Professor John Mackay

Wood Professor of Forest Science

Research Area

Genetics and molecular biology of forest trees

Research Description

Research in my group focuses on the adaptability of trees and forests, as relevant for sustainable use of forest lands. We use the tools of genetics and genomics to address these questions. The major themes are:

Genetic basis of adaptation: Role of gene expression variation in the adaptability of forest trees. Genes and genes networks that underpin responses to stress as well as growth and development

Forest health: Insect resistance in conifer trees.

Genetic basis of wood formation and properties: Regulation of gene expression in wood formation. Quantitative and association genetics of wood structure

Evolution of conifer genomes:  Genes and gene families. Copy number variation

Development of DNA-based tools for tree breeding: Insect resistance bio-markers in conifers. Genomic selection for wood and growth traits in spruce trees


SmarTForests Project:

ProCoGen Project:



Shanta N., Schwinghamer T., Backer R., Allaire S.E., Teshler I., Vanasse A., et al. (2016) Biochar and plant growth promoting rhizobacteria effects on switchgrass (Panicum virgatum cv. Cave-in-Rock) for biomass production in southern Québec depend on soil type and location. Biomass and Bioenergy, 95: 167-173

Verta, J.-P., Landry, C. R., MacKay, J. (2016) Dissection of eQTL allele-specificity using a haploid/diploid plant system – insights into compensatory evolution of transcriptional regulation within populations. The New Phytologist, 211: 159-171

Lamara M., Raherison E., Lenz P., Beaulieu J., Bousquet J., MacKay J. (2015) Genetic architecture of wood properties based on association analysis and co‐expression networks in white spruce. The New Phytologist, 210: 240-55.

Prunier J., Tessier G., Bousquet J., MacKay J. (2015) From genotypes to phenotypes: expression levels of genes encompassing adaptive SNPs in black spruce. Plant cell reports, 34: 2111-2125.

Prunier J., Verta J.-P., MacKay J.J. (2015) Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function. The New Phytologist (Tansley Review), 209: 44-62.

Warren R.L., Keeking C.I., Yuen M.M.S., Raymond A., Taylor G.A., Vandervalk B.P., Hamid Mohamadi H., Paulino D., Chiu R., Jackman S.D. et al. (2015) Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer defense metabolism. The Plant Journal, 83: 189-212.

Raherison, E.S.M., Guiguère I., Caron S., Lamara M., MacKay, J., (2015) Modular organization of the white spruce (Picea glauca (Moench) Voss) transcriptome reveals functional organization and evolutionary signatures. The New Phytologist, 207: 172-87

Beaulieu, J., Doerksen, T.K., MacKay, J., Rainville, A., Bousquet, J., (2014). Genomic selection accuracies within and between environments and small breding groups in white spruce. BMC Genomics, 15:1048

Allaire, S.E., Baril, B., Vanasse, A., Lange, S.F., MacKay, J., Smith, D.L. (2014) Carbon dynamic under switchgrass produced in a loamy soil amended with biochar. Canadian Journal of Soil Science,

De La Torre A.R., Birol I., Bousquet J., Ingvarsson P.K., Jansson S., Jones S.J.N., Keeling C.I., MacKay J., Nilsson O., Ritland K., Street N., Yanchuk A., Zerbe P., Bohlmann J. (2014) Insights into Conifer Giga-Genomes. Plant Physiology,

Mageroy, M.H., Parent, G.J., Germanos, G., Giguère, I., Delvas, N., Maaroufi, H., Bauce, É., Bohlmann, J., Mackay J. (2014) Expression of the beta-glucosidase gene Pgbglu-1 underpins natural resistance of white spruce against spruce budworm. Plant Journal,

Lenz, P., Deslauriers, M., Ung, C.-H., MacKay, J., Beaulieu, J. (2014) What do ecological regions tell us about wood quality? A case study in eastern Canadian white spruce. Canadian Journal of Forest Research, 44:1383-1393

Beaulieu, J., Doerksen, T.K., Clément, S., Mackay, J., Bousquet, J. (2014) Accuracy of genomic prediction for growth and wood traits in the context of progeny testing of half-sib families in white spruce. Heredity, 113: 343–352.

Sena, J., Giguère, I., Boyle, B., Rigault, P., Birol, I., Zuccolo, A., Ritland, K., Ritland, C., Bohlmann, J. Jones, S.J., Bousquet, J., MacKay, J. (2014). Evolution of gene structure in the conifer Picea glauca: A comparative analysis with angiosperms. BMC Plant Biology. 14: 95.

Duval I., Lachance D., Giguère I., Bomal C., Morency M.-J., Pelletier G., Boyle B., MacKay J.J., Séguin A. (2014) Large-scale screening of transcription factor – promoter interactions in spruce revealed a transcriptional network involved in vascular development. Journal of Experimental Botany, 65: 2319-2333.

Bomal, C., Duval, I., Giguère, I., Fortin, É., Caron, S., Boyle, B., Séguin, A., MacKay, J. (2014). Opposite action of R2R3-MYBs from different subgroups on common key genes from shikimate and monolignol pathways in spruce. Journal of Experimental Botany, 65:495-508

Beaulieu, J., Giguère, I., Deslauriers, M., Boyle, B., MacKay, J. (2013) Differential gene expression patterns in white spruce newly formed tissue on board the International Space Station. Advances in Space Research, 52: 760-772.

Pavy, N., Deschênes, A., Blais, S., Lavigne, P., Beaulieu, J., Isabel, N., MacKay, J., Bousquet J. (2013). The landscape of nucleotide polymorphism among13,500 genes of the conifer Picea glauca, relationships with functions and comparison with Medicago truncatula. Genome Biology and Evolution, 5: 1910-1925.

