New publications


2020

Chamberland, V., F. Robichaud, M. Perron, N, Gélinas, J. Bousquet & J. Beaulieu. 2020. Conventional versus genomic selection for white spruce improvement: a comparison of costs and benefits of plantations on Québec public lands. Tree Genetics and Genomes 16: 17 (16p.).

Depardieu, C., M.P. Girardin, S. Nadeau, P. Lenz, J. Bousquet & N. Isabel. 2020. Adaptive genetic variation to drought in a widely distributed conifer suggests a potential for increasing forest resilience in a drying climate. New Phytologist 227: 427–439.

Isabel, N., J.A. Holliday & S.N. Aitken. 2020. Forest genomics: advancing climate adaptation, forest health, productivity and conservation. Presentation of the Evolutionary Applications Special Issue of January 2020. Evolutionary Applications 13: 3-10.

Jackman, S.D., L. Coombe, R.L. Warren, H. Kirk, E. Trinh, T. McLeod, S. Pleasance, P. Pandoh, Y. Zhao, R.J. Coope, J. Bousquet, J. Bohlmann, S.J.M. Jones & I. Birol. 2020. Complete mitochondrial genome of a gymnosperm, Sitka spruce (Picea sitchensis), indicates a complex physical structure. Genome Biology and Evolution (in press) (doi.org/10.1093/gbe/evaa108).

Lenz, P.R.N., S. Nadeau, M.-J. Mottet, M. PerronN. IsabelJ. Beaulieu & J. Bousquet. 2020. Multi-trait genomic selection for weevil resistance, growth and wood quality traits in Norway spruce. Evolutionary Applications 13: 76-94.

Lenz, P.R.N., S. Nadeau, A. Azaïez, S. Gerardi, M. Deslauriers, M. PerronN. IsabelJ. Beaulieu & J. Bousquet. 2020. Genomic prediction for hastening and improving efficiency of forward selection in conifer polycross mating designs: an example from white spruce. Heredity 124: 562-578.

Parent, G., C. Méndez-Espinoza, I. Giguère, M. Mageroy, M. Charest, E. Bauce, J. Bohlmann & J. Mackay. 2020. Hydroxyacetophenone defenses in white spruce against spruce budworm. Evolutionary Applications 13: 62-75.


2019

Hassegawa, M., M. Savard, P.R.N. Lenz, E. Duchateau, N. Gelinas, J. Bousquet & A. Achim. 2019. White spruce wood quality for lumber products: priority traits and their enhancement through tree improvement. Forestry. 93: 16-37.

Lin, D.L. CoombeS. JackmanK. Gagalova, R. Warren, S Hammond, H. McDonald, H. Kirk, P. Pandoh, Y. Zhao, R. Moore, A. Mungall, C. Ritland, T. Doerksen, B. Jaquish, J. Bousquet, S. Jones, J. Bohlmann & I. Birol. 2019. Complete chloroplast genome sequence of an Engelmann spruce (Picea engelmannii) genotype from western Canada. Microbiology Resource Announcements. 8(24):e00382-19 (3p).

Lin, D., L. Coombe, S. Jackman, K. Gagalova, R. Warren, S Hammond, H. McDonald, H. Kirk, P. Pandoh, Y. Zhao, R. Moore, A. Mungall, C. Ritland, N. Isabel, B. Jaquish, J. Bousquet, S. Jones, J. Bohlmann & I. Birol. 2019. Complete chloroplast genome sequence of a white spruce (Picea glauca) genotype from eastern Canada. Microbiology Resource Announcements. 8(23): e00381-19 (4p.).

Tran, H., S. Kanzaki, L. Triest, I. Hormoza, N.J. Kuk, R. Ming, J. BousquetD. Khasa & P. Van Damme. 2019. Analysis of genetic diversity analysis of lychee (Litchi chinensis Sonn.) and wild forest relatives in the Sapindaceae from Vietnam using microsatellites. Genetic Resources and Crop Evolution. 66: 1653-1669.

Van Ghelder, C., G.J. Parent, P. Rigault, J. Prunier, I. Giguère, S. Caron, J. Stival Sena, A. Deslauriers, J. Bousquet, D. Esmenjaud & J. Mackay. 2019. The large repertoire of conifer NLR resistance genes includes drought responsive and highly diversified RNLs. Scientifc Reports. 9: 11614 (13p.).

Warren, R.L., L. Coombe, H. Mohamadi, J. Zhang, B. Jaquish, N. Isabel, S.J.M. Jones, J. Bousquet, J. Bohlmann & I. Birol. 2019. NtEdit: scalable genome assembly polishing. Bioinformatics. 35: 4430-4432.


