Schwab, O. and T. Maness (2009). Rebuilding spatial forest inventories from aggregated data. Journal of Forestry. accepted July 27, 2009 (GELS research contribution)
Zulak KG, Lippert DN, Kuzyk M, Domanski D, Chou T, Borchers CH and J Bohlmann. Targeted proteomics using selected reaction monitoring (SRM) reveals the induction of specific terpene synthases in a multi-level study of methyl jasmonate treated Norway spruce (Picea abies). The Plant Journal, accepted September 1, 2009.
Lippert D, Yuen M, and J Bohlmann (2009) Spruce Proteome DB: A resource for conifer proteomics research. Tree Genetics and Genomes 5: 723 – 727. [Link to Article]
Hamberger B, Hall D, Yuen M, Oddy C, Hamberger B, Keeling CI, Ritland C, Ritland K and J Bohlmann (2009) Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome. BMC Plant Biology 9:106. [Link to Article]
Schwab, O., T. Maness, G. Bull and D. Roberts (2009). Modeling the effect of changing market conditions on mountain pine beetle salvage harvesting and structural changes in the British Columbia forest products industry. Canadian Journal of Forest Research. Accepted June 8, 2009.
Bohlmann J and J Gershenzon (2009) Old substrates for new enzymes of terpenoid biosynthesis. Proceedings of the National Academy of Sciences USA 26: 10402-10403 (invited commentary).
Rokneddin Albouyeh and Kermit Ritland. 2009. Estimating Heritability of Gene Expression Using Parent–Offspring Regression with 2-Channel Microarrays. J. Heredity 100(1):114–118.
Liewlaksaneeyanawin C, Zhuang J, Tang M, Lueng G, Oddy C, Findlay S, Farzaneh N, Ritland CE, Bohlmann J, and K Ritland. (2009) Identification and validation of COS markers in Pinaceae. Tree Genetics & Genomes 5: 5:247-255.
Lippert D, Ralph SG, Phillips M, White R, Smith D, Hardie D, Gershenzon J, Ritland K, Borchers CH, and J Bohlmann. Quantitative iTRAQ proteome and comparative transcriptome analysis of elicitor-induced Norway spruce (Picea abies) cells reveals elements of calcium signaling in the early conifer defense response. Proteomics, In press (2009)
Bohlmann J and CI Keeling (2008) Terpenoid biomaterials. The Plant Journal 54: 656-669.
Bohlmann J (2008) Insect-induced terpenoid defenses in spruce. In: “Induced Plant Resistance to Herbivory" A. Schaller (ed.) Springer Science, pages 173 - 187.
Ralph SG, Chun HJE, Kolosova N, Cooper D, Oddy C, Ritland CE, Kirkpatrick R, Moore R, Barber S, Holt RA, Jones SJM, Marra MA, Douglas CJ, Ritland K and J Bohlmann (2008) A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics 9:484 (17 pages, doi:10.1186/1471-2164-9-484)
Aitken, S.N., S. Yeaman, J.A. Holliday, T. Wang and S. Curtis-McLane. Adaptation, migration or extirpation: Climate change outcomes for tree populations. Evolutionary Applications 1: 95-111.
Holliday J.A., Ralph S., White R., Bohlmann J. and Aitken, S.N. (2008) Global monitoring of gene expression during autumn cold acclimation among rangewide populations of Sitka spruce [Picea sitchensis (Bong.) Carr.] New Phytologist. 178:103-122
Keeling C, Bohlmann J (2008) Terpenoids in Plants. Wiley Encyclopedia of Chemical Biology, John Wiley & Sons, Inc. In Press.
Keeling C, Weisshaar S, Lin R, Bohlmann J (2008) Functional plasticity of paralogous diterpene synthases involved in conifer defense. PNAS 105(3): 1085-1090. [Link to Article]
Bérubé Y, Zhuang J, Ralph S, Rungis D, Bohlmann J, Ritland K (2007) Characterization of EST-SSRs in loblolly pine and spruce. Tree Genetics & Genomics 3: 251-259. [Link to article]
Bohlmann J. Insect-induced terpenoid defenses in spruce. Submitted for publication in: “Induced Plant Resistance to Herbivory" A. Schaller (ed.) Springer, New York. June 8, 2007.
