looking at the plant hormone auxin, which among other things controls the amount of biomass that the trees accumulate above and below ground. A study of the dozens of genes that regulate auxin showed that reducing the activity of one of those genes made the trees add more biomass to their trunks. "So if you want a tree that is economically better, short and stout is better than tall and thin in terms of harvesting costs," Tuskan says. "We were able to do that in an amazingly short amount of time. If we had done this through conventional genetics, it would have taken five to 10 years to get this far."

In 2008, the U.S. DOE Bioenergy Science Center at ORNL will be using the genome to study poplar's recalcitrance, or the difficulty of extracting fermentable sugars from plant tissues with microbes or enzymes. "We've taken the whole genome microarray, the metabolic profile, the transcript profile, the DNA annotation sequence and assembly, and we are bringing all of those resources to bear on the issue of recalcitrance," Tuskan says.