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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]

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]

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]

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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]

As boreal forests face significant threats from climate change, understanding evolutionary trajectories of coniferous species has become fundamental to adapting management and conservation to a drying climate. We examined the genomic architecture underlying adaptive variation related to drought tolerance in 43 populations of a widespread boreal conifer, white spruce (Piceaglauca [Moench] Voss), by combining genotype–environment associations, genotype–phenotype associations, and transcriptomics. Adaptive genetic variation was identified by correlating allele frequencies for 6,153 single nucleotide polymorphisms from 2,606 candidate genes with temperature, precipitation and aridity gradients, and testing for significant associations between genotypes and 11 dendrometric and drought‐related traits (i.e., anatomical, growth response and climate‐sensitivity traits) using a polygenic model. We identified a set of 285 genes significantly associated with a climatic factor or a phenotypic trait, including 110 that were differentially expressed in response to drought under greenhouse‐controlled conditions. The interlinked phenotype–genotype–environment network revealed eight high‐confidence genes involved in white spruce adaptation to drought, of which four were drought‐responsive in the expression analysis. Our findings represent a significant step toward the characterization of the genomic basis of drought tolerance and adaptation to climate in conifers, which is essential to enable the establishment of resilient forests in view of new climate conditions. see also the Perspective by Lars Opgenoorth and Christian Rellstab [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]

Understanding tree vulnerability to freezing temperatures will help resource managers to mitigate the effects of climatic variability. To test the effectiveness of tissue dehardening curves to represent whole seedling responses, we tested the cold tolerance of 4 conifer species to a range of freezing temperatures, − 15, − 25, and − 35 °C in late March, and − 5, − 10, and − 15 °C in early May. Results show that, after a 30-min exposure to freezing temperatures, needle mortality started at − 25 °C in late March (early spring dehardening) before budbreak activation and at − 10 °C in early May (late spring dehardening) when pine buds had flushed and white spruce (Picea glauca) buds had started swelling. Freezing temperatures delayed the timing of budbreak; increased needle, terminal bud, and seedling mortality; and reduced shoot growth and number of top laterals. White spruce and lodgepole pine (Pinus contorta) were more sensitive to freezing in terms of needle, terminal bud, and seedling mortality and growth reduction. The effects of March freezing were generally detected in the first year, whereas those of the May freezing were still evident in the second year on the shoot growth of black spruce (Picea mariana) and jack pine (Pinus banksiana). Although they seem relatively hardier based on first year post-freezing assessments (i.e., less immediate physical damage from freezing), black spruce and jack pine may have sustained more internal or physiological shock/damage. Our study results support the use of tissue cold hardiness–forcing temperature relationships to assess the risk of freezing damage for conifer seedlings. [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]

• We exposed seedlings of conifer species to three realistic simulated future climates. • Seedlings of conifer species experienced high mortality (75%) induced by drought. • Conifer species are highly vulnerable at the seedling stage to future drought. • Hydraulic safety margins are good indicators of mortality risk for conifer species. The future climate of northern temperate forests is projected to be drier and warmer by the end of this century. As a result, more drought-induced forest dieback events are anticipated in northeastern North America, and assessing the vulnerability of dominant tree species to drought is critical for understanding the future composition of these forests. In a greenhouse experiment, we exposed two-year-old seedlings of Picea glauca (Moench) Voss, Picea mariana (Mill.) B.S.P. and Pinus strobus L. to three future climate treatments for southern Quebec, Canada, and evaluated their mortality, growth, and foliage water status responses to soil water availability and atmospheric drought. Using a unique approach, climate treatments emulated droughts of different frequencies, durations, and intensities. Treatments closely simulated one growing season, with changes in air temperature and relative humidity every six hours and daily adjustment in the amount of water delivered to the seedlings. The three species experienced high mortality (75%) in all water-limited treatments compared to a control treatment that provided non-limiting soil moisture (0% mortality). The biomass of the seedlings that survived was 40% lower than that of control seedlings. Our results confirmed that the hydraulic safety margins, defined as the difference between seasonal minimum water potential and xylem water potential leading to 12, 50 and 88% of hydraulic conductivity loss, were good predictors of probability of tree mortality. Therefore, hydraulic safety margins are useful functional traits that can be used to compare the vulnerability of various species to drought and then provide crucial information to practitioners and policymakers to adjust forest management to climate change. We showed that three dominant conifer species of northern temperate forests were highly vulnerable to drought in future climates. Because drought is projected to be a significant threat to forests, understanding potentially adaptive physiological responses to drought, such as hydraulic safety margins of tree seedlings, is important for predicting the response of forest regeneration and composition in warmer and drier climates. [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]