Bousquet J, Isabel N, Pelgas B, Cottrell J, Rungis D, Ritland K (2007) Spruce. In Genome Mapping and Molecular Breeding in Plants, Volume 7 Forest Trees C. Kole (Ed.) Springer-Verlag Berlin Heidelberg (22 pages, in press) (This publication resulted from a collaboration with the Arborea project).
DiGuistini S, Ralph S, Lim Y, Holt R, Jones S, Bohlmann J, Breuil C (2007) Generation and annotation of lodgepole pine and oleoresin-induced expressed sequences from the blue-stain fungus Ophiostoma clavigerum, a Mountain Pine Beetle-associated pathogen. FEMS Microbiology Letters 267: 151-158. (Work described here used approaches developed in the present project) [Link to article]
Friedmann M, Ralph SG, Aeschliman D, Zhuang J, Ritland K, Ellis BE, Bohlmann J, Douglas CJ (2007) Microarray gene expression profiling of the developmental transition from primary to secondary growth and constitutive defence in Sitka spruce (Picea sitchensis) apical shoots.Journal of Experimental Botany 58: 593-614. [Link to article]
Godard KA, Byun-McKay A, Levasseur C, Plant A, Séguin A, Bohlmann J (2007) Testing of a heterologous, wound- and insect-inducible promoter for functional genomics studies in conifer defense. Plant Cell Reports 26(12): 2083-2090. [Link to article]
Holliday JA, Ralph SG, White R, Bohlmann J, Aitken SN. Global monitoring of autumn gene expression withi and among phenotypically divergent populations of Sitka spruce [Picea sitchensis (Bong.) Carr.]. Submitted to New Phytologist, May 14 2007.
Huber DPW, Erickson ML, Leutenegger CM, Bohlmann J, Seybold SJ (2007) Isolation and extreme sex-specific expression of cytochrome P450 genes in the bark beetle, Ips paraconfusus, following feeding on the phloem of host ponderosa pine, Pinus ponderosa. Insect Molecular Biology 16: 335-349. (Work described here used approaches developed in the present project) [Link to article]
Li S-H, Schneider B, Gershenzon J (2007) Microchemical analysis of laser-microdissected stone cells of Norway spruce by cryogenic nuclear magnetic resonance spectroscopy. Planta 225:772-779 (This publication is from our Max Planck co-funder.) [Link to article]
Lippert D, Chowrira S, Ralph SG, Zhuang J, Aeschliman D, Ritland C, Ritland K, Bohlmann J (2007) Conifer defense against insects: Proteome analysis of Sitka spruce (Picea sitchensis) bark induced by mechanical wounding or feeding by white pine weevils (Pissodes strobi). Proteomics 7: 248-270. [Link to article]
Phillips MA, Walter MH, Ralph SG, Dabrowska P, Luck K, Urós EM, Boland W, Strack D, Rodríguez-Conceptión M, Bohlmann J, Gershenzon J (2007) Functional identification and differentential expression of 1-deaoxy-D-xylulose-5-phosphate synthase in induced terpenoid resin formation of Norway spruce (Picea abies). Plant Molecular Biology 65(3): 243-257. (Publication resulted from collaboration with the Max Planck co-funder) [Link to article]
Ralph SG, Hudgins JW, Jancsik S, Franceschi VR, Bohlmann J (2007) Aminocycloprpane carboxylate synthase is a regulated step in ethylene-dependent induced conifer defense. Full-length cDNA cloning of a multigene family, differential constitutive and wound- and insect-induced expression, and cellular and subcellular localizatiob in spruce and Douglas fir. Plant Physiology 143:410-424. [Link to article]
Ralph SG, Jancsik S, Bohlmann J (2007) Dirigent proteins in conifer defense II: Extended gene discovery, phylogeny, and constitutive and stress-induced gene expression in spruce (Picea spp.). Phytochemistry 68:1974-1990. [Link to article]
Ralph SG, Keeling CI, Jancsik S, Kolosova N, Cooper D, Oddy C, Ritland CE, Kirkpatrick R, Chun HJE, Palmquist D, Wynhoven B, Butterfield YSN, Liu J, Stott J, Yang G, Barber S, Siddiqui A, Holt RA, Jones SJM, Marra MA, Douglas CJ, Ritland K, Bohlmann J. A high-quality full-length cDNA and EST resource for spruce and its utility for conifer gene annotation and characterization of insect-induced defenses.Submitted to Plant Physiology, June 25 2007.
