Project Leaders:
Carl Douglas, Brian Ellis, Joerg Bohlmann, Kermit Ritland

Lead Institution: 
University of British Columbia

Technology Applications:  comparative genomics, forest health markers, wood quality markers, tree microarrays

Research Funding Program:
Competition I

Project Website: 
Treenomix

Sustainable forestry in Canada will benefit from a genomic understanding of trees. The researchers have chosen two tree species, spruce and popular, plus an applicable and biologically well-characterized model plant, Arabidopsis, to form a comprehensive program of forestry genomics.

Spruce is the cornerstone of the Canadian forest industry and provides the springboard to other conifer species such as pine, and with comparative information, to all pine family members. Poplar is harvested across Canada and is globally the most intensively managed tree. It has rapid growth, desirable wood quality traits and rapid generation time. Despite Arabidopsis being an herbaceous annual plant with a different life cycle and appearance, research has demonstrated that it contains the basic genes for wood formation.

This project will use a combination of structural and functional genomics tools for cross-species comparisons to address key questions in forest tree biology. It is likely that mechanisms controlling wood formation and wood quality are homologous across spruce, poplar and Arabidopsis. In contrast, because defense-related genes evolve quickly in response to changing biotic pressures, the different species have probably evolved unique mechanisms for defense against insects and disease.

Using gene and protein expression data, this project will determine which markers correlate with desirable traits. This information will help develop marker-aided breeding programs, where adult traits can be predicted in seedlings. This speeds up conventional breeding programs using naturally occurring variation. The project will also provide improved knowledge of the benefits vs. compromises of desired breeding characteristics, such as increased growth rate and wood quality.

“We use paper and high-quality paper much more than we did 25 years ago,” says Dr. Joerg Bohlmann, a faculty member in the Biotechnology Laboratory at the University of British Columbia. “Our need for high quality solid wood for building materials is also greater. Pressure by human demand on natural forests is increasing, at the same time as outbreaks of pests and global climate change creates uncertainties for natural and planted forests.” This project is essential for sustainable management, harvest and future improvement of Canada’s largest natural, renewable resource.

Project publications:
Bohlmann, J., Martin, D.M., Miller, B., & Huber, D.P.W. (2004). Terpenoid synthases in conifers and poplars. In C. Walter & M. Carson (Eds.), Plantation Forest Biotechnology for the 21st Century (pp.181-201). Kerala, India: Research Signpost.

Byun-McKay, A., Godard, K.-A., Toudefallah, M., Martin, D.M., Alfaro, R., King, J., Bohlmann, J., & Plant, A. L. (2006). Wound-induced terpene synthase gene expression in Sitka spruce that exhibit resistance or susceptibility to attack by the white pine
weevil. Plant Physiology, 140 , 1009-1021 .

Douglas, C.J. & Ehlting, J. (2005). Arabidopsis thaliana full genome longmer microarrays: a powerful gene discovery tool for agriculture and forestry. Transgenic Research, 14 , 551-561.

Ehlting, J., Mattheus, N., Aeschliman, D.S., Li, E., Hamberger, B., Cullis, I.F., Zhuang, J., Kaneda, M., Mansfield, S.D., Samuels, A.L., Ritland, K., Ellis, B.E., Bohlmann, J., & Douglas, C.J. (2005). Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation. The Plant Journal, 42 , 618-640.

Gilchrist, E.J., Haughn, G.W., Ying, C.C., Otto, S.P., Zhuang, J., Cheung, D., Hamberger , B., Aboutorabi, F., Kalynyak, T., Johnson, L., Bohlmann, J., Ellis, B.E., Douglas, C.J. & Cronk, Q.C.B. (2006). Use of EcoTILLING as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa . Molecular Ecology , 15 , 1365-1376.

Hamel, L.-P., Nicole, M.-C., Sritubtim, S., Morency, M.-J., Ellis, M., Ehlting, J., Beaudoin, N., Barbazuk, B., Klessig, D., Lee, J., Martin, G., Mundy, J., Ohashi, Y., Scheel, D., Sheen, J., Xing, T., Zhang, S., Seguin A., & Ellis, B.E. (2006). Ancient signals: Comparative genomics of plant MAPK and MAPKK gene families. Trends in Plant Science, 11 (4), 192-198.

Huber, D.P.W. & Bohlmann, J. (2006). The role of terpene synthases in the direct and indirect defense of conifers against insect herbivory and fungal pathogens. In S. Tuzun & E. Bent (Eds.), Multigenic and Induced Systemic Resistance in Plants (pp.296-313). New York: Springer.

Huber, D.P., Ralph, S. & Bohlmann, J. (2004). Genomic hardwiring and phenotypic plasticity of terpenoid-based defenses in conifers. Journal of Chemical Ecology, 30(12) , 2399-2418.

