Domesticated tree crops may be the 'future of forestry'

The trees of the future may stem from advances in gene discovery research at Purdue University that could lead to domesticated trees, the forestry equivalent of crop plants like corn and soybeans.

"I think this is the future of forestry," said Richard Meilan, an associate professor of molecular physiology with Purdue's Hardwood Tree Improvement and Regeneration Center who has demonstrated a way to rapidly identify genes in poplar trees and determine their function.

"Our goal in gene discovery is to domesticate trees, just like we have domesticated corn over the past 5,000 years," he said. "If we can produce trees for specific purposes, like making furniture or plywood, and intensively manage those trees like agricultural row crops, we can make more efficient use of our limited land resources without treading on wilderness areas."

Identifying gene function is the first step in eventually developing trees with many ideal characteristics, such as insect resistance, improved wood properties or delayed flower production, and then producing multiple trees with those traits, he said.

Meilan and his colleagues used two related techniques known as "gene trapping" and "enhancer trapping" to identify genes in this study. He reported the application of these techniques in the current issue of the journal Plant Physiology.

While these techniques have previously been used to identify gene function in Arabidopsis, a common research plant, this is the first time these methods have been used in any type of tree, he said.

Gene and enhancer trapping are alternatives to classical approaches in developmental genetics, the field of biology that determines which genes activate various processes and pathways in living organisms.

Classical approaches typically require the production of numerous mutant plants and the identification of genes responsible for traits that differ between mutant and normal plants. This can be a long and laborious process - especially in plants such as trees, which have life spans ranging from decades to hundreds of years.

Gene and enhancer trapping remove the need to produce mutant plants and instead identify genes based solely on their activity patterns. These methods rely on the insertion of a foreign piece of DNA, called a "trap vector," at random throughout the genome. This trap vector has a unique DNA sequence and carries a gene called GUS, which results in a blue color when activated.

When the trap vector lands near or next to a plant gene, GUS is expressed in the same manner as its neighboring gene. For example, if GUS lands beside a gene active only in the veins of the plant's leaves, then GUS will be active only in those areas, producing a blue color in the veins.

Researchers can pinpoint where in the genome the trap vector landed since the vector has a known DNA sequence. This allows them to home in on the gene responsible for the trait - in the example above, a gene active in the veins.

Of the two methods, gene trapping is more specific than enhancer trapping, but both are effective in locating genes of interest throughout the genome, Meilan said

Once a gene that controls a desired trait is identified, Meilan said, scientists could manipulate that gene's activity and, for example, produce a tree that flowers at a different time than other trees of the same species. Scientists also could transfer genes of interest, such as genes for insect resistance, into trees that don't have them.

Meilan's current goal is to identify the genes responsible for root development in trees, making it possible for foresters and nursery managers to propagate trees that, through conventional breeding, have attained a desirable set of characteristics.

Currently, the nursery and forestry industries rely on conventional breeding - mating male and female trees with ideal growth characteristics, sowing their seeds and planting out seedlings. However, ideal parents are no guarantee that the next generation of trees will exhibit the same traits.

"The problem with conventional breeding is that you get a mix of the traits from the two parents, so for whatever qualities you're looking for, even if the parent plants have many highly desirable traits, their offspring may not exhibit all of the characteristics the parents have," Meilan said.

A solution, he said, is to find a way to propagate trees without the need for conventional breeding.

"With houseplants, you can take a cutting, put it in water, and it will root. That's called vegetative propagation," Meilan said.

"You can't do that with most trees. If you take a branch off of a walnut tree and stick it in water, it won't develop roots. We'd like to find the genes that cause root initiation so we can develop trees we could propagate, just like houseplants."

This would allow for the production of uniform fields of trees, all with the same suite of desirable characteristics, Meilan said.

The potential to engineer trees and other plants with valuable characteristics is not without controversy, and critics point out the risk of contaminating wild stands of trees with pollen from plants carrying novel genes. An answer to those critics, however, could lie within the process of gene discovery itself, Meilan said.

"If we're domesticating trees, it probably won't be for their flowers; it's for the wood. And if we can propagate them vegetatively, we won't need them to flower," he said. "To prevent gene flow, we could develop transgenic trees that don't flower or that flower at an unusual time.

"This would allow us to achieve what's known as 'bioconfinement' - preventing a gene you've introduced from escaping into the wild."

Meilan said he sees tree domestication as a partial solution to the myriad problems associated with human population growth, such as loss of agricultural lands, encroachment on wildlife areas and increased consumption of natural resources.

"I'm not suggesting that we have genetically engineered trees growing in all our national forests," he said. "But this kind of technology could allow us to increase our yields and create tailor-made trees to meet society's demands for forestry products without encroaching on wilderness areas."

The next step in Meilan's research will involve taking genes he identifies through gene and enhancer trapping, transferring those genes to trees that lack the desired trait and determining whether the trait is acquired.

Also contributing to this research were Andrew Groover, Joseph R. Fontana and Gayle Dupper with the U.S. Department of Agriculture Forest Service Institute of Forest Genetics; Caiping Ma and Steven Strauss with Oregon State University; and Robert Martienssen with Cold Spring Harbor Laboratory in New York.

Funding was partially provided by industrial members of the Tree Genetic Engineering Research Cooperative, sponsored by the National Science Foundation's Industry/University Cooperative Research Center, and the U.S. Department of Energy's Biomass Program through contract with Oak Ridge National Laboratory in Tennessee.

The blue color in the veins of the leaf pictured may contain the key to the trees of the future, says Purdue scientist Rick Meilan, who uses a type of molecular flag that produces a blue substance in his research in tree gene discovery. Meilan suggests his research could lead to the development of ideal characteristics, such as insect resistance or improved wood production, in trees that could be domesticated or "farmed," reducing the need to log wilderness areas. (Photo/Andrew Groover, USDA Forest Service, Institute of Forest Genetics, Davis, California)

ABSTRACT

Gene and enhancer trap tagging of vascular-expressed genes in poplar trees
Andrew Groover, Joseph R. Fontana, Gayle Dupper, Caiping Ma, Robert Martienssen, Steven Strauss, and Richard Meilan

We report a gene discovery system for poplar trees based on gene and enhancer traps. Gene and enhancer trap vectors carrying the -glucuronidase (GUS) reporter gene were inserted into the poplar genome via Agrobacterium tumefaciens transformation, where they reveal the expression pattern of genes at or near the insertion sites. Because GUS expression phenotypes are dominant and are scored in primary transformants, this system does not require rounds of sexual recombination, a typical barrier to developmental genetic studies in trees. Gene and enhancer trap lines defining genes expressed during primary and secondary vascular development were identified and characterized. Collectively, the vascular gene expression patterns revealed that approximately 40 percent of genes expressed in leaves were expressed exclusively in the veins, indicating that a large set of genes is required for vascular development and function. Also, significant overlap was found between the sets of genes responsible for development and function of secondary vascular tissues of stems and primary vascular tissues in other organs of the plant, likely reflecting the common evolutionary origin of these tissues. Chromosomal DNA flanking insertion sites was amplified by thermal asymmetric interlaced PCR and sequenced and used to identify insertion sites by reference to the nascent Populus trichocarpa genome sequence. Extension of the system was demonstrated through isolation of full-length cDNAs for five genes of interest, including a new class of vascular-expressed gene tagged by enhancer trap line cET-1-pop1-145. Poplar gene and enhancer traps provide a new resource that allows plant biologists to directly reference the poplar genome sequence and identify novel genes of interest in forest biology.