This study was conducted to quantify growth responses of three major commercial conifer species (lodgepole pine (Pinus contorta Douglas ex Loudon var. latifolia Engelm. ex S. Watson), interior Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco var. glauca (Beissn.) Franco), and spruce (white spruce (Picea glauca (Moench) Voss) and hybrid spruce (Picea engelmannii Parry ex. Engelm. × Picea glauca (Moench) Voss × Picea sitchensis (Bong.) Carrière))) to various fertilizer blends in interior British Columbia, Canada. Over 25 years, growth-response data were repeatedly collected across 46 installations. The fertilizer blends were classified into three groups: nitrogen only; nitrogen and sulfur combined; and nitrogen, sulfur, and boron combined. The growth responses for stand volume, basal area, and top height were calculated through absolute and relative growth rate ratios relative to a controlled group. Fertilizer blend, inverse years since fertilization, site index, stand density at fertilization, and their interactions with the fertilizer blend were used as explanatory variables. The magnitude and significance of volume and basal area growth responses to fertilization differed by species, fertilizer-blend groups, and stand-condition variables (i.e., site index and stand density). In contrast, the response in top height growth did not differ among fertilization blends, with the exception of the nitrogen and sulfur fertilizer subgroup for lodgepole pine. The models developed in this study will be incorporated into the current growth and yield fertilization module (i.e., Table Interpolation Program for Stand Yields (TIPSY)), thereby supporting guidance of fertilization applications in interior forests in British Columbia. [ABSTRACT FROM AUTHOR]

Mid-latitude forests commonly show increased productivity and ultimately produce larger trees on shaded, northern aspects compared with those on sunny, southern aspects. Little research has been conducted on this phenomenon at higher latitudes where solar radiation is less available. We examined patterns of canopy tree size in a set of 142 naturally regenerated, late-seral conifer stands in northwestern British Columbia, Canada, at latitudes of 54°N–56°N. The height, diameter, and total stem volume of three shade-tolerant conifers (western hemlock (Tsuga heterophylla (Raf.) Sarg.), subalpine fir (Abies lasiocarpa (Hook.) Nutt.), and hybrid spruce (Picea glauca × engelmannii (Moench) Voss)) and shade-intolerant lodgepole pine (Pinus contorta var. latifolia Engelm. ex S. Watson) were analyzed. In contrast to most previous studies, mean canopy tree height, diameter, and volume were greatest on southern aspects and lowest on northern aspects for the subset of sites with pronounced slopes (≥30%). There was some variation in patterns among species, with western hemlock responding most strongly to topography, and species-specific effects of topography on height–diameter allometry. We suggest that decreased levels of radiation at northern latitudes and increased light and warmer temperatures on steeper, southern aspects promote growth. In contrast, colder, shaded, northern aspects with increased snow accumulation, delayed snowmelt, and decreased nitrogen mineralization inhibit growth. Our results, together with published data, suggest that a latitudinal shift from higher forest productivity on northern aspects to higher productivity on southern aspects typically occurs between 40°N and 50°N. [ABSTRACT FROM AUTHOR]

The processes for producing conifer planting stock by somatic embryogenesis (SE) in conifers are described. Implementation of SE presents opportunities and limitations at various stages of the in vitro process. The topic of genetic stability, or somaclonal variation, is a particular concern and reviewed. Following the in vitro processes, several factors affect the successful acclimation, early growth and field performance of SE planting stock. Experiences with other conifer species in the context of commercial production are reviewed. While SE production has historically been a very labor-intensive process, recent advances have been made to automate the various steps. Developments to enable SE for Norway spruce in Sweden are described. [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]

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]

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 AUTHOR]

Next-generation sequencing (NGS) technologies are revolutionizing both medical and biological research through generation of massive SNP data sets for identifying heritable genome variation underlying key traits, from rare human diseases to important agronomic phenotypes in crop species. We evaluated the performance of genotyping-by-sequencing (GBS), one of the emerging NGS-based platforms, for genotyping two economically important conifer species, lodgepole pine ( Pinus contorta) and white spruce ( Picea glauca). Both species have very large genomes (>20,000 Mbp), are highly heterozygous, and lack reference sequences. From a small set (six accessions each) of independent replicated DNA samples and a 48-plex read depth, we obtained ~60,000 SNPs per species. After stringent filtering, we obtained 17,765 and 17,845 high-coverage SNPs without missing data for lodgepole pine and white spruce, respectively. Our results demonstrated that GBS is a robust and suitable method for genotyping conifers. The application of GBS to forest tree breeding and genomic selection is discussed. [ABSTRACT FROM AUTHOR]

