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Data from: A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids
Isabel, Nathalie; Lamothe, Manuel; Thompson, Stacey Lee — 2013-03-28 Rapid identification of Populus L. species and hybrids can be achieved with relatively little effort through the use of primer extension-based single nucleotide polymorphism (SNP) genotyping assays. We present an optimized set of 36 SNP markers from 28 gene regions that diagnose eight poplar species (Populus angustifolia James, Populus balsamifera L., Populus deltoides Bartram, Populus fremontii Watson, Populus laurifolia Ledeb., Populus maximowiczii Henry, Populus nigra L., and Populus trichocarpa Torr. & Gray). A total of 700 DNA sequences from six Populus species (1–15 individuals per species) were used to construct the array. A set of flanking and probe oligonucleotides was developed and tested. The accuracy of the SNP assay was validated by genotyping 448 putatively “pure” individuals from 14 species of Populus. Overall, the SNP assay had a high success rate (97.6 %) and will prove useful for the identification of all Aigeiros Duby and Tacamahaca Spach. species and their early-generation hybrids within natural populations and breeding programs. Null alleles and intraspecific polymorphisms were detected for a few locus/species combinations in the Aigeiros and Tacamahaca sections. When we attempted to genotype aspens of the section Populus (Populus alba L., Populus grandidentata Michx., Populus tremula L., and Populus tremuloides Michx.), the success rate of the SNP array decreased by 13 %, demonstrating moderate cross-sectional transferability. https://creativecommons.org/publicdomain/zero/1.0/
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How useful is genomic data for predicting maladaptation to future climate?
Lind, Brandon; Candido-Ribeiro, Rafael; Singh, Pooja; Lu, Mengmeng; Obreht Vidakovic, Dragana; Booker, Tom; Whitlock, Michael; Yeaman, Sam; Isabel, Nathalie; Aitken, Sally — 2024-04-17 <p>Methods using genomic information to forecast potential population maladaptation to climate change or new environments are becoming increasingly common, yet the lack of model validation poses serious hurdles toward their incorporation into management and policy. Here, we compare the validation of maladaptation estimates derived from two methods – Gradient Forests (GF<sub>offset</sub>) and the Risk Of Non-Adaptedness (RONA) – using exome capture pool-seq data from 35 to 39 populations across three conifer taxa: two Douglas-fir varieties and jack pine. We evaluate sensitivity of these algorithms to the source of input loci (markers selected from genotype-environment associations [GEA] or those selected at random). We validate these methods against two-year and 52-year growth and mortality measured in independent transplant experiments. Overall, we find that both methods often better predict transplant performance than climatic or geographic distances. We also find that GF<sub>offset</sub> and RONA models are surprisingly not improved using GEA candidates. Even with promising validation results, variation in model projections to future climates makes it difficult to identify the most maladapted populations using either method. Our work advances understanding of the sensitivity and applicability of these approaches, and we discuss recommendations for their future use.</p>
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Data from: Finding common ground: Toward comparable indicators of adaptive capacity of tree species to a changing climate
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Aubin, Isabelle; Royer-Tardif, Samuel; Boisvert-Marsh, Laura; Godbout, Julie; Isabel, Nathalie — 2022-08-02 <p>Adaptive capacity, one of the three determinants of vulnerability to climate change, is defined as the capacity of species to persist in their current location by coping with novel environmental conditions through acclimation and/or evolution. Although studies have identified indicators of adaptive capacity, few have assessed this capacity in a quantitative way that is comparable across tree species. Yet, such multi-species assessments are needed by forest management and conservation programs to refine vulnerability assessments and to <span style="background:white;">guide the choice of adaptation measures</span>. In this paper, we propose a framework to quantitatively evaluate five key components of tree adaptive capacity to climate change: individual adaptation through phenotypic plasticity, population phenotypic diversity as influenced by genetic diversity, genetic exchange within populations, genetic exchange between populations and genetic exchange between species. For each component, we define the main mechanisms that underlie adaptive capacity and present associated metrics that can be used as indices. To illustrate the use of this framework, we evaluate the relative adaptive capacity of 26 northeastern North American tree species using values reported in the literature. Our results show adaptive capacity to be highly variable among species and between components of adaptive capacity, such that no one species ranks consistently across all components. On average, the conifer <i>Picea glauca</i> and the broadleaf <i>Betula papyrifera </i>show the greatest adaptive capacity among the 26 species we documented, whereas the conifers <i>Picea rubens </i>and <i>Thuja occidentalis</i>,<i> </i>and the broadleaf <i>Ostrya virginiana</i> possess the lowest. We discuss limitations that arise when comparing adaptive capacity among species, including poor data availability and comparability issues in metrics derived from different methods or studies. The breadth of data required for such an assessment exemplifies the multidisciplinary nature of adaptive capacity and the necessity of continued cross-collaboration to better anticipate the impacts of a changing climate.</p>
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Data from: Fitness dynamics within a poplar hybrid zone: I. Prezygotic and postzygotic barriers impacting a native poplar hybrid stand.
