Project Overview

Forest Health in Canada and globally is facing severe challenges from outbreaks of insect pests and their associated fungal pathogens, and from the limits of adaptation of conifers to changing environments.  In combination with traditional approaches, genomics offers special opportunities to address these problems in conifers.  The inherent limitation of generation time in breeding is overcome and “immortal” populations for mapping and phenotyping can be established.  The fact that longer-lived plants cannot migrate in the face of climate change places additional importance on these organisms. 

The overall goal of the TREENOMIX: Conifer Forest Health Project is to deliver and apply new knowledge and tools from conifer genomics to spruce breeding programs in Canadian forest stewardship organizations.  Our project objectives are to:

  1. Develop gene, protein and metabolite expression profiles to spruce defense and resistance and gene expression structure and genome function;
  2. Develop knowledge of conifer genome structure and genome function;
  3. Apply the first two objectives in existing tree breeding programs; and
  4. Address economic, environmental, and social issues (GE3LS) via research and public participation.

Resource Development


The project is currently developing the following spruce genomic resources:

  • EST compilation and annotation: 75,000 additional ESTs and a central spruce database with improved gene annotation for >235,000 spruce ESTs.
  • Full Length cDNAs (FL-cDNAs): Sequencing and databasing of 10,000 FL-cDNAs, which should represent a large part of the expressed conifer genome.
  • Marker development and mapping: we are developing additional EST-SSR markers, COS (conserved orthologous set) markers, and SNPs from candidate genes for insect resistance; these markers are being placed on a spruce genetic map in collaboration with the Arborea project in Quebec
  • BAC library: construction of a BAC library, as a resource for spruce geneticists.  In Spring 2007, a 5X BAC library was constructed (140-160 kb insert size)
  • Proteomics: Innovative proteomics methods such as iTRAQ and MRM are being tested and used for the first time in conifers.
  • Metabolomics: GC/MS and LC/MS technologies are being used to profile and database spruce low molecular weight metabolites.