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]

Early establishment of competing vegetation often presents an obstacle to the success of planted white spruce ( Picea glauca (Moench) Voss) seedlings. We followed growth and development of white spruce and associated vegetation for up to 17 years in Alaska's boreal forests to quantify roles of overtopping plant cover in suppressing conifers. The three study areas represented a range of site conditions of varying productivity and species of competing cover, different site preparation and release treatments, and different bare-root and container white spruce stock types. Herbaceous overtopping peaked early after planting and decreased as white spruce were able to outgrow competitors. Overtopping by shrubs and hardwoods, especially aspen ( Populus tremuloides Michx.) and resin birch ( Betula neoalaskana Sarg.) peaked somewhat later than herbaceous overtopping and decreased over time for most sites and treatments. In a model that combined all sites, vegetation management treatments, and years, overtopping and previous year's volume explained approximately 85% of the variation in volume growth. Increasing the size of planting stock helped reduce overtopping, hence suppression, even in treatments dominated by hardwood species. Results suggested that control of overtopping was essential for maximum growth and long-term or increasing levels of overtopping severely suppressed white spruce seedling growth. [ABSTRACT FROM AUTHOR]

Context: It is widely accepted that ring area increment generally increases from the tree apex to the crown base and is more-or-less constant below the crown base (Pressler's law), but few quantitative models of this distribution have been developed. Aims: The aim of this study was to develop a model of ring area increment using easily obtained crown features and other tree or stand characteristics in order to further the understanding and prediction of tree growth, form, and wood quality. Methods: The models were fit to stem analysis observations from white spruce, black spruce, balsam fir, and lodgepole pine. Results: In the final model, which includes tree crown and stand variables, ring area increment within the crown region was slightly curvilinear, the slope of ring area increment below the crown was non-zero, and the effect of butt swell was appreciable up-to a relative height of 0.10. Conclusions: The high accuracy of the mixed effects model suggests that the three-component model form is appropriate for describing ring area profiles, whereas some tree-to-tree variation remains unexplained. The tree and stand variables used in these models can be easily measured in the field or obtained from remote sensing techniques. [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]

An endoconidial, black meristematic taxon gen. et. sp. nov. (Dothideales) from the black subicula found on twigs of declining white spruce, (Moench) Voss, in Alberta is described. It is morphologically distinguishable from other endoconidial taxa by the conidioma composed of clumps of endoconidial conidiogenous cells, scattered meristematically dividing cells, dematiaceous hyphae, abundant brown, granular matrix materials, and sometimes plant tissue. Endoconidia also occur in conidiogenous cellular clumps that are not organized into a conidioma but develop directly from stromatic cells on the bark. In culture, it forms similar endoconidial conidiomata and also a mycelial, blastic synanamorph that superficially resembles . is a member of the Dothideales and shows phylogenetic affinities to a clade of conifer-stem and -needle pathogens, including and , although no teleomorph was found either on the natural substrate or in culture. It has not been determined whether A. arboricola is pathogenic to its host, but the occurrence of abundant intracellular hyphae in the host periderm suggests that the fungus is at least parasitic. [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]

