Publications – Nathalie Isabel


Gagalova, K., R.L. Warren, L. Coombe, J. Wong, K.M. Nip, M.M. Saint Yuen, J. Whitehill, J.M. Celedon, C. Ritland, G.A. Taylor, D” Cheng, P. Plettner, S.A. Hammond, H. Mohamadi, Y. Zhao, R. A. Moore, A. J. Mungall, B. Boyle, J. Laroche, J. Cottrell, J. Mackay, M. Lamothe, S. Gérardi, N. Isabel, N. Pavy, S.J.M. Jones, J. Bohlmann, J. Bousquet & I. Birol. 2022. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. The Plant Journal 111 (17p.) doi:10.1111/tpj.15889

Goessen, R., N. Isabel, C. Wehenkel, N. Pavy, I. Giguère, M.-C. Gros-Louis, L. Touchette, J. Laroche, B. Boyle, L. Tischenko, R. Soolanayakanahally, K. Mock, J. Hernandez-Velasco, S.L. Simental-Rodriguez, J. Bousquet & I. Porth. 2022. Coping with environmental constraints: geographically divergent adaptive genetic evolution and germination plasticity in the transcontinental Populus tremuloides. Plant People Planet 4 (17p.) doi:10.1002/ppp3.10297

Laverdière, J.-P., P. Lenz, S. Nadeau, C. Depardieu, N. Isabel, M. Perron, J. Beaulieu & J. Bousquet. 2022. Breeding for adaptation to climate change: genomic selection for drought response in a white spruce multi-site polycross test. Evolutionary Applications 15: 383-402. 


Depardieu, C., S. Gérardi, S. Nadeau, G. Parent, J. Mackay, P. Lenz, J. Bousquet & N. Isabel. 2021. Connecting tree-ring phenotypes, association genomics, and transcriptomics to decipher the genomic architecture of drought tolerance in a widespread conifer. Molecular Ecology 30: 3898-3917 (cet article a été désigné pour la page de couverture du numéro du mois d’août 2021 du journal et a fait l’objet d’un commentaire éditorial publié aux pages 3893-95 de ce même numéro).

Girardin, M.P., N. Isabel, X.J. Guo, M. Lamothe, I. Duchesne & P. Lenz. 2021. Annual aboveground carbon uptake enhancements from assisted gene flow in boreal black spruce forests are not long-lasting. Nature Communications 12: 1169 (15p.)

Laoué, J., C. Depardieu, S. Gérardi, M. Lamothe, C. Bomal, A. Azaiez, M.C. Gros-Louis, J. Laroche, B. Boyle, A. Hammerbacher, N. Isabel & J. Bousquet. 2021. Combining QTL mapping and transcriptomics to decipher the genetic architecture of phenolic compounds metabolism in the conifer white spruce. Frontiers in Plant Science 112: 793 (20p.)

Thiffault, N., P. Raymond, J.-M. Lussier, I. Aubin, S. Roy-Tardif, A. D’Amato, F. Doyon, B. Lafleur, M. Perron, J. Bousquet, N. Isabel, S. Carles, P. Lupien & A. Malenfant. 2021. Adaptive silviculture for climate change: from concepts to reality. The Forestry Chronicle 97: 13-27

Thiffault, N., P. Raymond, J.-M. Lussier, I. Aubin, S. Roy-Tardif, A. D’Amato, F. Doyon, B. Lafleur, M. Perron, J. Bousquet, N. Isabel, S. Carles, P. Lupien & A. Malenfant. 2021. Sylviculture d’adaptation aux changements climatiques: des concepts à la réalité. The Forestry Chronicle 97: 28-42


Depardieu, C., M.P. Girardin, S. Nadeau, P. LenzJ. 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.

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.


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.).

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.


Housset, J. M., S. Nadeau, N. Isabel, C. Depardieu, I. Duchesne, P. Lenz,
& M.P. Girardin. 2018. Tree rings provide a new class of phenotypes for genetic
associations that foster insights into adaptation of conifers to climate
change. New Phytologist. 218:630–645.

Prunier, J., I. Giguère, N. Ryan, R. Guy, R. Soolanayakanahally, N. IsabelJ. MacKay & I. Porth. 2018. Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations. Molecular Ecology 28: 1476-1490.


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.

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.).

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.


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.


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.

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.

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.


Gauthier, S., P. Bernier, P.J. Burton, J. Edwards, K. Isaac, N. Isabel, K. Jayen, H. Le Goff & E.A. Nelson. 2014. Climate change vulnerability and adaptation in the managed Canadian boreal forest. Environmental Reviews 22: 256-285.

Meirmans, P.G., M.-C. Gros-Louis, M. Lamothe, M. Perron, J. Bousquet & N. Isabel. 2014. Rates of spontaneous hybridisation and hybrid recruitment in co-existing exotic and native mature larch populations. Tree Genetics & Genomes 10: 965-975.

