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The evolutionary dynamics of tree species are influenced by their specific climatic environments, and their ability to persist is determined by adaptive strategies such as broad climate tolerance, phenotypic plasticity or genetic differentiation. Biogeographical predictions indicate that populations located at the edges of their ranges are more likely to experience heightened vulnerability to climatic fluctuations due to approaching tolerance limits. However, if local phenotypic acclimation or genetic adaptation has taken place, trees near the edge of their range could demonstrate comparable sensitivity to freeze and drought as the rest of the sampled population. Nevertheless, there remains uncertainty regarding the extent of developmental and evolutionary adjustments in climate sensitivity across the entire ranges of many tree species.Here, we document the biogeography of tree growth sensitivity to freeze and soil water and vapour pressure deficits during 1950–2018 using an extensive multi‐species tree‐ring dataset of 35,784 trees at 4535 sites covering boreal, temperate conifer and temperate deciduous forests of Canada. We quantify the relationships between tree radial growth increment and seasonal climate variables and explore factors driving the observed patterns of annual growth and climate sensitivity such as species, regional climate and local site conditions, and tree age and size.Freeze and drought had widespread impacts on tree growth that were contingent on the presence of focal species in interaction with tree size. An indirect growth thermal limitation towards cold/wet edges, occurring through the site moisture conditions, was observed in seven widespread species (e.g. Picea glauca, Picea mariana and Larix laricina). Moreover, six species had negative drought impacts more strongly expressed towards their warm/dry edges (e.g. Abies balsamea, Betula papyrifera and Pseudotsuga menziesii). However, widespread Picea, Pinus and Populus species showed no indication of increased sensitivity to soil water conditions at these edges.Synthesis. Our findings support the idea of evolutionary or acclimatization adjustments in the development of populations in response to long‐term climate conditions experienced in their respective locations. This underscores the importance of incorporating phenotypic and genomic data into future analyses of climate change impacts, which would enhance our ability to predict potential ecological shifts. [ABSTRACT FROM AUTHOR]

In species with large and complex genomes such as conifers, dense linkage maps are a useful resource for supporting genome assembly and laying the genomic groundwork at the structural, populational, and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 single nucleotide polymorphism (SNP) markers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-seq and genotyping array SNP data for 528 individuals from 2 full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for P. sitchensis and Picea glauca based on 27,052 markers and 11,609 gene sequences. Altogether, these 2 linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed, herein, open new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species. [ABSTRACT FROM AUTHOR]

Tree improvement programs select genotypes for faster growth, at both early and late stages, to increase yields over unimproved material, and the improvement is frequently attributed to genetic control in growth parameters among genotypes. Underutilized genetic variability among genotypes also has the potential to ensure future gains are possible. However, the genetic variation in growth, physiology and hormone control among genotypes generated from different breeding strategies has not been well characterized in conifers. We assessed growth, biomass, gas exchange, gene expression and hormone levels in white spruce seedlings obtained from three different breeding strategies (controlled crosses, polymix pollination, open pollination) using parents grafted into a clonal seed orchard in Alberta, Canada. A pedigree-based best linear unbiased prediction (ABLUP) mixed model was implemented to quantify variability and narrow-sense heritability for target traits. The levels of several hormones and expression of gibberellinrelated genes in apical internodes were also determined. Over the first two years of development, the estimated heritabilities for height, volume, total dry biomass, above ground dry biomass, root:shoot ratio and root length, varied between 0.10 and 0.21, with height having the highest value. The ABLUP values showed large genetic variability in growth and physiology traits both between families from different breeding strategies, and within families. The principal component analysis showed that developmental and hormonal traits explained 44.2% and 29.4% of the total phenotypic variation between the three different breeding strategies and two growth groups. In general, controlled crosses from the fast growth group showed the best apical growth, with more accumulation of indole-3-acetic acid, abscisic acid, phaseic acid, and a 4-fold greater gene expression of PgGA3ox1 in genotypes from controlled crosses versus those from open pollination. However, in some cases, open pollination from the fast and slow growth groups showed the best root development, higher water use efficiency (iWUE and d13C) and more accumulation of zeatin and isopentenyladenosine. Inconclusion, tree domestication can lead to trade-offs between growth, carbon allocation, photosynthesis, hormone levels and gene expression, and we encourage the use of this phenotypic variation identified in improved and unimproved trees to advance white spruce tree improvement programs. [ABSTRACT FROM AUTHOR]

Introduction: Genomic selection is becoming a standard technique in plant breeding and is now being introduced into forest tree breeding. Despite promising results to predict the genetic merit of superior material based on their additive breeding values, many studies and operational programs still neglect non-additive effects and their potential for enhancing genetic gains. Methods: Using two large comprehensive datasets totaling 4,066 trees from 146 full-sib families of white spruce (Picea glauca (Moench) Voss), we evaluated the effect of the inclusion of dominance on the precision of genetic parameter estimates and on the accuracy of conventional pedigree-based (ABLUP-AD) and genomic-based (GBLUP-AD) models. Results: While wood quality traits were mostly additively inherited, considerable non-additive effects and lower heritabilities were detected for growth traits. For growth, GBLUP-AD better partitioned the additive and dominance effects into roughly equal variances, while ABLUP-AD strongly overestimated dominance. The predictive abilities of breeding and total genetic value estimates were similar between ABLUP-AD and GBLUP-AD when predicting individuals from the same families as those included in the training dataset. However, GBLUP-AD outperformed ABLUP-AD when predicting for new unphenotyped families that were not represented in the training dataset, with, on average, 22% and 53% higher predictive ability of breeding and genetic values, respectively. Resampling simulations showed that GBLUP-AD required smaller sample sizes than ABLUP-AD to produce precise estimates of genetic variances and accurate predictions of genetic values. Still, regardless of the method used, large training datasets were needed to estimate additive and non-additive genetic variances precisely. Discussion: This study highlights the different quantitative genetic architectures between growth and wood traits. Furthermore, the usefulness of genomic additive-dominance models for predicting new families should allow practicing mating allocation to maximize the total genetic values for the propagation of elite material. [ABSTRACT FROM AUTHOR]

Climate change is predicted to increase forest fires in boreal forests, which can threaten the sustainability of forest genetic resources. Wildfires can potentially impact genetic diversity and population structure in forest trees by creating population bottlenecks, and influencing demography, effective population size (Ne) and various evolutionary processes. We have investigated this critical issue in a widely-distributed, transcontinental, ecologically and economically important and fire-intolerant boreal conifer, white spruce (Picea glauca (Moench) Voss). We tested the hypothesis that in a predominantly outcrossing species with long distance gene flow, such as white spruce, located in primary undisturbed forests, normal forest fires do not adversely affect genetic diversity and population structure. We used 10 nuclear genic and genomic microsatellite loci to examine genetic diversity and population structure of post-fire pristine old-growth (PF-OG) and adjacent post-fire naturally regenerated young (PF-YR) stands. The genetic diversity, inbreeding and genetic differentiation levels, Bayesian population structure, Ne and latent genetic potential were statistically similar between the PF-OG and PF-YR populations. None of the microsatellites showed any signature of selection. Our study demonstrates that normal wild forest fires do not adversely affect genetic diversity, differentiation, and population genetic structure in white spruce. The results should have wide significance for sustainable forest management. [ABSTRACT FROM AUTHOR]

SUMMARY: Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non‐synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga‐genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response. Significance Statement: The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response. [ABSTRACT FROM AUTHOR]

