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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]

Contamination of soils with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX, Research Department Explosive) as a result of military applications is a large-area problem globally. Since coniferous trees dominate the vegetation of large areas of military land in Central Europe, particularly in Germany, the long-term fate of14C-RDX in the conifers Scots pine and Dwarf Alberta spruce was studied. Acetic acid was the most effective solvent for the removal of extractable RDX residues from homogenates of RDX-laden tree material (85%, 80–90% and 64–80% for roots, wood and needles, respectively). On average, only a fifth of RDX-derived14C was bound in non-extractable residues (NER). Within the main cell wall compartments, lignin was the dominant binding site for NER (needles: 32–62%; roots: 38–42%). Hemicellulose (needles: 11–18%; roots: 6–11%) and cellulose (needles: 12–24%; roots: 1–2%) were less involved in binding and a considerable proportion of NER (needles: 15–24%; roots: 59–51%) was indigestible. After three-year incubation in rot chambers, mineralisation of tree-associated14C-RDX to14CO2clearly dominated the mass balance in both tree species with 48–83%. 13–33% of14C-RDX-derived radioactivity remained in an unleachable form and the remobilisation by water leaching was negligible (< 2%). [ABSTRACT FROM PUBLISHER]

The article provides information on the infanticides committed by the male red squirrels before a mast year. Topics discussed include their anticipation for White Spruce's production of cones, the death of pups after the female stops lactating, and the infanticide occuring frequently in species in which the male can monopolize the female species.

Conifers possess a suite of physiochemical defenses that protect their subcortical tissues from bark beetle - fungal complexes. These defenses include rapid induction of terpenoids and phenolics at the site of attack. Studies of the distribution, induction, and bioactivity of conifer terpenoids have focused heavily on monoterpenes. We assessed induction of diterpene acids in white spruce ( Picea glauca) and red pine ( Pinus resinosa) to fungal associates of two bark beetles, and the responses of four spruce beetle ( Dendroctonus rufipennis)-associated fungi to three diterpene acids. Constitutive phloem contents differed between species, in that red pine had extremely low concentrations of diterpene acids, whereas white spruce had substantial constitutive levels. Induction differed quantitatively. Both red pine and white spruce exhibited marked increases, but red pine underwent greater increases and achieved higher concentrations than white spruce. Induction also differed qualitatively in that red pine showed lower diversity and fewer compositional changes during induction than white spruce. In red pine,fungal inoculation accompanying wounding elicited greater increases than wounding alone, but in white spruce total concentrations were higher following wounding alone. Spruce beetle fungal symbiont growth varied among species and compounds. Some diterpenes elicited both stimulatory and inhibitory effects on fungi, depending on concentration. All four fungi exhibited higher tolerances compared to those associated with pine bark beetles in previous studies. Variation in tolerances to, and potentially metabolism of, diterpene acids by symbionts may reflect differences in constitutive levels between spruce and pine, and partially explain differences in concentrations achieved during induction. [ABSTRACT FROM AUTHOR]

The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (>50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Piceagene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms. [ABSTRACT FROM AUTHOR]

The establishment of patterns of radial and longitudinal variations and the development of models to predict the wood anatomical properties, especially from juvenile wood, are of interest for both wood industry and researchers. Linear regressions were used to predict whole-tree, breast height and mature tracheid length and diameter in white spruce (Picea glauca (Moench) Voss) and the WBE model was used to predict the variation of tracheid diameter. Tracheid length and diameter increased from pith to bark. Tracheid length decreased, while tracheid diameter increased from apex to lower heights. Cambial age was the most important predictor of tracheid length. The final tracheid length models with either a log transformation or a third-order polynomial of cambial age explained 82% of the variation in the whole-tree tracheid length. At breast height, 83% of the variation in the whole tracheid length was explained using the juvenile value at a cambial age of 3 years. Up to 87% of the variation was explained by the model, including the average value of juvenile wood. However, mature wood tracheid length at breast height could not be predicted from juvenile wood. Distance from the apex predicted the tracheid widening in outer rings but failed to predict tracheid expansion of samples collected at fixed cambial ages. The WBE explained 86% of conduit widening in the outer rings. The sampling strategy, i.e. collecting samples longitudinally at a fixed cambial age vs. at a fixed calendar year is important in predicting tracheid diameter. [ABSTRACT FROM AUTHOR]