Roe, A.D., C.J.K. MacQuarrie, M.-C. Gros-Louis, J.D. Simpson, J. Lamarche, T. Beardmore, S.L. Thompson, P. Tanguay & N. Isabel. 2014. Fitness dynamics within a poplar hybrid zone: I. Prezygotic and postzygotic barriers impacting a native poplar hybrid stand. Ecology and Evolution 4: 1629–1647.

Roe, A.D., C.J.K. MacQuarrie, M.-C. Gros-Louis, J.D. Simpson, J. Lamarche, T. Beardmore, S.L. Thompson, P. Tanguay & N. Isabel. 2014. Fitness dynamics within a poplar hybrid zone: II. Impact of exotic sex on native poplars in an urban jungle. Ecology and Evolution 4: 1876–1889.


Isabel, N., M. Lamothe & S.L. Thompson. 2013. A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids. Tree Genetics & Genomes 9: 621-626.

LeBoldus, J.M., N. Isabel, K.D. Floate, P. Blenis & B.R. Thomas. 2013. Testing the ‘hybrid susceptibility’ and ‘phenological sink’ hypotheses using the P. balsamiferaP. deltoides hybrid zone and Septoria leaf spot [Septoria musiva]. PLoS One 8(12): e84437 (8p.).

Pavy, N., A. Deschênes, S. Blais, P. Lavigne, J. Beaulieu, N. Isabel, J. Mackay & J. Bousquet. 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.

Pavy, N., F. Gagnon, P. Rigault, S. Blais, A. Deschênes, B. Boyle, B. Pelgas, M. Deslauriers, S. Clément, P. Lavigne, M. Lamothe, J.E.K. Cooke, J.P. Jaramillo-Correa, J. Beaulieu, N. Isabel, J. Mackay & J. Bousquet. 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.

Prunier, J., B. Pelgas, F. Gagnon, M. Desponts, N. Isabel, J. Beaulieu & J. Bousquet. 2013. The genomic architecture and assocation genetics of adaptive characters using a candidate SNP approach in boreal black spruce. BMC Genomics 14: 368 (16p.).


Pavy, N., B. Pelgas, J. Laroche, P. Rigault, N. Isabel & J. Bousquet. 2012. A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers. BMC Biology 10: 84 (18p.).

Pavy, N., M.-C. Namroud, F. Gagnon, N. Isabel & J. Bousquet. 2012. The heterogenous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers. Heredity 108: 273-284.

Talbot, P., W. Schroeder, J. Bousquet & N. Isabel. 2012. When exotic poplars and native Populus balsamifera L. meet on the Canadian Prairies: spontaneous hybridization and establishment of interspecific hybrids. Forest Ecology and Management 285: 142-152.


MacKay, J., B. Boyle, W. El Kayal, M.-C. Namroud, T. Doerksen, J. Cooke, N. Isabel, J. Beaulieu, P. Rigault, P. Bicho & J. Bousquet. 2011. Gene mapping in white spruce (P. glauca): QTL and association studies integrating population and expression data. BMC Proceedings 5 (Suppl. 7): I6 (2p.).

Pelgas, B., J. Bousquet, P.G. Meirmans, K. Ritland & N. Isabel. 2011. QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments. BMC Genomics 12: 145 (23p.).

Ritland, K., K. Krutovsky, Y. Tsumura, B. Pelgas, N. Isabel & J. Bousquet. 2011. Chapter 5: Genetic mapping in conifers. In Genetics, Genomics and Breeding of Conifers (C. Plomion, J. Bousquet & C. Kole, Eds). Edenbridge Science Publishers & CRC Press, New York. Pp. 196-238.


Meirmans, P.G., M. Lamothe, M.-C. Gros-Louis, D.P. Khasa, P. Périnet, J. Bousquet & N. Isabel. 2010. Complex pattern of hybridization between exotic and native North American poplar species. American Journal of Botany 97: 1688-1697.

Namroud, M.-C., C. Guillet-Claude, J. MacKay, N. Isabel & J. Bousquet. 2010. Molecular evolution of regulatory genes in spruces from different species and continents: heterogeneous patterns of linkage disequilibrium and selection but correlated recent demographic changes. Journal of Molecular Evolution 70: 371-386.

Thompson, S.L., M. Lamothe, P.G. Meirmans, P. Périnet & N. Isabel. 2010. Repeated unidirectional introgression towards Populus balsamifera in contact zones of exotic and native poplars. Molecular Ecology 19: 132-145.


Meirmans, P.G., J. Bousquet & N. Isabel. 2009. A metapopulation model for the introgression from genetically modified plants into their wild relatives. Evolutionary Applications 2: 160-171.