Mechanistically predicting the evolutionary response of tree species to climate change requires an understanding of genetic variation in relevant traits. Here we compared the phenotypic and genetic variation in the Leaf Economics Spectrum (LES) traits and the response of gas exchange to vapour pressure deficit (VPD) in lodgepole pine (Pico) and white spruce (Pigl), an early and a late successional species dominating the boreal forests of western Canada.We measured gas exchange, foliar nitrogen and lamina mass to area ratio in 697 c. 30‐year‐old trees in two field progeny trials. We analysed the response of gas exchange rates to VPD using a novel quantitative genetic model, the function‐valued trait approach.Pico showed greater phenotypic variation in the LES traits and greater genetic variation in photosynthetic rate than Pigl, but the species showed no significant difference in their phenotypic correlations between the LES traits. Pico showed a less sensitive stomatal response to VPD than Pigl and no significant genetic variation in stomatal sensitivity. In contrast, Pigl showed a positive correlation between the genetic values of stomatal sensitivity to VPD and stomatal conductance under low VPD.Our study region is projected to see an increase in VPD with climate change; the less sensitive and genetically diverse stomatal response to VPD in Pico could make this species more vulnerable to climate‐change‐induced droughts. A free Plain Language Summary can be found within the Supporting Information of this article. [ABSTRACT FROM AUTHOR]

In an attempt to comprehensively study the dynamics of non-structural carbon compounds (NCCs), we measured the seasonal changes of soluble sugars, starch, lipids and sugar alcohols in the leaves, branches, stem and roots of the fast-growing Pinus contorta (Loudon) (pine) and slow-growing Picea glauca (Moench) Voss (spruce) trees growing in a boreal climate. In addition to measuring the seasonal concentrations of these compounds, the relative contribution of these compounds to the total NCC pool within the organs of trees (~8 m tall) was estimated and compared across different phenological and growth stages. Both species showed large seasonal shifts from starch to sugars from spring to fall in nearly all organs and tissues; most likely an adaptation to the cold winters. For both species, the total fluctuation of sugar + starch across the year (i.e. the difference between the minimum and maximum observed across collection times) was estimated to be between 1.6 and 1.8 kg for all NCCs. The fluctuation, however, was 1.40 times greater than the minimum reserves in pine, while only 0.72 times the minimum reserves in spruce. By tissue type, NCC fluctuations were greatest in the roots of both species. Roots showed a large build-up of reserves in late spring, but these reserves were depleted over summer and fall. Storage reserves in needles and branches declined over the summer, and this decline may be linked to the sink strength of the stem during diameter growth. Some notable highlights of this holistic study: a late winter build-up of sugars in the stem xylem of both species, but especially spruce; and an increase in sugar alcohols in the bark of spruce in very late winter, which could indicate mobilization to support early growth in spring and high lipid reserves in the bark of pine, which appeared not to be impacted by seasonal changes between summer and winter. Collectively, these observations point toward a more conservative NCC reserve strategy in spruce compared with pine, which is consistent with its stress tolerance and greater longevity. [ABSTRACT FROM AUTHOR]

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 (Picea glauca) 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. [ABSTRACT FROM AUTHOR]

Future warming may alter plant stress at high‐elevation treelines and forests, thereby changing plant–plant interactions. The relative importance of competition and facilitation may depend on the degree of resource or physical stress. According to the stress gradient hypothesis (SGH), physical stress on trees is more important at cold high elevations where facilitation predominates, and less important at low elevations where competition is the main interaction. Our goals were to investigate whether plant–plant interactions along elevational gradients corresponded to those predicted by the SGH, and to assess the effects of increasing temperatures on the growth of conifer seedlings in tundra–forest ecosystems in interior Alaska, USA. We established sites along two elevational gradients: one in tundra (four sites, 550–1170 m) and one in forest (three sites, 210–760 m). A field warming and neighbor removal experiment was conducted using transplanted seedlings of white spruce (Picea glauca). After three growing seasons, regardless of elevation, spruce seedling biomass was approximately 20% lower in seedlings with neighbor plants compared to those without neighbors. Therefore, there was no evidence for greater facilitation at high elevations across either tundra or forest elevational gradient. Seedlings in forest sites increased their shoot‐to‐root ratios and relative growth rates in height, suggesting competition for light, but this was not seen for seedlings growing in tundra sites. When warmed by greenhouses, seedling growth was stimulated in forests, especially at high elevations. In contrast, at tundra sites, warmed seedlings grew less than controls and the seedlings at high elevations showed water stress. Our results suggest that the resource stresses of low light and water availability are more important drivers of plant–plant interactions than the physical stress imposed by low temperature, possibly due to warming in the past 50 yr in this region. Further warming may increase growth of seedlings in forests, but is likely to decrease it in open tundra habitats, thereby slowing the upward movement of treeline in the near future. [ABSTRACT FROM AUTHOR]

Aims Black spruce (Picea mariana [Mill.] B.S.P.) and white spruce (Picea glauca [Moench] Voss.) are congeneric species. Both are moderately shade tolerant and widely distributed across North American boreal forests. Methods To understand light effects on their ecophysiological responses to elevated CO2, 1-year-old seedlings were exposed to 360 µmol mol−1 and 720 µmol mol−1 CO2 at three light conditions (100%, 50% and 30% of full light in the greenhouse). Foliar gas exchanges were measured in the mid- and late-growing season. Important Findings Elevated CO2 increased net photosynthesis (P n) and photosynthetic water use efficiency, but it reduced stomatal conductance and transpiration. The stimulation of photosynthesis by elevated CO2 was greatest at 50% light and smallest at 100%. Photosynthesis, maximum carboxylation rate (V cmax) and light-saturated rate of electron transport (J max) all decreased with decreasing light. Elevated CO2 significantly reduced V cmax across all light treatments and both species in mid-growing season. However, the effect of elevated CO2 became insignificant at 30% light later in the growing season, with the response being greater in black spruce than in white spruce. Elevated CO2 also reduced J max in white spruce in both measurements while the effect became insignificant at 30% light later in the growing season. However, the effect on black spruce varied with time. Elevated CO2 reduced J max in black spruce in mid-growing season in all light treatments and the effect became insignificant at 30% light later in the growing season, while it increased J max later in the season at 100% and 50% light. These results suggest that both species benefited from elevated CO2, and that the responses varied with light supply, such that the response was primarily physiological at 100% and 50% light, while it was primarily morphological at 30% light. [ABSTRACT FROM AUTHOR]

• Over many decades, red foxes increase nutrient concentrations and affect vegetation diversity on their dens in the boreal woodlands, a nutrient-poor environment. • Denning activity also affects the growth and reproduction of white spruce, a mast-seeding conifer. • White spruce on fox dens are taller and produce more cones in non-mast years than trees off dens. • The effects of denning are subject to the mast-seeding cycle, as cone production in mast years was not elevated on dens. Predators may act as ecosystem engineers by modifying their physical environment through non-trophic interactions. Red foxes (Vulpes vulpes) are ecosystem engineers in the boreal woodlands, a nutrient-poor environment, where their denning activity increases soil nutrient concentrations, affecting the diversity of vegetation around dens. Since dens can persist for many decades and tree growth is enhanced on dens, dens can be used to study the long term impacts of nutrient additions on community and ecosystem processes. We examined the reproductive output of a mast-seeding conifer, white spruce (Picea glauca), on 10 red fox dens and paired control sites at the boreal treeline near Churchill, Manitoba, in July 2019. We estimated cone production in both the current non-mast year (2019) and the previous mast year. The number of cones produced per tree and per hectare was significantly higher on dens than control sites in the non-mast year, but did not differ in the mast year. Higher cone production on dens was partly driven by trees being larger on dens. These results suggest that red fox ecosystem engineering activity affects white spruce reproduction, since increased soil nutrients on dens allow for higher cone production, but the effect of red fox denning is limited by interactions with mast-seeding mechanisms. For example, weather cues may override the effects of denning in mast years, while trees on dens may be able to allocate more resources to reproduction in non-mast years, but store the same amount of resources as trees off dens to produce similarly large cone crops in mast years. Altered resource availability in this nutrient-limited landscape could have additional ecological implications, by affecting the foraging patterns of seed predators and spruce range expansion. [ABSTRACT FROM AUTHOR]