Lenz, P., Auty, D., Achim, A., Beaulieu, J., Mackay J. (2013) Genetic improvement of white spruce mechanical wood traits – early screening by means of acoustic velocity. Forests, 4: 575-594.

Rutledge, R.G., Stewart, D., Caron, S., Overton, C., Boyle, B., MacKay, J., Klimaszewska, K. (2013) Potential link between biotic defense activation and recalcitrance to induction of somatic embryogenesis in shoot primordia from adult trees of white spruce (Picea glauca). BMC Plant Biology, 13: 16.

Birol, I., A. Raymond, S.D. Jackman, S. Pleasance, R. Coope, G.A. Taylor, M.M. Saint Yuen, C.I. Keeling, D. Brand, B.P. Vandervalk, H. Kirk, P. Pandoh, R.A. Moore, Y. Zhao, A.J. Mungall, B. Jaquish, A. Yanchuk, C. Ritland, B. Boyle, J. Bousquet, K. Ritland, J. MacKay, J. Bohlmann, Jones S.J.M. (2013). Shotgun sequencing and assembly of the 20 Gb white spruce (Picea glauca) genome. Bioinformatics, 29: 1492-1497.

Nystedt, N., N.R. Street, A. Wetterbom, A. Zuccolo, Y.-C. Lin, D.G. Scofield, F. Vezzi, A. Alexeyenko, S. Giacomello, N. Delhomme, R. Vicedomini, K. Sahlin, E. Sherwood, M. Elfstand, L. Gramzow, K. Holmberg, O. Keech, L. Klasson, M. Koriabine, M. Kucukoglu, M. Käller, J. Luthman, F. Lysholm, T. Niittylä, Å. Olson, C. Ritland, J.A. Rosselló, J. Sena, T. Svensson, C. Talavera-López, G. Theißen, H. Tuominen, K.Vanneste, Z.-Q. Wu, B. Zhang, P. Zerbe, L. Arvestad, R. Bhalerao, J. Bohlmann, J. Bousquet, R. Garcia Gil, T.R. Hvidsten, P. de Jong, J. MacKay, M. Morgante, K. Ritland, B. Sundberg, S. Lee Thompson, Y. Van de Peer, B. Andersson, O. Nilsson, P.K. Ingvarsson, J. Lundeberg, S. Jansson. (2013). Sequencing the 20 Gbp Norway spruce genome sheds light on conifer genome evolution. Nature, 497: 579-84.

Pavy, N., Gagnon, F., Rigault, P., Blais, S., Deschênes, A., Boyle, B., Pelgas, B., Deslauriers, M., Clément, S., Lavigne, P., Lamothe, M., Cooke, J.E.K., Jaramillo-Correa, J.-P., Beaulieu, J., Isabel, N., MacKay, J.J., Bousquet, J. (2013) Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners. Molecular Ecology Resources, 13: 324 -336.

Verta J.P., Landry C., MacKay J. 2013. Are long lived trees poised for evolutionary change? Single locus effects in the evolution of gene expression networks in spruce. Molecular Ecology (From the Cover), 22: 2369-2379.

Mackay, J., Dean, J.F.D., Plomion, C., Peterson, D.G., Cánovas, F.M., Pavy, N., Ingvarsson, P.K., Savolainen, O., Angeles Guevara, M., Fluch, S., Vinceti, B., Abarca, D., Díaz-Sala, C., Cervera, M.-T. (2012) Towards decoding the conifer giga-genome. Plant Molecular Biology, 80: 555-69.

Raherison E., Rigault P., Caron S., Poulin P.-L., Boyle B., Verta J.-P., Giguère I., Bomal C., Bohlmann B., MacKay, J. (2012). Transcriptome profiling in conifer trees and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression. BMC Genomics, 13: 434.

Rigault, P., Boyle, B., Lepage, P., Cooke, J., Bousquet, J., MacKay, J. (2011) A white spruce gene catalogue for conifer genome analyses. Plant Physiology, 157: 14-28.

Beaulieu, J., Doerksen, T., Boyle, B., Clément, S., Deslauriers, M., Beauseigle, S., Blais, S., Poulin, P.-L., Lenz, P., Caron, S., Rigault, P., Bicho, P., Bousquet, J., MacKay, J. (2011) Association genetics of wood physical traits in the conifer white spruce and relationships with gene expression. Genetics, 188: 197–214.

Bedon, F., C. Bomal, S. Caron, C. Levasseur, B. Boyle, S.D. Mansfield, A. Schmidt, J. Gershenzon, J. Grima-Pettenati, A. Séguin, J. MacKay. (2010) Subgroup 4 R2R3-MYBs in conifer trees: gene family expansion and contribution to the isoprenoid-oriented response. Journal of Experimental Botany, 61: 3847-3864

Boyle, B., N. Dallaire, J. MacKay (2009). Evaluation of the impact of single nucleotide polymorphisms and primer mismatches on quantitative PCR. BMC Biotechnology, 9: 75.

Bomal, C., F. Bedon, S. Caron, S.D. Mansfield, C. Levasseur, J.E.K. Cooke, S. Blais, L. Tremblay, M.-J. Morency, N. Pavy, J. Grima-Pettenati, A. Séguin, J. MacKay (2008). Involvement of Pinus taeda MYB1 and MYB8 in phenylpropanoid metabolism and secondary cell wall biogenesis: a comparative in planta analysis. Journal of Experimental Botany, 59: 3925–3939.

Pavy, N., B. Boyle, C. Nelson, C. Paule, I. Giguère, S. Caron, L.S. Parsons, N. Dallaire, F. Bedon, H. Bérubé, J.E.K. Cooke, J. MacKay (2008). Identification of conserved core xylem gene sets: conifer cDNA microarray development, transcript profiling and computational analyses. The New Phytologist, 180: 766-786.