2018

Azaiez, A., N. Pavy, S. Gérardi, J. Laroche, B. Boyle, F. Gagnon, M-J. Mottet, J. Beaulieu & J. Bousquet. 2018. A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies). BMC Genomics 19: 942 (13p.).

Benomar, L., MS. Lamhamedi, S. Pepin, A. Rainville, M-C. Lambert, HA. Margolis, J. Bousquet & J. Beaulieu. 2018. Thermal acclimation of photosynthesis and respiration of southern and northern white spruce seed sources tested along a regional climatic gradient indicates limited potential to cope with temperature warming. Annals of Botany 121: 443-457.

Gamal El-Dien, O., B. Ratcliffe, J. Klápště, I. Porth, C. Chen & YA. El-Kassaby. 2018. Multienvironment genomic variance decomposition analysis of open-pollinated Interior spruce (Picea glauca x engelmanii). Molecular Breeding 38:26 (16 p.).

Lamara, M., G.J. Parent, I. Giguère, J. Beaulieu, J. Bousquet & J.J. MacKay. 2018. Association genetics of acetophenone defence against spruce budworm in mature white spruce. BMC Plant Biology 18: 231 (15p.).

Otis Prud’homme, G., MS. Lamhamedi, L. Benomar, A. Rainville, J. DeBlois, J. Bousquet & J. Beaulieu. 2018. Ecophysiology and growth of white spruce seedlings from various seed sources along a climatic gradient support the need for assisted
migration. Frontiers in Plant Science 8: 2214 (17p.).

Porth, I., R. White, B. Jaquish & K. Ritland. 2018. Partial correlation analysis of transcriptomes helps detangle the growth and defense network in spruce. New Phytologist (in press). DOI: 10.1111/nph.15075.

Prunier, J., I. Giguère, N. Ryan, R. Guy, R. Soolanayakanahally, N. Isabel, J. MacKay & I. Porth. 2018. Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations. Molecular Ecology (in press). DOI: 10.1111/mec.14836.

Stival Sena, J., I. Giguère, P. Rigault, J. Bousquet & J. MacKay. 2018. Expansion of the dehydrin family in the Pinaceae is associated with considerable structural diversity and drought-responsive expression. Tree Physiology 38: 442-456.


2017

Du, R., S. Niu, Y. Liu, X. Sun, I. Porth, YA. El-Kassaby & W. Li. 2017. The gibberellin GID1-DELLA signalling module exists in evolutionary ancient conifers. Scientific Reports 7: 16637 (11p.).

De Lafontaine, G. & J. Bousquet. 2017. Asymmetry matters: genomic assessment of directional biases in gene flow between hybridizing spruces . Ecology and Evolution 7: 3883-3893.

Godbout, J., L. Tremblay, C. Levasseur, P. Lavigne, A. Rainville, J. MacKay, J. Bousquet & N. Isabel. 2017. Development of a traceability system based on a SNP array for large-scale production of high-value white spruce (Picea glauca). Frontiers in Plant Science 8: 1264 (13p.).

Lenz, P., J. Beaulieu, S. Clément, S. Mansfield, M. Desponts & J. Bousquet. 2017. Factors affecting the accuracy of genomic selection for growth and wood quality traits in an advanced-breeding population of black spruce (Picea mariana). BMC Genomics 18: 335 (17p.).

McKown, AD., J. Klápště, RD. Guy, RY. Soolanayakanahally, J. La Mantia, I. Porth, O. Skyba, F. Unda, CJ. Douglas, YA. El-Kassaby, RC. Hamelin, SD. Mansfield & QCB. Cronk. 2017. Sexual homomorphism in dioecious trees: extensive tests fail to detect sexual dimorphism in Populus. Scientific Reports 7: 1831 (14p.).

Pavy, N., M. Lamothe, B. Pelgas, F. Gagnon, I. Birol, J. Bohlmann, J. Mackay, N. Isabel & J. Bousquet. 2017. A high resolution reference genetic map positioning 8.8K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance. The Plant Journal 90: 189-203.

Prunier, J., S. Caron, M. Lamothe, S. Blais, J. Bousquet, N. Isabel & J. Mackay. 2017. Gene copy number variations and adaptive evolution: the genomic architecture of gene CNVs revealed by genetic mapping and their adaptive role in a non domesticated species, white spruce. Molecular Ecology 26: 5989-6001.

Prunier, J., S. Caron & J. MacKay. 2017. CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation. BMC Genomics 18:97.

Ratcliffe, B., O. Gamal El-Dien, E.P. Cappa, I. Porth, J. Klápště, C. Chen & Y. A. El-Kassaby. 2017. Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca. G3: 7 (33p.).