The southern range limit of white spruce (Picea glauca) in western Canada is believed to arise from effects of moisture limitation on seedling recruitment. Within stands near white spruce's range limit, the adverse effects of water limitation on seedling growth and survival may be compounded by competition from neighboring understory plants and trees. To test this hypothesis, we conducted a competition removal experiment on white spruce seedlings in the Cypress Hills, an isolated forest landscape within the Canadian Prairies. We measured the height and diameter at root collar of 371 natural seedlings, and then we manually cleared all vegetation within a 75‐cm radius of 83 seedlings to remove local competition from neighboring plants. In addition to removal of neighboring plants, we excavated a 75‐cm radius trench around another 46 of these seedlings to remove competition for belowground resources. We took hemispherical photographs above each seedling to calculate canopy openness (a proxy for light availability) and re‐measured height and diameter over two years to calculate pre‐ and post‐treatment growth. There was a pronounced difference in precipitation between the two years of our experiment, with spring–summer precipitation 58% higher than average in the pre‐treatment year and 62% lower than average in the post‐treatment year. The diameter growth and survival of seedlings growing without competition showed smaller decreases in the dry post‐treatment year than control seedlings. Removing competition by trenching increased the height growth of seedlings located under an open canopy, but not of those growing under heavy shade. These interactions suggest that white spruce regeneration in water‐limited areas is sensitive to both light availability and local competition. Competition exacerbated drought effects on seedlings, which suggests that frequent droughts could have greater negative impacts on boreal tree seedlings that are growing under a closed canopy. [ABSTRACT FROM AUTHOR]

The C5 hemiterpenes isoprene and 2-methyl-3-buten-2-ol (MBO) are important biogenic volatiles emitted from terrestrial vegetation. Isoprene is emitted from many plant groups, especially trees such as Populus , while emission of MBO is restricted to certain North American conifers, including species of Pinus. MBO is also a pheromone emitted by several conifer bark beetles. Both isoprene and MBO have typically been measured by proton-transfer reaction mass spectrometry (PTR-MS), but this method cannot accurately distinguish between them because of their signal overlap. Our study developed a method for using selective ion flow tube mass spectrometry (SIFT-MS) that allows simultaneous on-line measurement of isoprene and MBO by employing different reagent ions. The use of m / z (NO+) = 68 u for isoprene and m / z (O2+) = 71 u for MBO gave minimal interference between the compounds. We tested the suitability of the method by measuring the emission of young trees of Populus , Picea , and Pinus. Our results largely confirm previous findings that Populus nigra , Picea glauca , and Picea abies emit isoprene and Pinus ponderosa emits MBO, but we also found MBO to be emitted by Picea abies. Thus SIFT-MS provides a reliable, easy to use, on-line measuring tool to distinguish between isoprene and MBO. The method should be of use to atmospheric chemists, tree physiologists and forest entomologists, among others. [ABSTRACT FROM AUTHOR]

The methylerythritol 4-phosphate (MEP) pathway of isoprenoid biosynthesis produces chlorophyll side chains and compounds that function in resistance to abiotic stresses, including carotenoids, and isoprene. Thus we investigated the effects of moderate and severe drought on MEP pathway function in the conifer Picea glauca , a boreal species at risk under global warming trends. Although moderate drought treatment reduced the photosynthetic rate by over 70%, metabolic flux through the MEP pathway was reduced by only 37%. The activity of the putative rate-limiting step, 1-deoxy-D-xylulose-5-phosphate synthase (DXS), was also reduced by about 50%, supporting the key role of this enzyme in regulating pathway metabolic flux. However, under severe drought, as flux declined below detectable levels, DXS activity showed no significant decrease, indicating a much-reduced role in controlling flux under these conditions. Both MEP pathway intermediates and the MEP pathway product isoprene incorporate administered 13CO2 to high levels (75–85%) under well-watered control conditions indicating a close connection to photosynthesis. However, this incorporation declined precipitously under drought, demonstrating exploitation of alternative carbon sources. Despite the reductions in MEP pathway flux and intermediate pools, there was no detectable decline in most major MEP pathway products under drought (except for violaxanthin under moderate and severe stress and isoprene under severe stress) suggesting that the pathway is somehow buffered against this stress. The resilience of the MEP pathway under drought may be a consequence of the importance of the metabolites formed under these conditions. [ABSTRACT FROM AUTHOR]

Summary: Drought intensity and frequency are increasing under global warming, with soil water availability now being a major factor limiting tree growth in circumboreal forests. Still, the adaptive capacity of trees in the face of future climatic regimes remains poorly documented.Using 1481 annually resolved tree‐ring series from 29‐yr‐old trees, we evaluated the drought sensitivity of 43 white spruce (Picea glauca (Moench) Voss) populations established in a common garden experiment.We show that genetic variation among populations in response to drought plays a significant role in growth resilience. Local genetic adaptation allowed populations from drier geographical origins to grow better, as indicated by higher resilience to extreme drought events, compared with populations from more humid geographical origins. The substantial genetic variation found for growth resilience highlights the possibility of selecting for drought resilience in boreal conifers.As a major research outcome, we showed that adaptive genetic variation in response to changing local conditions can shape drought vulnerability at the intraspecific level. Our findings have wide implications for forest ecosystem management and conservation. [ABSTRACT FROM AUTHOR]

Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5-Mb mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads based on sequence homology to the white spruce mitochondrial genome. The assembly graph shows a multipartite genome structure, composed of one smaller 168-kb circular segment of DNA, and a larger 5.4-Mb single component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination. [ABSTRACT FROM AUTHOR]

Summary: Phenology is an important indicator of environmental variation and climate change impacts on tree responses. In conifers, monitoring phenology of photosynthesis through remote sensing has been unreliable, because needle foliage varies little throughout the year. This is challenging for modelling ecosystem carbon uptake and monitoring phenology for enhanced breeding (genomic selection) and forest health.Here, we demonstrate that drone‐based carotenoid‐sensitive spectral indices, such as the Chl/carotenoid index (CCI), can be used to track phenology in conifers by taking advantage of the close relationship between seasonally changing carotenoid levels and the variation of photosynthetic activity.Physiological ground measurements, including photosynthetic pigments and maximum quantum yield of Chl fluorescence, indicated that CCI tracked the variation of photosynthetic activity better than other vegetation indices for 30 white spruce seedlings measured over 1 yr. A machine‐learning approach, using CCI derived from drone‐based multispectral imagery, was used to model phenology of photosynthesis for the entire pedigree population (6000 seedlings).This high‐throughput drone‐based phenotyping approach is suitable for studying climate change impacts and environmental variation on the physiological status of thousands of field‐grown conifers at unprecedented speed and scale. [ABSTRACT FROM AUTHOR]

Background: The presupposition of genomic selection (GS) is that predictive accuracies should be based on population-wide linkage disequilibrium (LD). However, in species with large, highly complex genomes the limitation of marker density may preclude the ability to resolve LD accurately enough for GS. Here we investigate such an effect in two conifer species with ~ 20 Gbp genomes, Douglas-fir (Pseudotsuga menziesii Mirb. (Franco)) and Interior spruce (Picea glauca (Moench) Voss x Picea engelmannii Parry ex Engelm.). Random sampling of markers was performed to obtain SNP sets with totals in the range of 200–50,000, this was replicated 10 times. Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) was deployed as the GS method to test these SNP sets, and 10-fold cross-validation was performed on 1,321 Douglas-fir trees, representing 37 full-sib F1 families and on 1,126 Interior spruce trees, representing 25 open-pollinated (half-sib) families. Both trials are located on 3 sites in British Columbia, Canada. Results: As marker number increased, so did GS predictive accuracy for both conifer species. However, a plateau in the gain of accuracy became apparent around 10,000–15,000 markers for both Douglas-fir and Interior spruce. Despite random marker selection, little variation in predictive accuracy was observed across replications. On average, Douglas-fir prediction accuracies were higher than those of Interior spruce, reflecting the difference between full- and half-sib families for Douglas-fir and Interior spruce populations, respectively, as well as their respective effective population size. Conclusions: Although possibly advantageous within an advanced breeding population, reducing marker density cannot be recommended for carrying out GS in conifers. Significant LD between markers and putative causal variants was not detected using 50,000 SNPS, and GS was enabled only through the tracking of relatedness in the populations studied. Dramatically increasing marker density would enable said markers to better track LD with causal variants in these large, genetically diverse genomes; as well as providing a model that could be used across populations, breeding programs, and traits. [ABSTRACT FROM AUTHOR]