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Roe, Amanda D.; MacQuarrie, Chris J. K.; Gros-Louis, Marie-Claude; Simpson, J. Dale; Lamarche, Josyanne; Beardmore, Tannis; Thompson, Stacey L.; Tanguay, Philippe; Isabel, Nathalie — 2015-03-17 Hybridization and introgression are pervasive evolutionary phenomena that provide insight to the selective forces that maintain species boundaries, permit gene flow and control the direction of evolutionary change. Poplar trees (Populus L.) are well known for their ability to form viable hybrids and maintain their distinct species boundaries despite this interspecific gene flow. We sought to quantify the hybridization dynamics and postzygotic fitness within a hybrid stand of balsam poplar (Populus balsamifera L.), eastern cottonwood (P. deltoides Marsh.) and their natural hybrids to gain insight to the barriers maintaining this stable hybrid zone. We observed asymmetrical hybrid formation with P. deltoides acting as the seed parent, but with subsequent introgression biased towards P. balsamifera. Native hybrids expressed fitness traits intermediate to the parental species and were not universally unfit. That said, native hybrid seedlings were absent from the seedling population, which may indicate additional selective pressures controlling their recruitment. It is imperative that we understand the selective forces maintaining this native hybrid zone in order to quantify the impact of exotic poplar hybrids on this native system.
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Data from: Fitness dynamics within a poplar hybrid zone: II. Impact of exotic sex on native poplars in an urban jungle.
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Roe, Amanda D.; MacQuarrie, Chris J. K.; Gros-Louis, Marie-Claude; Simpson, J. Dale; Lamarche, Josyanne; Beardmore, Tannis; Thompson, Stacey L.; Tanguay, Philippe; Isabel, Nathalie; MacQuarrie, Chris J.K. — 2015-03-17 Trees bearing novel or exotic gene components are poised to contribute to the bioeconomy for a variety of purposes such as bioenergy production, phytoremediation, and carbon sequestration within the forestry sector, but sustainable release of trees with novel traits in large-scale plantations requires the quantification of risks posed to native tree populations. Over the last century, exotic hybrid poplars produced through artificial crosses were planted throughout eastern Canada as ornamentals or windbreaks and these exotics provide a proxy by which to examine the fitness of exotic poplar traits within the natural environment to assess risk of exotic gene escape, establishment, and spread into native gene pools. We assessed postzygotic fitness traits of native and exotic poplars within a naturally regenerated stand in eastern Canada (Quebec City, QC). Pure natives (P. balsamifera and P. deltoides spp. deltoides), native hybrids (P. deltoides × P. balsamifera), and exotic hybrids (trees bearing Populus nigra and P. maximowiczii genetic components) were screened for reproductive biomass, yield, seed germination, and fungal disease susceptibility. Exotic hybrids expressed fitness traits intermediate to pure species and were not significantly different from native hybrids. They formed fully viable seed and backcrossed predominantly with P. balsamifera. These data show that exotic hybrids were not unfit and were capable of establishing and competing within the native stand. Future research will seek to examine the impact of exotic gene regions on associated biotic communities to fully quantify the risk exotic poplars pose to native poplar forests.
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Genes involved in the constitutive production of phenolic compounds in white spruce
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Gérardi, Sébastien; Laoué, Justine; Depardieu, Claire; Lamothe, Manuel; Bomal, Claude; Azaiez, Aïda; Gros-Louis, Marie-Claude; Laroche, Jerôme; Boyle, Brian; Hammerbacher, Almuth; Isabel, Nathalie; Bousquet, Jean — 2021-05-13 <p>Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (<em>Picea glauca</em>) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.</p>

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(auteur : Isabel, Nathalie)

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