Although many studies have examined the phenological mismatches between interacting organisms, few have addressed the potential for mismatches between phenology and seasonal weather conditions. In the Arctic, rapid phenological changes in many taxa are occurring in association with earlier snowmelt. The timing of snowmelt is jointly affected by the size of the late winter snowpack and the temperature during the spring thaw. Increased winter snowpack results in delayed snowmelt, whereas higher air temperatures and faster snowmelt advance the timing of snowmelt. Where interannual variation in snowpack is substantial, changes in the timing of snowmelt can be largely uncoupled from changes in air temperature. Using detailed, long-term data on the flowering phenology of four arctic plant species from Zackenberg, Greenland, we investigate whether there is a phenological component to the temperature conditions experienced prior to and during flowering. In particular, we assess the role of timing of flowering in determining pre-flowering exposure to freezing temperatures and to the temperatures experienced prior to flowering. We then examine the implications of flowering phenology for flower abundance. Earlier snowmelt resulted in greater exposure to freezing conditions, suggesting an increased potential for a mismatch between the timing of flowering and seasonal weather conditions and an increased potential for negative consequences, such as freezing damage. We also found a parabolic relationship between the timing of flowering and the temperature experienced during flowering after taking interannual temperature effects into account. If timing of flowering advances to a cooler period of the growing season, this may moderate the effects of a general warming trend across years. Flower abundance was quadratically associated with the timing of flowering, such that both early and late flowering led to lower flower abundance than did intermediate flowering. Our results indicate that shifting the timing of flowering affects the temperature experienced during flower development and flowering beyond that imposed by interannual variations in climate. We also found that phenological timing may affect flower abundance, and hence, fitness. These findings suggest that plant population responses to future climate change will be shaped not only by extrinsic climate forcing, but also by species' phenological responses. [ABSTRACT FROM AUTHOR]

The position of the Arctic treeline, which is a key regulator of surface energy exchange and carbon cycling, is widely thought to be controlled by temperature. Here, we present evidence that soil nutrient availability, rather than temperature, may be the proximate control on growth of treeline trees at our study site in northwest Alaska. We examined constraints on growth and allocation of white spruce in three contrasting habitats. The habitats had similar aboveground climates, but soil temperature declined from the riverside terrace to the forest to the treeline. We identified six lines of evidence that conflict with the hypothesis of direct temperature control and/or point to the importance of soil nutrient availability. First, the magnitude of aboveground growth declined from the terrace to the forest to the treeline, along gradients of diminishing soil nitrogen (N) availability and needle N concentration. Second, peak rates of branch extension, main stem radial and fine-root growth were generally not coincident with seasonal air and soil temperature maxima. At the treeline, in particular, rates of aboveground and fine-root growth declined well before air and soil temperatures reached their seasonal peaks. Third, in contrast with the hypothesis of temperature-limited growth, growing season average net photosynthesis was positively related to the sum of normalized branch extension, main stem radial and fine-root growth across trees and sites. Fourth, needle nonstructural carbohydrate concentration was significantly higher on the terrace, where growth was greatest. Fifth, annual branch extension growth was positively related to snow depth, consistent with the hypothesis that deeper snow promotes microbial activity and greater soil nutrient availability. Finally, the tree ring record revealed a large growth increase during late 20th-century climate warming on the terrace, where soil N availability is relatively high. Meanwhile, trees in the forest and at the treeline showed progressively smaller growth increases. Our results suggest temperature effects on tree growth at our study sites may be mediated by soil nutrient availability, making responses to climate change more complex and our ability to interpret the tree ring record more challenging than previously thought. [ABSTRACT FROM AUTHOR]

White spruce (Picea glauca (Moench) Voss) trees that are resistant or susceptible to spruce budworm (Choristoneura fumiferana (Clem.)) attack were identified in a southern Quebec plantation. Due to high mortality-induced selective pressures imposed by resistant trees on spruce budworm larvae, insects that survive on resistant trees exhibited greater biological performance than those on susceptible trees. We tested the hypothesis that this better biological performance is maintained across generations when progeny were subjected to nutritional stress. We collected pupae from resistant and susceptible trees (phenotype). Adults were reared under controlled laboratory conditions. Progeny were subsequently reared on two types of artificial diet (high vs. low quality). Low quality diet simulated food quality deterioration during outbreak conditions. Results confirmed that surviving insects collected from resistant trees have better performance than those from susceptible trees. Offspring performance (pupal mass, developmental time) was affected only by diet quality. These results suggest that adaptive advantages that would be acquired from parents fed on resistant trees are lost when progeny are exposed to nutritionally-imbalanced food, but the effects persist when larvae are fed a balanced diet. Offspring mortality, fecundity and fertility were positively influenced by parental origin (tree phenotype). [ABSTRACT FROM AUTHOR]

Tree improvement programs aim to develop families that are well-adapted to future growing conditions. To gain insight into the stability of the family genetic response to climate change, white spruce (Picea glauca) seedlings from 60 full-sib families were subjected to a combination of two temperature regimes and two levels of CO2over two growing seasons. There was positive effect of warmer temperatures and higher CO2on some growth variables but no significant family × treatment interactions. Instantaneous water use efficiency was the only physiological trait that was affected positively by the CO2treatment, showing a 51% increase that was consistent across families. [ABSTRACT FROM PUBLISHER]