The spruce budworm, Choristoneura fumiferana, is presumed to be panmictic across vast regions of North America. We examined the extent of panmixia by genotyping 3,650 single nucleotide polymorphism (SNP) loci in 1975 individuals from 128 collections across the continent. We found three spatially structured subpopulations: Western (Alaska, Yukon), Central (southeastern Yukon to the Manitoba–Ontario border), and Eastern (Manitoba–Ontario border to the Atlantic). Additionally, the most diagnostic genetic differentiation between the Central and Eastern subpopulations was chromosomally restricted to a single block of SNPs that may constitute an island of differentiation within the species. Geographic differentiation in the spruce budworm parallels that of its principal larval host, white spruce (Picea glauca), providing evidence that spruce budworm and spruce trees survived in the Beringian refugium through the Last Glacial Maximum and that at least two isolated spruce budworm populations diverged with spruce/fir south of the ice sheets. Gene flow in the spruce budworm may also be affected by mountains in western North America, habitat isolation in West Virginia, regional adaptations, factors related to dispersal, and proximity of other species in the spruce budworm species complex. The central and eastern geographic regions contain individuals that assign to Eastern and Central subpopulations, respectively, indicating that these barriers are not complete. Our discovery of previously undetected geographic and genomic structure in the spruce budworm suggests that further population modelling of this ecologically important insect should consider regional differentiation, potentially co‐adapted blocks of genes, and gene flow between subpopulations. [ABSTRACT FROM AUTHOR]

Plant defenses often involve specialized cells and tissues. In conifers, specialized cells of the bark are important for defense against insects and pathogens. Using laser microdissection, we characterized the transcriptomes of cortical resin duct cells, phenolic cells and phloem of white spruce ( Picea glauca) bark under constitutive and methyl jasmonate (MeJa)-induced conditions, and we compared these transcriptomes with the transcriptome of the bark tissue complex. Overall, ~3700 bark transcripts were differentially expressed in response to MeJa. Approximately 25% of transcripts were expressed in only one cell type, revealing cell specialization at the transcriptome level. MeJa caused cell-type-specific transcriptome responses and changed the overall patterns of cell-type-specific transcript accumulation. Comparison of transcriptomes of the conifer bark tissue complex and specialized cells resolved a masking effect inherent to transcriptome analysis of complex tissues, and showed the actual cell-type-specific transcriptome signatures. Characterization of cell-type-specific transcriptomes is critical to reveal the dynamic patterns of spatial and temporal display of constitutive and induced defense systems in a complex plant tissue or organ. This was demonstrated with the improved resolution of spatially restricted expression of sets of genes of secondary metabolism in the specialized cell types. [ABSTRACT FROM AUTHOR]

Within a plantation of clonal somatic embryo-derived white spruce trees that belonged to four genotypes, one genotype (G6) has consistently responded for the last 16 years, to the induction of somatic embryogenesis within primordial shoot explants. Analysis of fourteen individuals within this genotype subsequently revealed a group of clonal trees that were nonresponsive. This in turn provided a unique opportunity to conduct differential gene expression analysis in the absence of genotype-specific factors. Absolute qPCR was first used to expand the analysis of several genes previously identified via microarray analysis to be differentially expressed during SE induction, along with the inclusion of two nonresponsive genotypes. While this demonstrated a high level of repeatability within, and between, responsive and nonresponsive genotypes, it did not support our previous contention that an adaptive stress response plays a role in SE induction responsiveness, at least with respect to the candidate genes we analyzed. RNAseq analysis was then used to compare responsive and nonresponsive G6 primordial shoots during the somatic embryogenesis induction treatment. Although not analyzed in this study, this included samples of callus and embryonal masses previously generated from G6 explants. In addition to revealing a large number of differentially expressed genes, de novo assembly of unmapped reads was used to generate over 25,000 contigs that potentially represent previously unidentified transcripts. This included a MADS-domain gene that was found to be the most highly differentially expressed gene within responsive shoot explants during the first seven days of the induction treatment. [ABSTRACT FROM AUTHOR]

Conifers' exceptionally large genome (20-30 Gb) is scattered with 60% retrotransposon (RT) components and we have little knowledge on their origin and evolutionary implications. RTs may impede the expression of flanking genes and provide sources of the formation of novel small RNA (sRNAs) populations to constrain events of transposon (TE) proliferation/transposition. Here we show a declining expression of 24-nt-long sRNAs and low expression levels of their key processing gene, pgRTL2 (RNASE THREE LIKE 2) at seed set in Picea glauca. The sRNAs in 24-nt size class are significantly less enriched in type and read number than 21-nt sRNAs and have not been documented in other species. The architecture of MIR loci generating highly expressed 24-/21-nt sRNAs is featured by long terminal repeat-retrotransposons (LTR-RTs) in families of Ty3/Gypsy and Ty1/Copia elements. This implies that the production of sRNAs may be predominantly originated from TE fragments on chromosomes. Furthermore, a large proportion of highly expressed 24-nt sRNAs does not have predictable targets against unique genes in Picea, suggestive of their potential pathway in DNA methylation modifications on, for instance, TEs. Additionally, the classification of computationally predicted sRNAs suggests that 24-nt sRNA targets may bear particular functions inmetabolic processes while 21-nt sRNAs target genes involved inmany different biological processes. This study, therefore, directs our attention to a possible extrapolation that lacking of 24-nt sRNAs at the late conifer seed developmental phase may result in less constraints in TE activities, thus contributing to the massive expansion of genome size. [ABSTRACT FROM AUTHOR]

* Background and Aims Trees invest in both primary (e.g. height) and secondary (e.g. diameter) growth. The trade-off between these investments varies between species and changes with the tree growing environment. To better establish this trade-off, readily available allometric exponents relating height to diameter at breast height (γh,dbh) and stem volume to diameter at breast height (αvdbh) were simultaneously studied. * Methods Allometric exponents αv,dbh and γh,dbh were obtained from 8893 individual tree stem analyses from two broadleaved species (Betula papyrifera, Populus tremuloides) and four conifers (Picea glauca, Picea mariana, Pinus banksiana, Abies balsamea) in the temperate and boreal forests of the province of Quebec, Canada. αvdbh and γh,dbh were related to tree age, stand density index (SDI), and mean temperature (TGS) and total precipitation (PGS) of the growing season. * Key Results αv,jdbh and γh,dbh were found to be invariant with PGS and positively related to SDI and TGS for all species except Pinus banksiana. The parameter values associated with SDI and TGS were of higher value for conifers than for broadleaved species. * Conclusions This suggests that conifers and broadleaved species have different growth patterns. This could be explained by their different mode of development, the conifer species having a stronger apical dominance than broadleaved species. Such results could be further considered in allocation studies to quantify future carbon stocks in managed forests. [ABSTRACT FROM AUTHOR]

White spruce ( Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western ( PG29) and eastern ( WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation. [ABSTRACT FROM AUTHOR]

