The Forest for the Trees
Nicholas School to Host Forestry Genomics Forum at Duke
This article originally appeared in GenomeLife, Issue 11.
Are genetically engineered corn and soybeans a boon to farmers and consumers or a threat to the environment that's being foisted on an unsuspecting populace? The answer, not surprisingly, depends upon whom you ask; agriculture biotech giant Monsanto and environmental activist group Greenpeace are sure to give radically different answers. Claire Williams has followed the crop controversy with interest and wonders whether the prospect of genetically modified trees will provoke a similar tempest.
Williams is a Visiting Professor in the Nicholas School of the Environment and Earth Sciences and was formerly full professor at Texas A&M in genetics and forestry. Her expertise is in the field of landscape genomics, an emerging area at the interface of natural resources management and the genome sciences. As with modified crops, the biological, societal and political issues relevant to genetically modified trees are viewed differently by different constituencies, including environmental groups, timber companies, biotechnology firms, genome scientists and government regulators. Like Monsanto and Greenpeace, Williams says that many of these groups are "diametrically opposed to one another." Can they be brought together without starting a forest fire?
Williams intends to find out. She has organized The Nicholas Environmental Leadership Forum on "Landscapes, Genomics and Transgenic Conifer Forests," which will take place November 17-19 at the Washington Duke Inn.
The size of some organisms' genomes, in base pairs Conifers and Their Genomes: Size Matters
Williams' trees of choice are conifers - pine cone-bearing, forestland trees that include both the loblolly pines that preside over Duke Forest and the towering Redwoods and Giant Sequoias in the Pacific Northwest . They also include shrubs such as the yew and juniper as well as the Douglas Fir, Norway Spruce, and assorted cedar and cypress trees. Most of the 550 species are evergreen. Conifers are used in paper, especially paper bags and shipping materials, as well as in furniture and construction materials. Medicine, too: Taxol, used to treat various cancers, is isolated from the Pacific yew tree.
Bill Schlesinger, James B. Duke Professor of Biogeochemistry and Dean of the Nicholas School, sees genetically modified conifers as having the potential to address some of forestry's problems in an environmentally sound way. "The rising human population will demand more products from managed forests," he says. "It would be nice to be able to grow the highest yielding timber varieties we can engineer on the smallest area of land." Given conifers' economic importance and the potential of genome technology, both industry and academic scientists have shown an interest in trying to improve the conifer genome.
Williams shares that interest; however, she points to several problems, not the least of which are technical. First, the smallest conifer genome still adds up to some 14,000 megabases, or more than four times the size of the human genome; loblolly pines have even larger genomes, on the order of 21,000 megabases. Worse, much of that DNA is repetitive, so assembling it in the proper order becomes a major headache.
Conifer genomics also suffers from a lack of comparative species data to use as reference points. Williams notes that the poplar genome has been sequenced; however, a 200-million-year evolutionary divide separates it from its conifer cousins. Will the poplar genome be useful for conifer sequencers? "I don't know," she says, citing the fact that the common ancestors of conifers and poplars, the protogymnosperms, have been extinct for at least 150 million years. Given the depth of this phylogenetic divide between conifers and poplars, Williams speculates that the conifer community might find the genome of the small annual weed Arabidopsis thaliana, which has already been fully sequenced, to be at least as useful as the poplar genome.
Williams and others have been working on developing shortcuts to get at the gene-rich parts of the conifer genome. One method involves trying to remove the methylated parts of the genome, that is, those parts that are less likely to be transcribed into RNA and translated into protein. Another involves using biochemical approaches to enrich for the non-repetitive portion of the conifer genome. But even that still leaves one with 4000 megabases. "Right now," says Williams, "the conifer sequence is on a slimming diet."
Trees Are Not Crops
As towering as the conifer genome is, the policy issues may be even more foreboding. For Williams, part of the impetus behind the forum is to discuss whether or not it's appropriate to deal with transgenic trees the way genetically modified crops are dealt with. Currently, if only as a matter of convenience, US Department of Agriculture policy says 'yes.' Williams and most of her peers say 'no.' She cites several reasons.
"Two of the main questions are about chain of custody and liability. If you plant a transgenic tree, that land may be sold before the tree is ever harvested. So how do you keep track of what's there [and who it belongs to]? Those are iceberg issues that set forestry apart from agriculture." Williams notes that the chain of custody question is complicated by the fact that most US forestland is public, not private, whereas most agriculture takes place on private land. Then there's the longevity issue. "A loblolly pine can live 400 years," says Williams-far longer than any governmental regulator. Not only that, each conifer may produce a million wind-dispersed seeds a year. If a seed escapes into an unmanaged ecosystem during a tree's long lifetime, Williams wonders where it will go, what the consequences will be and who will take responsibility for it.
Let a Thousand Conifers Bloom
Schlesinger believes that stakeholders in the development of genetically modified trees have an opportunity to learn from the mistakes of the purveyors of genetically engineered crops such as corn and soybeans. "With trees, we have a chance to do a better job understanding some of the potential impacts of genetic modification before we introduce large numbers of them into the wild."
Williams, too, hopes the forum will provide an opportunity to get, if not consensus, at least a number of diverse opinions on how forest genomics should proceed. "No one has really thought all the way through from genomics to deliverables," she says, "except to follow the example of agriculture. I hope that we can talk about all of this at the forum…and still be friends at the end."