Mineral soils exposed by fire are often covered by a layer of ash due to complete consumption of the forest floor (litter and duff). To assess the possible effects of ash on seed germination and viability of jack pine (Pinus banksiana Lamb.), black spruce (Picea mariana (Mill.) Britton, Sterns, Poggenb.), white spruce (Picea glauca (Moench) Voss), and balsam fir (Abies balsamea (L.) Mill.), a laboratory experiment was conducted using ash derived from three types of forest floor samples. The samples represented areas of high conifer concentration, high aspen concentration, and mixed aspen and conifer and were collected from five mature aspen (Populus tremuloides Michx.) – conifer mixedwood stands in southeastern Manitoba. Ash derived from each forest floor type neither prohibited nor delayed conifer germination, except that of balsam fir. Balsam fir had significantly less germination on ash derived from forest floor samples with high aspen concentration. When corrected for seed viability, balsam fir had significantly less germination on all three ash types compared with jack pine, black spruce, and white spruce. However, the impact of ash on balsam fir is unlikely to have meaningful ecological implications, as balsam fir is a climax species and will establish in undisturbed mature forests. Le sol minéral exposé par le feu est souvent recouvert d’une couche de cendre due à la combustion de la couverture morte (litière et humus). Les effets de la cendre sur la viabilité et la germination des graines de pin gris (Pinus banksiana Lamb.), d’épinette noire (Picea mariana (Mill.) Britton, Sterns, Poggenb.), d’épinette blanche (Picea glauca (Moench) Voss) et de sapin baumier (Abies balsamea (L.) Mill.) ont été évalués. Une expérience en laboratoire a été réalisée en utilisant de la cendre provenant de trois types d’échantillons de couverture morte, représentatifs de zones avec une concentration élevée de conifères (HC), de peupliers (LC) et d’un mélange de peupliers et de conifères (MC) prélevés dans cinq peuplements mixtes matures de peuplier faux-tremble (Populus tremuloides Michx.) dans le sud-est du Manitoba. La cendre provenant de chacun des types de couverture morte n’a ni inhibé ni retardé la germination des conifères à l’exception du sapin baumier. Les graines de sapin baumier germaient significativement moins bien sur la cendre provenant du type de couverture morte LC. Lorsqu’elle était corrigée pour la viabilité des graines, la germination du sapin baumier était significativement plus faible sur les trois types de cendre comparativement au pin gris, à l’épinette noire et à l’épinette blanche. L’impact de la cendre sur le sapin baumier a peu de chances d’avoir des implications écologiques significatives étant donné que le sapin baumier est une espèce climacique qui s’établira dans les forêts matures non perturbées. [ABSTRACT FROM AUTHOR]

Abstract: This work aimed to compare radial growth–climate relationships among three coexisting coniferous tree species across a wide geographic and climate range from southern British Columbia (BC) to central Yukon, Canada. Tree-ring data were collected from 20 mature stands of white spruce (Picea glauca), lodgepole pine (Pinus contorta var. latifolia), and subalpine fir (Abies lasiocarpa). Linear relationships between annual growth variation and monthly and seasonal climate were quantified with correlation and regression analyses, and variation in climate–growth responses over a climatic gradient were quantified by regressing growth responses against local mean climatic conditions. Temperatures had more consistent and stronger correlations with growth for all three species than precipitation, but growth–climate responses varied among species and among sites. In particular, pine and fir populations showed different responses between BC and Yukon, whereas spruce showed a more consistent response across the study domain. Results indicate that (1) the response and sensitivity of trees to seasonal climate variables vary among species and sites and (2) winter temperatures prior to growth may have significant impacts on pine and fir growth at some sites. The capacity to adapt to climate change will likely vary among the study species and across climatic gradients, which will have implications for the future management of mixed-species forests in Yukon and BC. [Copyright &y& Elsevier]

Abstract: This study reports 14th-year response of a boreal mixedwood stand to different harvest intensities (uncut, 50% partial cut with and without removal of residuals after 3 years, and clearcut), spot site preparation treatments (none and scalped), and chemical weeding frequencies (none, single, and multiple) in northeastern Ontario. The response variables include the survival and growth of planted white spruce (Picea glauca [Moench] Voss) and jack pine (Pinus banksiana Lamb.), height and density of natural regeneration and shrubs, and cover of shrubs and non-woody vegetation. Harvesting and weeding generally improved survival and growth of planted trees, although white spruce survival did not significantly differ among the three weeding frequencies. Harvesting tended to increase heights of hardwood (mostly trembling aspen (Populus tremuloides Michx.)) and conifer (largely balsam fir (Abies balsamea (L.) Mill.).) natural regeneration, cover and density of shrubs, and cover of herbs, lichens, and ferns. Chemical weeding reduced height, density and cover of shrubs, height and density of hardwood regeneration, and fern cover, but increased moss and lichen cover. Spot scalping did not significantly affect planted seedling, natural regeneration, or the vegetation. Maximum survival and growth of planted white spruce and jack pine were achieved using a combination of clearcutting and multiple weeding. However, partial cutting followed by a single weeding produced acceptable survival and reasonable growth of planted trees, particularly for white spruce. Partial canopy removal alone substantially reduced the amount of hardwood regeneration, relative to clearcutting, but did not adequately suppress understory shrubs. Significant improvement in seedling growth following multiple weedings was evident primarily in the complete canopy removal treatments: 50% partial cut with removal of residuals after 3 years and clearcut. While the effects of harvesting and weeding on planted crop trees found in the 5th-year assessments generally persisted at year 14, survival decreased, likely due to light competition from developing hardwood and shrubs. [Copyright &y& Elsevier]