• Transcript profiling has shown the molecular bases of several biological processes in plants but few studies have developed an understanding of overall transcriptome variation. We investigated transcriptome structure in white spruce (Picea glauca), aiming to delineate its modular organization and associated functional and evolutionary attributes. • Microarray analyses were used to: identify and functionally characterize groups of coexpressed genes; investigate expressional and functional diversity of vascular tissue preferential genes which were conserved among Picea species, and identify expression networks underlying wood formation. • We classified 22 857 genes as variable (79%; 22 coexpression groups) or invariant (21%) by profiling across several vegetative tissues. Modular organization and complex transcriptome restructuring among vascular tissue preferential genes was revealed by their assignment to coexpression groups with partially overlapping profiles and partially distinct functions. Integrated analyses of tissue-based and temporally variable profiles identified secondary xylem gene networks, showed their remodelling over a growing season and identified PgNAC-7 (no apical meristerm (NAM), Arabidopsis transcription activation factor (ATAF) and cup-shaped cotyledon (CUC) transcription factor 007 in Picea glauca) as a major hub gene specific to earlywood formation. • Reference profiling identified comprehensive, statistically robust coexpressed groups, revealing that modular organization underpins the evolutionary conservation of the transcriptome structure. [ABSTRACT FROM AUTHOR]

Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world's forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20-30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine ([Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes. [ABSTRACT FROM AUTHOR]

Background and Aims MADS-box genes comprise a gene family coding for transcription factors. This gene family expanded greatly during land plant evolution such that the number of MADS-box genes ranges from one or two in green algae to around 100 in angiosperms. Given the crucial functions of MADS-box genes for nearly all aspects of plant development, the expansion of this gene family probably contributed to the increasing complexity of plants. However, the expansion of MADS-box genes during one important step of land plant evolution, namely the origin of seed plants, remains poorly understood due to the previous lack of whole-genome data for gymnosperms. Methods The newly available genome sequences of Picea abies, Picea glauca and Pinus taeda were used to identify the complete set of MADS-box genes in these conifers. In addition, MADS-box genes were identified in the growing number of transcriptomes available for gymnosperms. With these datasets, phylogenies were constructed to determine the ancestral set of MADS-box genes of seed plants and to infer the ancestral functions of these genes. Key Results Type I MADS-box genes are under-represented in gymnosperms and only a minimum of two Type I MADS-box genes have been present in the most recent common ancestor (MRCA) of seed plants. In contrast, a large number of Type II MADS-box genes were found in gymnosperms. The MRCA of extant seed plants probably possessed at least 11–14 Type II MADS-box genes. In gymnosperms two duplications of Type II MADS-box genes were found, such that the MRCA of extant gymnosperms had at least 14–16 Type II MADS-box genes. Conclusions The implied ancestral set of MADS-box genes for seed plants shows simplicity for Type I MADS-box genes and remarkable complexity for Type II MADS-box genes in terms of phylogeny and putative functions. The analysis of transcriptome data reveals that gymnosperm MADS-box genes are expressed in a great variety of tissues, indicating diverse roles of MADS-box genes for the development of gymnosperms. This study is the first that provides a comprehensive overview of MADS-box genes in conifers and thus will provide a framework for future work on MADS-box genes in seed plants. [ABSTRACT FROM AUTHOR]

Conifer needles have been reported to absorb water under certain conditions. Radial water movement across needle tissues is likely influenced by aquaporin ( AQP) water channels., Foliar water uptake and AQP localization in Picea glauca needles were studied using physiological and microscopic methods. AQP expression was measured using quantitative real-time PCR. Members of the AQP gene family in spruce were identified using homology search tools., Needles of drought-stressed plants absorbed water when exposed to high relative humidity ( RH). AQPs were present in the endodermis-like bundle sheath, in phloem cells and in the transfusion parenchyma of needles. Up-regulation of AQPs in high RH coincided with embolism repair in stem xylem. The present study also provides the most comprehensive functional and phylogenetic analysis of spruce AQPs to date. Thirty putative complete AQP sequences were found., Our findings are consistent with the hypothesis that AQPs facilitate radial water movement from the needle epidermis towards the vascular tissue. Foliar water uptake may occur in late winter when needles are covered by melting snow and may provide a water source for embolism repair before the beginning of the growing season. [ABSTRACT FROM AUTHOR]

Background A positive relationship between genome size and intron length is observed across eukaryotes including Angiosperms plants, indicating a co-evolution of genome size and gene structure. Conifers have very large genomes and longer introns on average than most plants, but impacts of their large genome and longer introns on gene structure has not be described. Results Gene structure was analyzed for 35 genes of Picea glauca obtained from BAC sequencing and genome assembly, including comparisons with A. thaliana, P. trichocarpa and Z. mays. We aimed to develop an understanding of impact of long introns on the structure of individual genes. The number and length of exons was well conserved among the species compared but on average, P. glauca introns were longer and genes had four times more intronic sequence than Arabidopsis, and 2 times more than poplar and maize. However, pairwise comparisons of individual genes gave variable results and not all contrasts were statistically significant. Genes generally accumulated one or a few longer introns in species with larger genomes but the position of long introns was variable between plant lineages. In P. glauca, highly expressed genes generally had more intronic sequence than tissue preferential genes. Comparisons with the Pinus taeda BACs and genome scaffolds showed a high conservation for position of long introns and for sequence of short introns. A survey of 1836 P. glauca genes obtained by sequence capture mostly containing introns <1 Kbp showed that repeated sequences were 10× more abundant in introns than in exons. Conclusion Conifers have large amounts of intronic sequence per gene for seed plants due to the presence of few long introns and repetitive element sequences are ubiquitous in their introns. Results indicate a complex landscape of intron sizes and distribution across taxa and between genes with different expression profiles. [ABSTRACT FROM AUTHOR]

Redundancy and competition between R2R3-MYB activators and repressors on common target genes has been proposed as a fine-tuning mechanism for the regulation of plant secondary metabolism. This hypothesis was tested in white spruce [Picea glauca (Moench) Voss] by investigating the effects of R2R3-MYBs from different subgroups on common targets from distinct metabolic pathways. Comparative analysis of transcript profiling data in spruces overexpressing R2R3-MYBs from loblolly pine (Pinus taeda L.), PtMYB1, PtMYB8, and PtMYB14, defined a set of common genes that display opposite regulation effects. The relationship between the closest MYB homologues and 33 putative target genes was explored by quantitative PCR expression profiling in wild-type P. glauca plants during the diurnal cycle. Significant Spearman’s correlation estimates were consistent with the proposed opposite effect of different R2R3-MYBs on several putative target genes in a time-related and tissue-preferential manner. Expression of sequences coding for 4CL, DHS2, COMT1, SHM4, and a lipase thio/esterase positively correlated with that of PgMYB1 and PgMYB8, but negatively with that of PgMYB14 and PgMYB15. Complementary electrophoretic mobility shift assay (EMSA) and transactivation assay provided experimental evidence that these different R2R3-MYBs are able to bind similar AC cis-elements in the promoter region of Pg4CL and PgDHS2 genes but have opposite effects on their expression. Competitive binding EMSA experiments showed that PgMYB8 competes more strongly than PgMYB15 for the AC-I MYB binding site in the Pg4CL promoter. Together, the results bring a new perspective to the action of R2R3-MYB proteins in the regulation of distinct but interconnecting metabolism pathways. [ABSTRACT FROM PUBLISHER]

