CORVALLIS, Ore. - Researchers in Sweden and the United States have publicly released a new database of many of the most important genes in a tree genome. This collection of genes, which includes a large proportion of those expressed during tree growth, is among the best for any plant species.
"This is an important fundamental step towards doing the type of genetic and biotechnology research with trees that we've been able to do with only the most scientifically well-known plants," said Steven Strauss, a professor of forest science at Oregon State University.
Strauss is one of the co-authors on a paper that was just published on this advance in a professional journal, Proceedings of the National Academy of Sciences.
"There's still an enormous amount we don't know about the genetic function of trees at the most basic levels," Strauss said. "But advances such as this will narrow the gap between the scientific research we can undertake with trees and the studies that are possible with traditional model plant species, such as rice, corn, and Arabidopsis - a tiny plant in the mustard family that is the lab rat for all plants."
The database just announced, which was produced by a research group in Sweden with collaboration by researchers at OSU, describes about 102,000 sequences of the most commonly expressed genes in the genus "Populus," which includes cottonwoods and aspens. In living organisms, the genes which are "expressed" are only a fraction of the total DNA in cells. But they are most important to determining an animal or plant's function - in the case of a tree, forming its bark, leaves, roots and wood, and enabling it to respond to environmental stresses.
The study also compared many of these gene sequences to those found in Arabidopsis, and found that nearly all the genes were functionally common between the two, even though they have been separated by about 100 million years of evolution and look completely different. Arabidopsis is the most frequently used plant in the world for basic genetic research on plant structure and function, and being able to compare its genetics to those of a tree will greatly speed genetic research with trees, Strauss said.
It also indicates that the large majority of transfers of genes between widely separated plant species via genetic engineering would not produce novel characteristics, but simply modify existing genetic characteristics, he said.
Just as Arabidopsis is the most commonly studied plant in the world with respect to molecular genetics, poplar is the most commonly studied tree, Strauss said.
Trees, which are among the most ancient of plant life forms, also have a very complex genetic makeup that so far has resisted many of the traditional genetic research techniques that are used with other plants which have short life cycles.
Knowing so many genes in a tree, and being able to modify them easily in poplars with asexual biotechnology methods such as gene transfer, provides a tremendous advance for basic research in trees. Even if regulations continue to present strong obstacles to use of gene transfer methods for commercial purposes, it can still be used to learn a great deal about tree biology, Strauss said.
The new study, along with advances that are expected soon to describe the entire Populus genome DNA sequence, will help scientists find specific genes in a matter of minutes using computational approaches. Such discoveries would have taken decades or centuries prior to these databases, Strauss said.
"Once you know a lot of gene sequences and can study thousands of genes at a time, you can start to really explore how trees might respond on a basic genetic level to such stresses as drought, exposure to cold, and pest attack," Strauss said.
Using the expression of thousands of genes as "metabolic fingerprints," a method that is becoming routine with the advent of gene chips, researchers can also make major strides in understanding the physiological changes that take place as trees age, Strauss said.
"Do very old trees effectively oxidize over time, like humans do?" he said. "Or can they renew their cellular integrity continuously despite living for centuries to millennia? These are the kinds of questions we can start to ask and answer, in ways that we never could before."
Ultimately, the researchers believe that a more comprehensive understanding of tree genetics should allow controlled gene transfer, both as a research and biotechnology tool. It could take the type of conventional plant breeding that has been done with trees for centuries but control the process more scientifically, modifying the expression of specific natural or native genes for desired purposes.
For example, the structure and chemical makeup of trees could be modified for a variety of uses: bioremediation to eliminate pollutants from soil, or the production of renewable feedstocks for bioenergy and fiber products, including paper and chemicals. This process, where only native gene functions are modified, is quite different from transferring novel proteins across vastly different kinds of species, which is a large part of the unease about the use of genetically engineered crops in agriculture, Strauss said.
The researchers in their new report pointed to trees as "a life form of paramount importance for terrestrial ecosystems and human societies," because of their ecological dominance and provision of so much energy and industrial materials for human societies.
"Arabidopsis is still the plant model that will first give us the basic answers to how plants function," Strauss said. "But it is very exciting to see the knowledge it is yielding being applied to trees, such an important and difficult life form. For many environmental and economic reasons trees are one group of plants that we want to be able to breed more scientifically, and we're now getting closer to the day we can really do that."