Thistlethwaite, FR., B. Ratcliffe, J. Klápště, I. Porth, C. Chen, MU. Stoehr & YA. El-Kassaby. 2017. Genomic prediction accuracies in space and time for height and wood density of Douglas-fir using exome capture as the genotyping platform. BMC Genomics 18: 930 (16p.).


2016

Benomar, L., M. S. Lamhamedi, A. Rainville, J. Beaulieu, J. Bousquet & H.A. Margolis. 2016. Genetic adaptation versus ecophysiological plasticity of photosynthetic-related traits in young Picea glauca trees along a regional climatic gradient. Frontiers in Plant Science 7: 48 (15p.).

Gamal El-Dien O., B. Ratcliffe, J. Klápště, I. Porth, C. Chen & Y. A. El-Kassaby. 2016. Implementation of the Realized Genomic Relationship Matrix to Open-Pollinated White Spruce Family Testing for Disentangling Additive from Non-additive Genetic Effects. G3 6: 743-753.

Herath, P., S. Beauseigle, B. Dhillon, D.I. Ojeda, G. Bilodeau, N. Isabel, M.-C. Gros-Louis, H. Kope, S. Zeglen, R.C. Hamelin & N. Feau. 2016. Anthropogenic signature in the incidence and distribution of an emerging pathogen of poplars. Biological Invasions 18: 1147-1161.

Jackman, S.D., R. Warren, E. Gibb, B.P. Vandervalk, J. Mohanadi, J. Chu, A. Raymond, S. Pleasance, R. Coope, M.R. Wildung, C. Ritland, J. Bousquet, SJM Jones, JC Bohlmann & I. Birol. 2016. Organellar genomes of white spruce (Picea glauca): Assembly and annotation. Genome Biology and Evolution 8: 29-41.

Lamara, M., E. Raherison, P. Lenz, J. Beaulieu, J. Bousquet & J. MacKay. 2016. Genetic architecture of wood properties based on association analysis and co-expression networks in white spruce. New Phytologist 210: 240-255.

Niu S, H. Yuan, X. Sun, I. Porth, Y. Li, Y.A. El-Kassaby & W. Li. 2016. A transcriptomics investigation into pine reproductive organ development. New Phytologist 209: 1278–1289.

Park, Y.S., J. Beaulieu & J. Bousquet. 2016. Multi-varietal forestry integrating genomic selection and somatic embryogenesis. In Y.-S. Park, J. Bonga & H.K. Moon (eds). Vegetative Propagation of Forest Trees. National Institute of Forest Science, Seoul, South Korea. Pp. 302-322 (invited).

Pavy, N., F. Gagnon, A. Deschênes, B. Boyle, J. Beaulieu & J. Bousquet. 2016. Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana). Molecular Ecology Resources 16: 588–598.

Prunier J., J-P. Verta & J.J. MacKay. 2016. Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function. New Phytologist 209: 44-62.

Villeneuve, I., M.S. Lamhamedi, L. Benomar, A. Rainville, J. Deblois, J. Beaulieu, J. Bousquet, M.-C. Lambert & H.A Margolis. 2016. Morpho-physiological variation of white spruce seedlings from various seed sources and implications for deployment under climate change. Frontiers in Plant Science 7: 1450 (15p.).

Warren, É., G. de Lafontaine, S. Gérardi, S. Senneville, J. Beaulieu, M. Perron, J.P. Jaramillo-Correa & J. Bousquet. 2016. Joint inferences from cytoplasmic DNA and fossil data provide evidence for glacial vicariance and contrasted postglacial dynamics in tamarack, a transcontinental conifer. Journal of Biogeography 43: 1227-1241.


2015

Beaulieu, J. & J. Bousquet. 2015. Genomic selection – Potential and current limits of application in boreal conifer breeding programs. In Proc. 34th Meeting of the Canadian Forest Genetics Association, Univ. of New Brunswick, Fredericton, August 17-20. Part II. Ed. D. Simpson. Canadian Forest Service, Fredericton. 10p.

Benomar, L., M.S. Lamhamedi, I. Villeneuve, A. Rainville, J. Beaulieu, J. Bousquet &  H.A. Margolis. 2015. Fine-scale geographic variation in photosynthetic-related traits of Picea glauca seedlings indicates local adaptation to climate. Tree Physiology 35: 864-878.

Carles, S., D. Boyer-Groulx, M.S. Lamhamedi, A. Rainville, J. Beaulieu, P.Y. Bernier, J. Bousquet & H.A. Margolis. 2015. Family variation in the morphology and physiology of white spruce (Picea glauca) seedlings in response to elevated CO2 and temperature. Journal of Sustainable Forestry 34: 169-198.

Cinget, B., G. de Lafontaine, S. Gérardi & J. Bousquet. 2015. Integrating phylogeography and paleoecology to investigate the origin and dynamics of hybrid zones: insights from two widespread North American firs. Molecular Ecology 24: 2856-2870.