Background EST (expressed sequence tag) sequences and their annotation provide a highly valuable resource for gene discovery, genome sequence annotation, and other genomics studies that can be applied in genetics, breeding and conservation programs for non-model organisms. Conifers are long-lived plants that are ecologically and economically important globally, and have a large genome size. Black spruce (Picea mariana), is a transcontinental species of the North American boreal and temperate forests. However, there are limited transcriptomic and genomic resources for this species. The primary objective of our study was to develop a black spruce transcriptomic resource to facilitate on-going functional genomics projects related to growth and adaptation to climate change. Results We conducted bidirectional sequencing of cDNA clones from a standard cDNA library constructed from black spruce needle tissues. We obtained 4,594 high quality (2,455 5' end and 2,139 3' end) sequence reads, with an average read-length of 532 bp. Clustering and assembly of ESTs resulted in 2,731 unique sequences, consisting of 2,234 singletons and 497 contigs. Approximately two-thirds (63%) of unique sequences were functionally annotated. Genes involved in 36 molecular functions and 90 biological processes were discovered, including 24 putative transcription factors and 232 genes involved in photosynthesis. Most abundantly expressed transcripts were associated with photosynthesis, growth factors, stress and disease response, and transcription factors. A total of 216 full-length genes were identified. About 18% (493) of the transcripts were novel, representing an important addition to the Genbank EST database (dbEST). Fifty-seven di-, tri-, tetra- and penta-nucleotide simple sequence repeats were identified. Conclusions We have developed the first high quality EST resource for black spruce and identified 493 novel transcripts, which may be species-specific related to life history and ecological traits. We have also identified full-length genes and microsatellite-containing ESTs. Based on EST sequence similarities, black spruce showed close evolutionary relationships with conspecific Picea glauca and Picea sitchensis compared to other Pinaceae members and angiosperms. The EST sequences reported here provide an important resource for genome annotation, functional and comparative genomics, molecular breeding, conservation and management studies and applications in black spruce and related conifer species. [ABSTRACT FROM AUTHOR]

The identification of promoters is an essential step in the genome annotation process, providing a framework for gene regulatory networks and their role in transcription regulation. Despite considerable advances in the high-throughput determination of transcription start sites (TSSs) and transcription factor binding sites (TFBSs), experimental methods are still time-consuming and expensive. Instead, several computational approaches have been developed to provide fast and reliable means for predicting the location of TSSs and regulatory motifs on a genome-wide scale. Numerous studies have been carried out on the regulatory elements of mammalian genomes, but plant promoters, especially in gymnosperms, have been left out of the limelight and, therefore, have been poorly investigated. The aim of this study was to enhance and expand the existing genome annotations using computational approaches for genome-wide prediction of TSSs in the four conifer species: loblolly pine, white spruce, Norway spruce, and Siberian larch. Our pipeline will be useful for TSS predictions in other genomes, especially for draft assemblies, where reliable TSS predictions are not usually available. We also explored some of the features of the nucleotide composition of the predicted promoters and compared the GC properties of conifer genes with model monocot and dicot plants. Here, we demonstrate that even incomplete genome assemblies and partial annotations can be a reliable starting point for TSS annotation. The results of the TSS prediction in four conifer species have been deposited in the Persephone genome browser, which allows smooth visualization and is optimized for large data sets. This work provides the initial basis for future experimental validation and the study of the regulatory regions to understand gene regulation in gymnosperms. [ABSTRACT FROM AUTHOR]

Summary: •The evolution of compositional polymers and their complex arrangement and deposition in the cell walls of terrestrial plants included the acquisition of key protein functions.•A membrane‐bound endoglucanase, termed Korrigan (KOR), has been shown to be required for proper cellulose synthesis. To date, no extensive characterization of the gymnosperm KOR has been undertaken.•Characterization of the white spruce (Picea glauca) gene encoding KOR (PgKOR) shows conserved protein features such as polarized targeting signals and residues predicted to be essential for catalytic activity. The rescue of the Arabidopsis thaliana kor1‐1 mutant by the expression of PgKOR suggests gene conservation, providing evidence for functional equivalence. Analyses of endogenous KOR expression in white spruce revealed the highest expression in young developing tissues, which corresponds with primary cell wall development. Additionally, RNA interference of the endogenous gymnosperm gene substantially reduced growth and structural glucose content, but had no effect on cellulose ultrastructure.•Partial functional conservation of KOR in gymnosperms suggests that its role in cell wall synthesis dates back to 300 million yr ago (Mya), predating angiosperms, which arose 130 Mya, and shows that proteins contributing to proper cellulose deposition are important conserved features of vascular plants. [ABSTRACT FROM AUTHOR]

Managing boreal mixed stands of trembling aspen (Populus tremuloides Michx.) and white spruce (Picea glauca [Moench] Voss) is more likely to sustain a diversity of values and has the potential to increase productivity at both the site and landscape levels compared with pure broadleaf or conifer management. In this study, we examine growth of white spruce and aspen after 11 growing seasons over a range of aspen densities created by spot and broadcast treatment of broadleaves using manual and chemical means, aspen spacing, and an untreated control. Results indicate that survival and growth of both spruce and aspen were similar across the range of treatments. Spruce groundline diameter was greater, and height to groundline diameter ratio was lower, for the treatments in which aspen was chemically controlled or uniformly spaced compared with the control. Light measurements at the individual tree level suggested that increased light availability improved white spruce diameter growth. Spruce height growth did not vary by treatment. The status of these experimental mixedwoods was compared with current conifer and mixedwood regeneration evaluations, as well as the preharvest composition of the original stand. After 11 growing seasons, growth of aspen and white spruce indicated that opportunities exist to further modify aspen density to enhance treatment longevity and effectiveness to produce a greater range of boreal mixedwood stand types. [ABSTRACT FROM AUTHOR]

Background: The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. Results: Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers. For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs) were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies. Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. Conclusions: This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic reference to functional and association genetic studies of adaptation and growth in Picea taxa. The putative QTNs identified will be tested for associations in natural populations, with potential applications in molecular breeding and gene conservation programs. QTLs mapping consistently across years and environments could also be the most important targets for breeding, because they represent genomic regions that may be least affected by G × E interactions. [ABSTRACT FROM AUTHOR]

Conifers are among the most genetically diverse plants but show the lowest levels of genetic differentiation, even among geographically distant populations. High gene flow among populations may be one of the most important factors in maintaining these genetic patterns. Here, we provide empirical evidence for extensive pollen-mediated gene dispersal between natural stands of a widespread northern temperate/boreal conifer, Picea glauca. We used 6 polymorphic allozyme loci to quantify the proportion of seeds sired by pollen originating from different sources in a landscape fragmented by agriculture in North Central Ontario, Canada. In 7 stands, a small proportion of seeds were sired by self-pollen or neighboring trees but 87.1% (±1.7% standard error [SE]) of seeds were sired by pollen from at least 250 to 3000 m away. In 4 single isolated trees, self-fertilization rates were low and more than 96% (±1.3% SE) of seeds were sired by immigrant pollen. The average minimum pollen dispersal distance in outcrossed matings was 619 m. These results provide strong evidence that extensive long-distance pollen dispersal plays a primary role in maintaining low genetic differentiation among natural populations of P. glauca and helps maintain genetic diversity and minimize inbreeding in small stands in a fragmented landscape. [ABSTRACT FROM AUTHOR]

Questions: Can a statistical model be designed to represent more directly the nature of organismal response to multiple interacting factors? Can multiplicative kernel smoothers be used for this purpose? What advantages does this approach have over more traditional habitat modelling methods? Methods: Non-parametric multiplicative regression (NPMR) was developed from the premises that: the response variable has a minimum of zero and a physiologically-determined maximum, species respond simultaneously to multiple ecological actors, he response to any one factor is conditioned by the values of other factors, and that if any of the factors is intolerable then the response is zero. Key features of NPMR are interactive effects of predictors, no need to specify an overall model form in advance, and built-in controls on overfitting. The effectiveness of the method is demonstrated with simulated and real data sets. Results: Empirical and theoretical relationships of species response to multiple interacting predictors can be represented effectively by multiplicative kernel smoothers. NPMR allows us to abandon simplistic assumptions about overall model form, while embracing the ecological truism that habitat factors interact. [ABSTRACT FROM AUTHOR]

