Forestry: the new high-tech frontier

Genes may hold the secret to forest survival

Zoom in—way in—from the macro view of B.C.’s vast forests, right down to the micro level where researchers are looking into genes that could lead to  improved forest health, productivity and economic opportunities.

UBC researchers are leading four massive projects to sequence the genes of thousands of trees. With co-funding from Genome BC as a result of Genome Canada’s 2010 Large-Scale Applied Research Project Competition, the results sought are to tackle emerging challenges such as climate change, fuel shortages and declining natural resources.

Sally Aitken, a professor in the Department of Forest Sciences and University of Alberta colleague Andreas Hamann are collaborating on a project to better understand how trees adapt to local climatic conditions.

As climate change alters forest environments, trees that have adapted to the climate in one geographic area may not be well suited to thrive there in 30 or 40 years—a serious concern for an industry that plants 230 million trees in British Columbia every year.

Aitken’s team is looking for genetic variation in trees across Western Canada and comparing this to geographic information and differences in temperature, moisture and day length. Using climate change models, the team hopes to predict where trees with specific adaptations can thrive in the future.

“Ultimately we want to know where to find the seeds that are best adapted for the future climatic conditions of a region,” says Aitken.

Her team is working with the two most planted and economically important species in Western Canada: lodgepole pine and interior spruce. Because these trees are so abundant, they also play a key role in shaping forest habitat, affecting the carbon cycle, water flows, and snow melt.

In total, Aitken’s team will be sequencing and analyzing genes from more than 15,000 seedlings, mostly grown in a range of simulated climates in growth chambers in the basement of the Forest Sciences Centre.

“Research like this involves experts who have very different skill sets, knowledge and backgrounds. We don’t have enough resources to do this for every species so we’re hoping to find better ways to tackle the same questions in other trees,” she says.

Since 2001, UBC scientists have been awarded more than $65 million by Genome BC and Genome Canada for research in the forestry and bioenergy sectors.

In 2001, the “Treenomix” project became the first forestry genomics research project funded in Canada with an $11 million award from Genome BC and Genome Canada. It remains among the largest funding contracts awarded to any genomics research team in the province. Led by a team of UBC researchers including Joerg Bohlmann, Kermit Ritland, Brian Ellis, and Carl Douglas, the Treenomix project has set the groundwork for the success of forestry genomics in British Columbia.

“Forestry has been changing over the past 20 years, but the speed of change is accelerating,” said John Innes, dean of UBC’s Faculty of Forestry. “Increasingly, forest science is being recognized as a high-tech subject, using state-of-the-art equipment to unravel complex environmental problems. Genome BC has played a major part in encouraging this change by providing funding for advanced forest research.”

Genome BC In funding research, Genome BC and Genome Canada take a unique approach. Instead of issuing research grants, the organizations provide research contracts known as Collaborative Research Agreements that enable translatable research with socio-economic benefits. When a proposal is approved, Genome BC plays an integral role in the research process through milestone development and achievement, financial monitoring and facilitating follow up with potential end-users.

“Genome BC acts as a catalyst between government, academia and industry.  Our goal is to translate outstanding research carried out in universities into applications for users in industry, such as the Ministry of Forests,” said Dr. Alan Winter, President  & CEO of Genome BC.


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UBC Reports | Vol. 58 | No. 6 | Jun. 6, 2012

Sally Aiken will be analyzing genes from more than 15,000 lodgepole pine and interior spruce seedlings. Martin Dee Photograph

Sally Aiken will be analyzing genes from more than 15,000 lodgepole pine and interior spruce seedlings. Martin Dee Photograph

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UBC’s three other large-scale forest genomics projects

Fighting fungus

Richard Hamelin, a professor in the Department of Forest Sciences, is applying modern  techniques common in health sciences to forest health issues in an effort to protect B.C.’s trees from some of the most common fungal pathogens.

Working in partnership with researchers at the Michael Smith Genome Sciences Centre, Hamelin is sequencing the genomes of 20 fungal species, identifying the genes that make trees sick and looking for variation in these genes. He will then map the spread of disease using this information, in a sense studying tree epidemiology and using this to predict how the pathogen will spread.

Hamelin and his team will then develop DNA-based diagnostic tools that can be used for the treatment of these pathogens. Right now, trees infected with disease must be identified visually, which can be misleading or problematic if the tree is asymptomatic for a number of years. “Using these technologies from the medical field to generate actionable assays is a powerful approach,” said Hamelin.

Biofuel from poplar trees

In the ongoing pursuit to develop new products from forests, biofuel is an attractive option. UBC researchers Carl Douglas and Shawn Mansfield are identifying gene variations in the fast-growing poplar tree to select varieties with optimal characteristics for biofuel production. Their hope is to breed poplars with denser wood and higher cellulose content- the molecule that gets broken down into ethanol for biofuel. They’re also hoping to breed poplars with less lignin—a molecule that makes it difficult to convert cellulose into ethanol.

“We’re not just interested in how much trees grow but also in the chemistry and morphology of the wood,” said Douglas, a professor in the Department of Botany. He and Mansfield, a professor in the Department of Wood Science, will sequence the genomes of 700 trees—each tree has about 40,000 genes.
“We’ll have a catalogue of total genetic variation and also of trait variation in these trees so we can do a better job at identifying genetic variants that underlie differences in important wood and growth traits,” said Douglas.

Sustainable spruce forests

Joerg Bohlmann, a researcher at the Michael Smith Laboratories at UBC and a professor of Botany and Forest Sciences, and Laval University professor John MacKay, are working with a team of world-class co-investigators and end-users to develop applications from genomics research
in spruce trees. Spruce trees account for more than half of all the tree seedlings planted each year in Canada. The researchers aim to improve the yield and value of spruce forests.

The project, called SMarTForests, is sequencing the genome of white spruce and is using genomics to develop markers for improved insect resistance, growth, wood properties, and adaptation to climate. SMarTForests is part of an international consortium that will also be among the first in the world to sequence a conifer genome.

“Until recently, nobody would have been able to develop a decent genome sequence assembly for a conifer tree,” said Bohlmann. “These genomes are larger and more complex than anything that has ever been sequenced. Thanks to our collaboration with Dr. Steven Jones at the Michael Smith Genome Sciences Centre we are in an ideal position to take on this enormous challenge.”

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