Byun-McKayA, GodardK-A, ToudefallahM, Martin DM, AlfaroR, King J, Bohlmann J, Plant AL (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. (Work described in this paper started in Treenomix I) [Link to article]
Hamberger B, Bohlmann J (2006) Cytochrome P450 monooxygenases in conifer genomes: Discovery of members of the terpenoid oxygenase superfamily in spruce and pine. Biochemical Society Transactions 34: 1209-1214. [Link to article]
Huber DPW, Bohlmann J (2006) The role of terpene synthases in the direct and indirect defense of conifers against insect herbivory and fungal pathogens. In: “Multigenic and Induced Systemic Resistance in Plants.”S. Tuzun and E. Bent (eds.) Springer, New York. Pages: 296-313. [Link to article]
Hudgins JW, Ralph SG, Franceschi VR, Bolhmann J (2006) Ethylene in induced conifer defense response: FLcDNA cloning, wound-induced protien expression, and cellular and subcellular localization of 1-aminocyclopropane-carboxylic acid oxidase (ACO) in specialized resin duct cells and polyphenolic phloem parenchyma cells. Planta 224: 865-877
Keeling CI, Bohlmann J (2006a) Diterpene resin acids in conifers. Invited “Molecules of Interest” paper. Phytochemistry 67: 2415-2423. [Link to article]
Keeling CI, Bohlmann J (2006b) Genes, enzymes, and chemicals of terpenoid diversity in the constitutive and induced defence of conifers against insects and pathogens. New Phytologist 170: 657-675 (Invited Tansley Review). [Link to article]
Phillips M, Bohlmann J, Gershenzon J (2006) Molecular regulation of induced terpenoid biosynthesis in conifers. Phytochemical Reviews 5:179-189. (Publication co-authored with the Max Planck co-funder). [Link to article]
Ralph S, Park JY, Bohlmann J, Mansfield SD (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: 21-40. (Work described in this paper started in Treenomix I, was completed in Treenomix II and provided the foundation for new work in Treenomix II) [Link to article]
Ralph S, Yueh H, Friedmann MF,Aeschliman D, Zeznik JA, Nelson CC, Butterfield YSN, Kirkpatrick R, Liu J, Jones SJM, Marra MA, Douglas CJ, Ritland K, Bohlmann J (2006) Conifer defense against insects: Microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworm (Choristoneura occidentalis) or white pine weevil (Pissodes strobi) reveals large-scale changes of the host transcriptome. Plant, Cell and Environment 29: 1545-1570. [Link to article]
Ritland K, Ralph S, Lippert D, Rungis D, Bohlmann J (2006) A new direction in conifer genomics. In: “Landscapes, Genomics and Transgenic Conifer Forests” Claire Williams (ed.) Springer Publishers, Dordrecht Netherlands, pages 75-84.