Question: How do spatial patterns and associations of canopy and understorey vegetation vary with spatial scale along a gradient of canopy composition in boreal mixed-wood forests, from younger Aspen stands dominated by Populus tremuloides and P. balsamifera to older Mixed and Conifer stands dominated by Picea glauca? Do canopy evergreen conifers and broad-leaved deciduous trees differ in their spatial relationships with understorey vegetation? Location: EMEND experimental site, Alberta, Canada. Methods: Canopy and understorey vegetation were sampled in 28 transects of 100 contiguous 0.5 m × 0.5 m quadrats in three forest stand types. Vegetation spatial patterns and relationships were analysed using wavelets. Results: Boreal mixed-wood canopy and understorey vegetation are patchily distributed at a range of small spatial scales. The scale of canopy and understorey spatial patterns generally increased with increasing conifer presence in the canopy. Associations between canopy and understorey were highly variable among stand types, transects and spatial scales. Understorey vascular plant cover was generally positively associated with canopy deciduous tree cover and negatively associated with canopy conifer tree cover at spatial scales from 5-15 m. Understorey non-vascular plant cover and community composition were more variable in their relationships with canopy cover, showing both positive and negative associations at a range of spatial scales. Conclusions: The spatial structure and relation of boreal mixed-wood canopy and understorey vegetation varied with spatial scale. Differences in understorey spatial structure among stand types were consistent with a nucleation model of patch dynamics during succession in boreal mixed-wood forests. [ABSTRACT FROM AUTHOR]

A new member of the Argonaute (AGO) family of proteins was isolated from conifers and designated as PgAGO (Gene Bank Accession No. DQ068741; protein ID AAY67884). The complete coding sequence of PgAGO was obtained through screening cDNA libraries generated from white spruce (Picea glauca (Moench) Voss) somatic embryos. The PgAGO gene has an open reading frame of 2880 bp and encodes a protein of 960 amino acids. The predicted protein has an isolectric point of 9.17, a molecular mass of 107 kD and lacks prominent hydrophobic domains, which makes its cellular location inconclusive. The PgAGO protein contains the two conserved regions (the PAZ and PIWI domains) typically found in all members of the AGO family. The PAZ domain of PgAGO comprises 117 amino acid residues and shares a low degree of homology with similar domains in other species. The C-terminal PIWI domain contains 86 amino acids and is more conserved. Localization and transformation studies suggest that PgAGO is required for embryo development, specifically for proper shoot and root apical meristem differentiation. Based on RNA-in situ hybridization, the PgAGO transcripts are preferentially localized in cells of the shoot and root apical meristems from the early phases of embryo development. The RNA-mediated suppression of PgAGO results in severe abnormalities during embryo development, including the formation of poorly organized apical meristems. The root meristems lack the group of large central cells that separate the procambial region from the root cap, whereas the shoot meristem fails to differentiate apical initials. These abnormalities result in poor post-embryonic performance, leading to meristem abortion and growth cessation. [ABSTRACT FROM AUTHOR]

• Conifer foliage structures affect branch and bud temperature by altering the development and convective resistance of the thermal boundary layer. This paper examines foliage effects on forced convection in branches and buds of Picea glauca (Moench) Voss and Pinus contorta Dougl. Ex. Loud., two species that represent the range of variation in foliage structure among conifers. • Forced convection is characterized by a power law relating Nusselt (heat transfer) and Reynolds (boundary layer development) numbers. Data were collected in a laminar flow wind tunnel for free stream velocities of 0.16–6.95 m s−1. Scaling parameters were compared against literature values for silver cast branch replicas, a bed of real foliage, cylinders, and tube banks. • Foliage structures reduced Nusselt numbers (heat transfer) relative to cylinders, which are typically used to approximate leafless branches and buds. Significantly different scaling relationships were observed for all foliage structures considered. • Forced convection scaling relationships varied with foliage structure. The scaling relationships reported here account for variation within populations of branches and buds and can be used to characterize forced convection in a forest canopy. [ABSTRACT FROM AUTHOR]

Fire, which is the dominant disturbance in the boreal forest, creates substantial heterogeneity in soil burn severity at patch and landscape scales. We present results from five field experiments in Yukon Territory, Canada, and Alaska, USA that document the effects of soil burn severity on the germination and establishment of four common boreal trees: Picea glauca, Picea mariana, Pinus contorta subsp. latifolia, and Populus tremuloides. Burn severity had strong positive effects on seed germination and net seedling establishment after 3 years. Growth of transplanted seedlings was also significantly higher on severely burned soils. Our data and a synthesis of the literature indicated a consistent, steep decline in conifer establishment on organic soils at depths greater than 2.5 cm. A meta-analysis of seedling responses found no difference in the magnitude of severity effects on germination versus net establishment. There were, however, significant differences in establishment but not germination responses among deciduous trees, spruce, and pine, suggesting that small-seeded species experience greater mortality on lightly burned, organic soils than large-seeded species. Together, our analyses indicate that variations in burn severity can influence multiple aspects of forest stand structure, by affecting the density and composition of tree seedlings that establish after fire. These effects are predicted to be most important in moderately-drained forest stands, where a high potential variability in soil burn severity is coupled with strong severity effects on tree recruitment. [ABSTRACT FROM AUTHOR]

Herbivory by Zeiraphera canadensis Mut. & Free. (Lepidoptera: Tortricidae), an early season folivore of white spruce [ Picea glauca (Moench) Voss], has been associated with a shift in the timing of bud burst by its host during the subsequent year. We tested the hypothesis that a herbivory-induced shift in the phenology of bud development improves the window for colonisation of white spruce buds by Z. canadensis. Feeding on cortical tissue of elongating shoots caused the destruction of apical buds and an interruption of apical dominance in the year following herbivory. White spruce compensated for damage with the activation of dormant buds; mainly at proximal positions along shoots. As a result, half of all active buds on previously damaged branches were located immediately adjacent egg sites (i.e. previous year's bud scales), whereas <10% of active buds on intact shoots were situated there. More than 40% of newly emerged larvae colonised the basal buds of damaged shoots versus just 10% for intact shoots. Previous herbivory also influenced the initiation of bud burst. All buds flushed 2 days earlier on damaged shoots and date of bud burst was inversely correlated to bud density, indicating that short damaged shoots with large numbers of buds were stronger sinks for nutrients required for bud development. Egg hatch was best synchronized with early bursting buds on damaged branches. As a consequence, 89% of first-instar larvae successfully colonised buds on damaged branches while only 55% were successful on undamaged branches. Improved survival of larvae in the year following herbivory was a direct result of the evolved response by white spruce to the interruption of apical dominance. The pattern of herbivory by Z. canadensis may have evolved as a strategy to enhance the quality of white spruce for their offspring. [ABSTRACT FROM AUTHOR]

Fungi colonizing fine roots of containerized Picea glauca seedlings were assessed in four large conifer nurseries in northern Alberta. PCR amplification of fungal rDNA (internal transcribed spacer and a portion of the 5? end of the large subunit gene) from random samples of fine feeder roots gave between 1 and 4 amplicons per seedling. Amplicons were either separated by electrophoresis and sequenced directly, or cloned and sequenced. The resulting sequences were compared to sequences obtained from cultures established from seedling roots and from GenBank by maximum parsimony analysis. ITS sequences formed 11 distinct clades, each including at least one reference sequence. The ectomycorrhizal basidiomycetes Thelephora americana and Amphinema byssoides were dominant, whereas ascomycetes were less common. Fungi with sequences similar to members of the Heleotiales which form ericoid mycorrhizas were also present. Correspondence analysis revealed strong positive and negative associations among fungal taxa as well as an influence of applied fertilizer level on fungal diversity and species composition. [ABSTRACT FROM AUTHOR]