Huber, D.P.W. & Bohlmann, J. (2004). Terpene synthases and the mediation of plant-insect ecological interactions by terpenoids: a mini-review. In Q.C.B. Cronck, J. Whitton, R.H. Ree, & I.E.P. Taylor (Eds.), Plant Adaptation: Molecular Genetics and Ecology (pp. 70 - 81). Ottawa, Ontario: NRC Research Press.

Keeling, C.I. & Bohlmann, J. (2006). Genes, enzymes, and chemicals of terpenoid diversity in the constitutive and induced defence of conifers against insects and pathogens. Tansley Review for the New Phytologist, 170 (4), 657-675 .

Kolosova, N., Miller, B., Ralph, S., Ellis, B.E, Douglas, C., Ritland, K. & Bohlmann, J. (2004). Isolation of high-quality RNA from gymnosperm and angiosperm trees. Biotechniques, 36(5) , 821-824.

Lippert, D., Zhuang, J., Ralph, S., Ellis, D.E., Gilbert, M., Olafson, R., Ritland, K., Ellis, B., Douglas, C.J. & Bohlmann, J. (2005). Proteome analysis of early somatic embryogenesis in Picea glauca . Proteomics, 5 (2), 461-473.

Martin, D. & Bohlmann, J. (2005). Molecular biochemistry and genomics of terpenoid defenses in conifers. Recent Advances in Phytochemistry, 39 , 29-56.

Miller, B., Madilao, L.L., Ralph, S. & Bohlmann, J. (2005). Insect-induced conifer defense. White pine weevil and methyl jasmonate induce traumatic resinosis, de novo formed volatile emissions, and accumulation of terpenoid synthase and putative octadecanoid pathway transcripts in Sitka spruce. Plant Physiology, 137 , 369-382.

Ralph, S., Park, J.Y., Bohlmann, J., & Mansfield, S.D. (2006). Dirigent proteins in conifer defense: gene discovery, phylogeny, and differential wound- and insect-induced expression of a family of DIR and DIR-like genes in spruce ( Picea spp.). Plant Molecular Biology, 60 (1), 21-40.

Ralph, S., Oddy, C., Cooper, D., Yueh, H., Jancsik, S., Kolosova, N., Philippe, R.N., Aeschliman, D., White, R., Huber, D., Ritland, C.E., Benoit, F., Rigby, T., Nantel, A., Butterfield, Y.S.N., Kirkpatrick, R., Chun, E., Liu, J., Palmquist, D., Wynhoven, B., Stott, J., Yang, G., Barber, S., Holt, R.A., Siddiqui, A., Jones, S.J.M., Marra, M.A., Ellis, B.E., Douglas, C.J., Ritland, K. & Bohlmann, J. (2006). Genomics of hybrid poplar ( Populus trichocarpa x deltoides ) interacting with forest tent caterpillars ( Malacosoma disstria ): Normalized and full-length cDNA libraries, expressed sequence tags (ESTs), and a cDNA microarray for the study of insect-induced defenses in poplar. Molecular Ecology, 15 ,1275-1297 .

Ritland, K., Ralph,S., Lippert, D., Rungis, D., & Bohlmann, J. (2006). A new direction in conifer genomics. In C. Williams (Ed.), Landscapes, Genomics and Transgenic Conifer Forests (pp. 75-84). Dordrecht Netherlands: Springer.

Ro, D.-K., Ehlting, J., Keeling, C.I., Lin, R., Mattheus, N. & Bohlmann, J. (2006). Microarray expression profiling and functional characterization of AtTPS genes: Duplicated Arabidopsis thaliana sesquiterpene synthase genes At4g13280 and At4g13300 encode root-specific and wound-inducible ( Z )-g-bisabolene synthases.
Archives of Biochemistry and Biophysics , 448 (1-2), 104-116 .

Ro, D.-K., Arimura, G.-I., Lau, S.Y.W., Piers, E., & Bohlmann, J. (2005). Loblolly pine abietadienol/abietadienal oxidase PtAO is a multifunctional, multi-substrate cytochrome P450 monooxygenase. Proceedings of the National Academy of Sciences USA, 102 , 8060-8065.

Rungis, D., Hamberger, B., Bérubé, Y., Wilkin, J., Bohlmann, J. & Ritland, K. (2005). Efficient genetic mapping of single nucleotide polymorphisms based upon DNA mismatch digestion. Molecular Breeding, 16 , 261-270.

Rungis,D., Bérubé, Y., Zhuang, J., Ralph, S., Ritland, C.E., Ellis B.E., Douglas, C., Bohlmann, J. & Ritland, K. (2004). Robust simple sequence repeat (SSR) markers for spruce (Picea spp.) from expressed sequence tags (ESTs). Theoretical and Applied Genetics, 109 :1283-1294.