Ro D-K, Bohlmann J (2006) Diterpene resin acid biosynthesis in loblolly pine (Pinus taeda): Functional characterization of abietadiene/levopimaradiene synthase (PtTPS-LAS) cDNA and subcellular targeting of PtTPS-LAS and abietadienol/abietadienal oxidase (PtAO, CYP720B1). Phytochemistry 67(15):1572-1578. [Link to article]
Seybold SJ, Huber DPW, Lee LC, Bohlmann J (2006) Pine monoterpenes and pine bark beetles: A marriage of convenience for defense and chemical communication. Phytochemical Reviews 5:143-178. [Link to article]
Articles and Book Chapters Published 2008
Ralph SG, Chun HJE, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJM, Marra MA, Bohlmann J (2008) Analysis of 4,664 High-Quality Sequence-Finished Poplar Full-length cDNA Clones and their Utility for the Discovery of Genes Responding to Insect Feeding. BMC Genomics 9: 57. [Link to article]
Articles and Book Chapters Published 2007
Behnke K, Ehlting B, Teuber M, Bauerfeind M, Louis S, Hänsch R, Polle A, Bohlmann J, Schnitzler J-P (2007) Transgenic, non-isoprene emitting poplars don’t like it hot. The Plant Journal 51(3): 485-499. [Link to article]
Kelleher C, Chiu R, Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin TM, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, Lee D, Mathewson CA, Olson T, O’Connor K, Prabhu A-L, Smailus DE, Stott JM, Tsai M, Wye NH, Yang GS, Zhuang J, Holt RA, Putnam NH, Vrebalov J, Giovannoni JJ, Grimwood J, Schmutz J, Rokhsar D, Jones SJM, Marra MA, Tuskan GA, Bohlmann J, Ellis BE, Ritland K, Douglas CJ, Schein JE (2007) A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. The Plant Journal 50: 1063-1078. [Link to article]
Miranda M, Ralph SG, Mellway R, Heath M, Bohlmann J, Constabel P (2007) The transcriptional response of hybrid poplar (Populus trichocarpa x P. deltoides) to infection by Melampsora medusae leaf rust involves induction of flavonoid pathway genes leading to the accumulation of proanthocyanidins. Molecular Plant-Microbe Interactions 20: 816-831. [Link to article]
Philippe RN, Bohlmann J. Genomics of poplar defense against insects. Submitted to Canadian Journal of Botany, March 15 2007.
Articles and Book Chapters Published 2006
Gilchrist EJ, Haughn GW, Ying CC, Otto SP, Zhuang J, Cheung D, Hamberger B, Aboutorabi F, Kalynyak T, Johnson L, Bohlmann J, Ellis BE, Douglas CJ, Cronk QCB (2006) Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Molecular Ecology 15: 1367-1378. [Link to article]
Ralph S, Oddy C, Cooper D, Yueh H, Jancsik S, Kolosova N, Philippe RN, Aeschliman D, White R, Huber D, Ritland CE, Benoit F, Rigby T, Nantel A, Butterfield YSN, Kirkpatrick R, Chun E, Liu J, Palmquist D, Wynhoven B, Stott J, Yang G, Barber S, Holt RA, Siddiqui A, Jones SJM, Marra MA, Ellis BE, Douglas CJ, 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. [Link to article]
Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, A. Salamov, J. Schein, L. Sterck, A. Aerts, R. R. Bhalerao, R. P. Bhalerao, D. Blaudez, W. Boerjan, A. Brun, A. Brunner, V. Busov, M. Campbell, J. Carlson, M. Chalot, J. Chapman, G.-L. Chen, D. Cooper, P. M. Coutinho, J. Couturier, S. Covert, Q. Cronk, R. Cunningham, J. Davis, S. Degroeve, A. Déjardin, C. dePamphilis, J. Detter, B. Dirks, I. Dubchak, S. Duplessis, J. Ehlting, B. Ellis, K. Gendler, D. Goodstein, M. Gribskov, J. Grimwood, A. Groover, L. Gunter, B. Hamberger, B. Heinze, Y. Helariutta, B. Henrissat, D. Holligan, R. Holt, W. Huang, N. Islam-Faridi, S. Jones, M. Jones-Rhoades, R. Jorgensen, C. Joshi, J. Kangasjärvi, J. Karlsson, C. Kelleher, R. Kirkpatrick, M. Kirst, A. Kohler, U. Kalluri, F. Larimer, J. Leebens-Mack, J.-C. Leplé, P. Locascio, Y. Lou, S. Lucas, F. Martin, B. Montanini, C. Napoli, D. R. Nelson, C. Nelson, K. Nieminen, O. Nilsson, V. Pereda, G. Peter, R. Philippe, G. Pilate, A. Poliakov, J. Razumovskaya, P. Richardson, C. Rinaldi, K. Ritland, P. Rouzé, D. Ryaboy, J. Schmutz, J. Schrader, B. Segerman, H. Shin, A. Siddiqui, F. Sterky, A. Terry, C.-J. Tsai, E. Uberbacher, P. Unneberg, J. Vahala, K. Wall, S. Wessler, G. Yang, T. Yin, C. Douglas, M. Marra, G. Sandberg, Y. Van de Peer, and D. Rokhsar (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw). (Cover paper, Science Sept. 15) Science 313: 1596-1604. [Link to article]