Pavy, N., B. Pelgas, S. Beauseigle, S. Blais, F. Gagnon, I. Gosselin, M. Lamothe, N. Isabel & J. Bousquet. 2008. Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce. BMC Genomics 9: 21 (17p.).


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.

Meirmans, P.G., M. Lamothe, P. Périnet & N. Isabel. 2007. Species-specific single nucleotide polymorphism markers for detecting hybridization and introgression in poplar. Canadian Journal of Botany 85: 1082-1091.


Pelgas, B., S. Beauseigle, V. Acheré, S. Jeandroz, J. Bousquet & N. Isabel. 2006. Comparative genome mapping among Picea glauca, P. abies and P. mariana X rubens, and correspondance with other Pinaceae. Theoretical and Applied Genetics 113: 1371-1393.


Gros-Louis, M.-C., J. Bousquet, L.E. Paques & N. Isabel. 2005. Species-specific diagnostic markers in Larix spp. based on RAPDs and nuclear, cpDNA, and mtDNA gene sequences, and their phylogenetic implications. Tree Genetics & Genomes 1: 50-63.

Koubaa, A., N. Isabel, S.Y. Zhang, J. Beaulieu & J. Bousquet. 2005. Transition from juvenile to mature wood in Picea mariana. Wood and Fiber Science 37: 445-455.

Pelgas, B., J. Bousquet, S. Beauseigle & N. Isabel. 2005. A composite linkage map from two crosses for the species complex Picea mariana [Mill.] B.S.P. x P. rubens (Sarg.) and analysis of synteny with other Pinaceae. Theoretical and Applied Genetics 111: 1466-1488.


Guillet-Claude, C., N. Isabel, B. Pelgas & J. Bousquet. 2004. The evolutionary implications of knox-I gene duplications in conifers: correlated evidence from phylogeny, gene mapping, and analysis of functional divergence. Molecular Biology and Evolution 21: 2232-2245.

Pelgas, B., N. Isabel & J. Bousquet. 2004. Efficient screening for expressed sequence tag polymorphisms (ESTP) by DNA pool sequencing and denaturing gradient gel electrophoresis in spruces. Molecular Breeding 13: 263-279.


Jaramillo-Correa, J.P., J. Bousquet, J. Beaulieu, N. Isabel, M. Perron & M. Bouillé. 2003. Cross-species amplification of mitochondrial DNA sequence-tagged-site markers in conifers: the nature of polymorphism and variation within and among species in Picea. Theoretical and Applied Genetics 106: 1353-1367.


Fournier, D., D.J. Perry, J. Beaulieu, J. Bousquet & N. Isabel. 2002. Optimizing expressed sequence tag polymorphisms by single-strand conformation polymorphism in spruces. Forest Genetics 9: 11-18.

Gosselin, I., Y. Zhou, J. Bousquet & N. Isabel. 2002. Megagametophyte-derived linkage maps of white spruce (Picea glauca) based on RAPD, SCAR and ESTP markers. Theoretical and Applied Genetics 104: 987-997.


Koubaa, A., S.Y. Zhang, N. Isabel, J. Beaulieu & J. Bousquet. 2000. Phenotypic correlations between juvenile-mature wood density and growth in black spruce. Wood Fiber Science 32: 61-71.


Isabel, N., J. Beaulieu, P. Thériault & J. Bousquet. 1999. Direct evidence for biased gene estimates from dominant random amplified polymorphic DNA (RAPD) fingerprints. Molecular Ecology 8: 477-483.

Perry, D.J., N. Isabel & J. Bousquet. 1999. Sequence-tagged-site (STS) markers of arbitrary genes: the amount and nature of variation revealed in Norway spruce. Heredity 83: 239-248.


Isabel, N., R. Boivin, C. Lebvasseur, P.-M. Charest, J. Bousquet & F.M. Tremblay. 1996. Occurence of somaclonal variation among somatic embryo-derived white spruces (Picea glauca, Pinaceae). American Journal of Botany 83: 1121-1130.


Isabel, N., J. Beaulieu & J. Bousquet. 1995. Complete congruence between gene diversity estimates derived from genotypic data at enzyme and RAPD loci in black spruce. Proceedings of the National Academy of Sciences of USA 92: 6369-6373.

Isabel, N., R. Boivin, C. Levasseur, P.-M. Charest, J. Bousquet & F.M. Tremblay. 1995. Evidence of somaclonal variation in somatic embryo-derived plantlets of white spruce (Picea glauca (Moench) Voss.). In Current Issues in Plant Molecular & Cellular Biology (M. Terzi, R. Cella & A. Falavigna, Eds). Kluwer, Boston. Pp. 247-252.


Isabel, N., L. Tremblay, M. Michaud, F.M. Tremblay & J. Bousquet. 1993. RAPDs as an aid to evaluate the genetic integrity of somatic embryogenesis-derived populations of Picea mariana (Mill.) B.S.P. Theoretical and Applied Genetics 86: 81-87.