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Sept 9, 2013 - The use of genomics as a tool for forest management garnered much attention in recent years. Genomics is the study of genetic information of an organism encoded in its DNA and corresponding counterparts such as RNA, proteins, and metabolites. These components work together to define the physiology and behaviour of all species such as microorganisms, plants, animals, and humans.

The current work on the mountain pine beetle (MPB) epidemic is an example of the how genomics has been used in the forestry industry. The MPB is a natural part of the forest ecosystem, and carries with it the tree-killing blue stain fungus. Together, this beetle/fungal complex has infested more than 15 million hectares of pine forest in British Columbia and Alberta, and it continues to spread – how this is happening is where genomics is coming in to help.

Without new genomic tools, evidence of expansion of MPB into a new host species, the jack pine, would have taken longer to identify. This range expansion means that MPB now has the potential to move unimpeded across Canada, well into the Eastern Maritimes. Lodgepole pine and jack pine form a large hybrid zone in Alberta and the Northwest Territories where accurate identification of individual tree species is difficult due to an overlap in the morphological characteristics between them. To differentiate between the species, Tria Project researchers at the University of Alberta developed a series of genetic markers (www. thetriaproject.ca). Using these markers to look at the ancestry of affected trees, the Tria team provided the first example of an MPB attack on jack pine trees and further evidence that they are indeed suitable as hosts for the beetles and fungus.

Genomics was also used in the project to identify variations in tree populations that relate to or influence the continued spread of the insect. If this variation is mixed across the landscape, e.g. areas of high and low susceptibility, the risk of spread can be estimated. Given jack pine's naivety to the insect, researchers presume that the spread risk will be different between lodgepole pine, hybrid pine and jack pine. They sampled across Alberta, British Columbia and Saskatchewan and developed a model that would predict the genetic ancestry (and therefore risk) of an un-sampled region. Since lodgepole and jack pine are adapted to different environmental conditions, the predictive model uses habitat characteristics such as elevation, temperature, and moisture to evaluate susceptibility.

From this, a spatial probability map of Alberta was created, enabling researchers to measure MPB risk.
The research doesn't stop at trees though; the Tria Project (tria meaning three in Latin) is also looking at the use of genomics to characterize the fungus and the beetle. Genomic research on the beetle, for example, is investigating key physiological factors that influence population dynamics. Mortality of larvae during the winter is extremely important in anticipating the spread of subsequent generations. The current MPB epidemic has seen successful spread of the beetle to more northern areas (and colder climates) than previously observed. Detailed investigations into the molecular basis of over-wintering physiology and cold-tolerance are critical to understanding potential population levels of emerging broods as well as the potential, and direction, for future spread.

Genomic studies into other aspects of beetle physiology are ongoing, including how they detect volatile cues from suitable host trees or pheromones from other beetles (olfaction), and how the attacking beetle/fungal complex is able to survive the myriad of host tree defences (detoxification). The ability of attackers to tolerate these toxic defense compounds and even use the host tree terpenoids in pheromone production plays a large role in successful colonization of host trees and resulting beetle populations.

So what happens now - with all of these great findings how do we create tools to put into the hands of forest managers and the like?

This is one of the reasons why the Genome Canada 'Genomic Applications Partnership Program' was created. It's an opportunity for a company, industry, or provincial/federal forest managers to use the expertise of a Canadian academic and leverage their investment to create a product, process, or tool based in genomics that addresses a challenge or opportunity that they face. In this case – it could be the creation of a forestry risk management program, or a tool that surveyors could use to rapidly identify a tree species or infestation, both enabled by genomic research.

There is $30 million available nationally for budgets as small as $300,000 and as large as $6 million. However, Genome Canada's contribution must be leveraged by at least 2 parts industry or partner funding to 1 part Genome Canada funds. Projects can be as short as 6 months and can span up to 3 years.

To learn more about the GAPP and how your company can get involved, please visit www.genomecanada.ca


September 9, 2013
By Adrianna Clapp and Amy Noel

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