Cinget, B., S. Gérardi,  J. Beaulieu & J. Bousquet. 2015. Less pollen-mediated gene flow for more signatures of glacial lineages: congruent evidence from balsam fir cpDNA and mtDNA for multiple refugia in eastern and central North America. PLoS ONE 10(4): e0122815 (25p.).

De Lafontaine, G., J. Prunier, S. Gérardi & J. Bousquet. 2015. Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana × P. rubens). Molecular Ecology 24: 5229-5247.

Floate K.D., J. Godbout, M.K. Lau, N. Isabel & T.G. Whitham. 2015. Plant-herbivore interactions in a trispecific hybrid swarm of Populus: assessing support for hypotheses of hybrid bridges, evolutionary novelty and genetic similarity. New Phytologist 209: 832-844.

Hornoy, B., N. Pavy, S. Gérardi, J. Beaulieu & J. Bousquet. 2015. Genetic adaptation to climate in white spruce involves small to moderate allele frequency shifts in functionally diverse genes. Genome Biology and Evolution 7: 3269–3285.

Jaramillo-Correa, J.P., S. Gérardi, J. Beaulieu, F.T. Ledig & J. Bousquet. 2015. Inferring and outlining past population declines with linked microsatellites: a case study in two spruce species. Tree Genetics & Genomes 11: 9 (12p.).

Lupi, C., G. Larocque, A. DesRochers, M. Labrecque, A. Mosseler, J. Major, J. Beaulieu, M.F. Tremblay, A.M. Gordon, B.R. Thomas, A. Vezina, H. Bouafif, D. Cormier, D. Sidders, R. Krygier, N. Thevathasan, M. Riopel & B. Ferland-Raymond.  2015. Evaluating sampling designs and deriving biomass equations for young plantations of poplar and willow clones. Biomass and Bioenergy, 83: 196-205.

Mageroy, M.H., G. Parent, G. Germanos, I. Giguère, N. Delvas, H. Maaroufi, E. Bauce, J. Bohlmann & J.J. Mackay. 2015. Expression of the β-glucosidase gene Pgβglu-1 underpins natural resistance of white spruce against spruce budworm. The Plant Journal 81: 68-80.

Mamashita, T., G.R. Larocque, A. DesRochers, J. Beaulieu, B.R. Thomas, A. Mosseler, J. Major & D. Sidders. 2015. Short-term growth and morphological responses to nitrogen availability and plant density in hybrid poplars and willows. Biomass and Bioenergy, 81: 88-97.

Mvolo, C.S., A. Koubaa, J. Beaulieu, A. Cloutier & M.J. Mazerolle. 2015. Variation in wood quality in white spruce (Picea glauca (Moench) Voss). Part I. Defining the juvenile-mature wood transition based on tracheid length. Forest 6: 183-202.

Nadeau, S., J. Godbout, M. Lamothe, M.-C. Gros-Louis, N. Isabel & K. Ritland. 2015. Contrasting patterns of genetic diversity across the ranges of Pinus monticola and P. strobus: A comparison between eastern and western North American postglacial colonization histories. American Journal of Botany 102: 1342-1355.

Porth, I., J. Klapste, A.D. McKown, J. La Mantia, R.D. Guy, P.K. Ingvarsson, R. Hamelin, S.D. Mansfield, J. Ehlting, C.J. Douglas & Y.A. El-Kassaby. 2015. Evolutionary quantitative genomics of Populus trichocarpa. PLoS ONE 10(11): e0142864 (25p.).

Prunier, J., G. Tessier, J. Bousquet & J. Mackay. 2015. From genotypes to phenotypes: expression levels of genes encompassing adaptive SNPs in black spruce. Plant Cell Reports 34: 2111-2125 (15p.).

Raherison E.S., I. Giguère, S. Caron, M. Lamara & J.J. MacKay. 2015. Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures. New Phytologist 207: 172-187.

Taft, S., A. Najar, J. Godbout, J. Bousquet & N. Erbilgin. 2015. Variations in foliar monoterpenes across the range of jack pine reveal three widespread chemotypes: implications to host expansion of invasive mountain pine beetle. Frontiers in Plant Science 6: 342 (12p.).

Warren R.L., C.I Keeling, M.M. Yuen, A. Raymond, G.A. Taylor, B.P. Vandervalk, H. Mohamadi, D. Paulino, R. Chiu, S.D. Jackman, G. Robertson, C. Yang, M. Hoffmann, D. Weigel, D.R. Nelson, C. Ritland, N. Isabel, B. Jaquish, A. Yanchuk, J. Bousquet, S.J. Jones, J. MacKay, I. Birol & J. Bohlmann. 2015. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. The Plant Journal 83: 189-212.

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