Effects of drying and cryopreservation on survival of spruce (Picea glauca (Moench) Voss and Picea glauca × engelmannii complex) somatic embryos (SEs) were investigated with the aim of developing simple and robust protocols for embryo storage. Somatic embryos dried over salt solutions of known water potential (Ψ) survived removal of virtually all free water, to a relative water content (RWC) of approximately 0.13, a value similar to that for spruce zygotic embryos from dry seed. Desiccated SEs also survived subsequent freezing in liquid nitrogen, without the addition of cryoprotectant or pre-culture steps. Highest survival (> 80%) after freezing in liquid nitrogen was in embryos pre-dried to Ψ of –15 to –20 MPa, which yielded RWC close to predicted bound (apoplastic) water values. Low (< 35%) or no survival after freezing was observed in embryos pretreated at higher Ψ (above –5 MPa) or at very low Ψ (–540 MPa, using silica gel), respectively. [ABSTRACT FROM PUBLISHER]

It has previously been shown that exogenous applications of ascorbic acid (AA) increase the conversion frequency of somatic embryos of white spruce (Picea glauca (Moench) Voss). To determine whether ascorbic acid alters purine metabolism during the early phases of embryo germination, the relative rates of purine salvage and degradation were investigated by following the metabolic fates of exogenously applied [8-14C]adenine, [8-14C]adenosine, and [8-14C]inosine, and the activities of several key enzymes. We demonstrated that both the salvage and the degradation pathways operate during germination. Specifically, adenine and adenosine were mainly salvaged to nucleotides and nucleic acids, whereas an appreciable amount of inosine was degraded to CO2 and ureides. Comparisons of purine metabolism between control and AA-treated embryos showed that exogenous applications of ascorbic acid enhanced the ability of the embryos to take up adenine and adenosine throughout the germination period. Furthermore, the higher enzymatic activities of adenosine kinase and adenine phosphoribosyltransferase were responsible for the larger proportion of adenine and adenosine being salvaged in AA-treated embryos compared with control embryos. Thus, there was a positive correlation between the ability to anabolize purine precursors and successful embryo conversion. [ABSTRACT FROM AUTHOR]

Significant reductions in needle water content were observed in white spruce (Picea glauca (Moench) Voss), black spruce (Picea mariana (Mill) B.S.P.), and jack pine (Pinus banksiana Lamb.) seedlings in response to a 10-day drought, although turgor was apparently maintained. When the seedlings were re-watered after the drought, jack pine needles regained their original saturated volume, whereas white spruce and black spruce needles did not. Significant drought-induced reductions in turgor-loss volume (i.e., tissue volume at the point of turgor loss) were observed in shoots of all three species, especially jack pine. Repeated exposure to 7 days of drought or treatment with the cytochrome P450 inhibitor, paclobutrazol ((2RS,3RS)-1-(4-chlorophenyl)-4,4-dimethyl-2-(1,2,4-triazol-1-yl)-pentan-3-ol), reduced seedling height relative to that of untreated controls in all three species. The reductions in saturated and turgor-loss needle volumes in the paclobutrazol-treated seedlings were comparable with those of seedlings subjected to a 10-day drought. The treatment-induced reductions in shoot and needle water contents enabled seedlings to maintain turgor with tissue volumes close to, or below, the turgor-loss volume of untreated seedlings. Paclobutrazol-treated seedlings subsequently survived drought treatments that were lethal to untreated seedlings. [ABSTRACT FROM AUTHOR]

Simple Summary: Leaves can only toughen after they have finished growing and, as a result, many herbivorous insects specialize in newly developing leaves because softer leaves are easier to chew. The foliage of conifer trees is particularly tough, and so one would expect conifers to invest more defensive chemicals into soft vulnerable growing needles than into tough mature ones. We summarize the literature describing how chemical defenses of foliage change during the growing season in white spruce, an economically important conifer tree. We next report measurements of the toughness of white spruce buds as they swell, burst, and grow into young needles. As expected, buds soften as they swell in spring, but after budburst, needles become tougher until they are similar to previous-year foliage in mid-summer. Leaves grown in the sun are slightly tougher than leaves grown in the shade. However, there was no indication that trees invest more in chemical defense of growing leaves than of mature leaves. Changes during leaf ontogeny affect palatability to herbivores, such that many insects, including the eastern spruce budworm (Choristoneura fumiferana (Clem.)), are specialist feeders on growing conifer leaves and buds. Developmental constraints imply lower toughness in developing foliage, and optimal defense theory predicts higher investment in chemical defense in these vulnerable yet valuable developing leaves. We summarize the literature on the time course of defensive compounds in developing white spruce (Picea glauca (Moench) Voss) needles and report original research findings on the ontogeny of white spruce needle toughness. Our results show the predicted pattern of buds decreasing in toughness followed by leaves increasing in toughness during expansion, accompanied by opposite trends in water content. Toughness of mature foliage decreased slightly during the growing season, with no significant relationship with water content. Toughness of sun-grown leaves was slightly higher than that of shade-grown leaves. However, the literature review did not support the expected pattern of higher defensive compounds in expanding leaves than in mature leaves, suggesting that white spruce might instead exhibit a fast-growth low-defense strategy. [ABSTRACT FROM AUTHOR]

Models of forest growth and yield (G&Y) are a key component in long-term strategic forest management plans. Models leveraging the industry-standard "empirical" approach to G&Y are frequently underpinned by an assumption of historical consistency in climatic growing conditions. This assumption is problematic as forest managers look to obtain reliable growth predictions under the changing climate of the 21st century. Consequently, there is a pressing need for G&Y modelling approaches that can be more robustly applied under the influence of climate change. In this study we utilized an established forest gap model (JABOWA-3) to simulate G&Y between 2020 and 2100 under Representative Concentration Pathways (RCP) 2.6, 4.5, and 8.5 in the Canadian province of Newfoundland and Labrador (NL). Simulations were completed using the province's permanent sample plot data and surface-fitted climatic datasets. Through model validation, we found simulated basal area (BA) aligned with observed BA for the major conifer species components of NL's forests, including black spruce [Picea mariana (Mill.) Britton et al.] and balsam fir [Abies balsamea (L.) Mill]. Model validation was not as robust for the less abundant species components of NL (e.g., Acer rubrum L. 1753, Populus tremuloides Michx., and Picea glauca (Moench) Voss). Our simulations generally indicate that projected climatic changes may modestly increase black spruce and balsam fir productivity in the more northerly growing environments within NL. In contrast, we found productivity of these same species to only be maintained, and in some instances even decline, toward NL's southerly extents. These generalizations are moderated by species, RCP, and geographic parameters. Growth modifiers were also prepared to render empirical G&Y projections more robust for use under periods of climate change. [ABSTRACT FROM AUTHOR]

The increasing use of unmanned aerial vehicles (UAV) and high spatial resolution imagery from associated sensors necessitates the continued advancement of efficient means of image processing to ensure these tools are utilized effectively. This is exemplified in the field of forest management, where the extraction of individual tree crown information stands to benefit operational budgets. We explored training a region-based convolutional neural network (Mask R-CNN) to automatically delineate individual tree crown (ITC) polygons in regenerating forests (14 years after harvest) using true colour red-green-blue (RGB) imagery with an average ground sampling distance (GSD) of 3 cm. We predicted ITC polygons to extract height information using canopy height models generated from digital aerial photogrammetric (DAP) point clouds. Our approach yielded an average precision of 0.98, an average recall of 0.85, and an average F1 score of 0.91 for the delineation of ITC. Remote height measurements were strongly correlated with field height measurements (r2 = 0.93, RMSE = 0.34 m). The mean difference between DAP-derived and field-collected height measurements was −0.37 m and −0.24 m for white spruce (Picea glauca) and lodgepole pine (Pinus contorta), respectively. Our results show that accurate ITC delineation in young, regenerating stands is possible with fine-spatial resolution RGB imagery and that predicted ITC can be used in combination with DAP to estimate tree height. [ABSTRACT FROM AUTHOR]