Research Activities

 

Research Activities Overview

Treenomix II seeks to develop and apply the tools of genomics to identify mechanisms of resistance to the spruce shoot weevil (a.k.a. white pine weevil, Pissodes strobi), and to understand the genomic basis of tree adaptation to local climate.  The spruce shoot weevil and other insects are some of the most destructive pests of spruce forests worldwide. 

Weevil damage is a major risk factor in plantations of the most valuable timber trees in Canada: Sitka spruce (Picea sitchensis), white spruce (P. glauca) and interior spruce (P. glauca x P. engelmanni).  Identification of resistance mechanisms and the implementation of such knowledge into tree breeding and forest management would go a long way towards increasing the health and productivity of Canada’s forests. 

Likewise, adaptational genomics will aid in understanding the genomic basis of genetic variation to cold acclimation and growth phenology.  This is particularly important with the threat of rapid climate change.

The two main species of study in this research project are Sitka spruce and white spruce.  Compared to Treenomix I (funded by Genome Canada 2001-2005) which focused on resource development in spruce, poplar and Arabidopsis, Treenomix II involves much more targeted resource development and intensive, genome-level experimental studies. 

We integrate data from the different ‘omics: proteomics, metabolomics, and gene expression, and functional gene characterization.  Advances are also taking place in the area of statistical genomics, as the outbred nature of conifers and the nature of material in the breeding programs pose unique problems. 

To learn more about the various aspects of our project, click on the links below or the tabs on the left:

Below is a diagram outlining the levels of discovery and organization of our project (note, for simplicity, we have not included all collaborators and platform services in the schematic, please see our Research Team and Technology Platforms for a complete list):

Treenomix II Levels of Discovery and Organization

 

Previous Activities

Previous research activities can be seen in the archive.

 

Integrated Canadian Conifer Genomics Efforts

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The Conifer Forest Health (Treenomix II) and Arborea II projects each have distinct research objectives, but there are opportunities to synergistically join efforts and coordinate activities such as data sharing and creating common resources.  The four main areas of collaboration are outlined below.

1.  Merging spruce EST sequences
Trace files for EST sequence data have been exchanged from our Genome Canada competition I projects and current projects, and we will assemble or cluster the sequences, in order to best annotate genes and assemble our next-generation microarray.

The Arborea sequences are from white spruce (Picea glauca; approximately 50% 5’ and 3) and the Treenomix sequences (mostly 3’ reads) are from white spruce / interior spruce (hybrid of P. glauca x P. engelmanni) and Sitka spruce (P. sitchensis). The strategy for the merging this multi-species data begins with integration of the extensive white spruce / interior spruce data sets. Other species, most prominently Sitka spruce will be added to the white spruce framework.  This work requires considerable coordination of bioinformatics strategies. 

 

Number of sruce ESTs (thousands) from each project.
Spruce Species  Treenomix Sequences Arborea Sequences Total
  Phase 1 Phase 2 Phase 1 Phase 2  

Picea glauca /

P. glauca x P. Engelmanni

 118 N/A 70 150 338

P. sitchensis

 

 128* 97* 0 0 225*

* including end sequencing for FLcDNA selection.

2.  Annotation and Databasing the merged EST sequence data

We are integrating information and annotations on assemblies, contigs/clusters, and consensus sequences in a platform that supports advanced queries, enables curation of data, and ensures easy access and mining of merged datasets for both projects. This also involves developing pre-requisite methods for functional annotation and the databasing tools.  For example, we are using Discovery Space developed at the Vancouver Michael Smith Genome Sciences Centre for spruce EST annotation, along with expert curator annotation. Final consensus clusters and assemblies are also in the works. 

3. Development of oligonucleotide (long-mer) spotted microarrays

Together with the Arborea II project a next-generation microarray will be developed to achieve a broader representation of expressed spruce genes and a higher degree of specificity. Design of oligo synthesis will be based on the joint Treenomix and Arborea sequence data. Merged datasets of white spruce and Sitka spruce will be used to design the first set oligonucleotides; synthesis of oligos and printing of arrays will follow.

4. Marker development and genetic maps

A common set of gene-based markers between the Arborea and the Treenomix projects and a composite genetic map of the white spruce genome with all of the genes mapped in both projects will be built.  A comparison of candidate gene lists between projects indicates relatively little overlap (ca. 10%); a low level is actually advantageous as a means of verifying associations across populations. To date, a composite linkage map of white spruce has been assembled, containing 836 expressed gene loci and 126 genes in common between the Treenomix and Arborea pedigrees. SNP genotyping for these 126 genes was done by Treenomix and assembly of the joint map performed by Arborea (please contact K Ritland for more information about the map). The Arborea project will also include DNA samples from 11 parents from Treenomix pedigrees for testing with its next 1536-SNP array.

Other collaborative activities:

  • Book Chapter. An invited book chapter on spruce structural genomics and molecular breeding has been written (Bousquet, J., N. Isabel, B. Pelgas, J. Cottrell, D. Rungis & K. Ritland. 2007. Chapter 3 Spruce In: Genome Mapping and Molecular Breeding in Plants, Vol. 7 Forest Trees, C.Kole (Ed). Springer-Verlag, Berlin-Heidelberg. Pp. 93-114).
  • Joint National Workshop. Arborea and Treenomix will co-host a workshop in August 2008 in Quebec City, within the context of an International Union of Forest Research Organizations (IUFRO) Workgroup meeting.  The topic of this workgroup includes genomics and molecular breeding, and it is expected to attract 300 scientists internationally, allowing us an excellent opportunity to showcase our work.
  • Joint Steering Committee Meetings. Joint Steering Committee meetings between the two projects are held every 3 months. The Committee is composed of the four PIs of the two projects, and representatives from Genome BC and Genome Quebec.
  • Scientific Advisory Boards. The SABs of the two projects have two international members in common to provide recommendations on collaborative activities and help materialize new opportunities.