In Isle Royale National Park, heavy moose browsing over the past 100 years has suppressed the regeneration of many tree species, gradually resulting in a shift towards more open forests and savannas. By 1996, 16% of the forests at the southwestern end of Isle Royale had become savanna and another 20% of forests were starting to have canopy breakup. The changes in understory vegetation brought about by savanna formation have received little attention, even though the future of moose and wolf populations on Isle Royale is tied to these vegetation changes. This study examined the vegetation of savannas ranging in age (date since formation) from <10 years to 80 years to examine how the ground flora changes over time from initial forest canopy breakup, to extensive grassland, and finally to a zootic subclimax dubbed 'moose-spruce savanna.' Ordination techniques were used to describe plant communities and to identify environmental variables that influence vegetation development. Nonparametric multiplicative regression was used to predict how these variables influenced individual plants and structure within the communities. Plant communities had a notable shift from forest herbs to ruderal species, especially non-native plants. This succession was influenced strongly by the underlying bedrock and hydrology-altering moisture regimes and plant communities. Picea glauca (Moench) Voss. and Poa pratensis L. competed in a dynamic inhibitory relationship. The former facilitated forest plants while the latter out-competed other plants and promoted open swards. These interactions are dramatically changing the character of Isle Royale's upland plant communities and will have important trophic consequences for the island. [ABSTRACT FROM AUTHOR]

Peat-mineral soil mix (PMM) over tailings sand (TS) or overburden (OB) is a commonly used prescription for oil sands reclamation. The TS and OB (the substrates) often have unfavorable conditions such as high salinity, soil compaction, low nutrient availability in OB, and low nutrient and water availabilities in TS, which may limit tree growth. The objective of this study was to identify limiting factors for growth of lodgepole pine ( Pinus contorta ) on PMM over TS and white spruce ( Picea glauca ) on PMM over OB in the Athabasca oil sands region, Alberta, Canada. In the pine sites, mean annual growth of height (HG), diameter at breast height (DBHG) and aboveground biomass (ABG) were significantly correlated with volumetric water content (VWC) in PMM and foliar δ 13 C in current-year needles. Sites with high productivities had the lowest foliar δ 13 C relative to sites with low and medium productivities. The VWC and dissolved organic carbon (DOC) together explained 80% of the variation in both the current annual increment of height (HI) ( p = 0.007) and aboveground biomass (ABI) ( p = 0.008). In the spruce sites, foliar potassium (K) and foliar and soil nitrogen (N) concentrations were positively correlated with HG, DBHG and ABG, consistent with patterns in K and inorganic N (the sum of NH 4 + -N and NO 3 − -N) concentrations in PMM in those sites. Soil electrical conductivity (EC) and bulk density (Db) were greater in low than in medium and high productivity sites. The Db and inorganic N concentration together explained 67% of the variation in HI ( p = 0.037), while Db and EC together explained 79% of the variation in ABI ( p = 0.009). In conclusion, lodgepole pine trees planted on PMM over TS sites were limited by low water availability, while low soil N availability and high salinity limited the growth of white spruce trees planted on PMM over OB sites. Reclamation practices need to address water and nutrient limitations to ensure the success of reclaiming disturbed areas in the oil sands region. [ABSTRACT FROM AUTHOR]

The contribution of hyphae to water transport in ectomycorrhizal ( ECM) white spruce ( Picea glauca) seedlings was examined by altering expression of a major water-transporting aquaporin in Laccaria bicolor., Picea glauca was inoculated with wild-type ( WT), mock transgenic or L. bicolor aquaporin -overexpressing ( OE) strains and exposed to root temperatures ranging from 5 to 20°C to examine the root water transport properties, physiological responses and plasma membrane intrinsic protein ( PIP) expression in colonized plants., Mycorrhization increased shoot water potential, transpiration, net photosynthetic rates, root hydraulic conductivity and root cortical cell hydraulic conductivity in seedlings. At 20°C, OE plants had higher root hydraulic conductivity compared with WT plants and the increases were accompanied by higher expression of P. glauca PIP GQ03401_ M18.1 in roots. In contrast to WT L. bicolor, the effects of OE fungi on root and root cortical cell hydraulic conductivities were abolished at 10 and 5°C in the absence of major changes in the examined transcript levels of P. glauca root PIPs., The results provide evidence for the importance of fungal aquaporins in root water transport of mycorrhizal plants. They also demonstrate links between hyphal water transport, root aquaporin expression and root water transport in ECM plants. [ABSTRACT FROM AUTHOR]

Periodic outbreaks of spruce budworm ( SBW) affect large areas of ecologically and economically important conifer forests in North America, causing tree mortality and reduced forest productivity. Host resistance against SBW has been linked to growth phenology and the chemical composition of foliage, but the underlying molecular mechanisms and population variation are largely unknown. Using a genomics approach, we discovered a β-glucosidase gene, Pgβglu-1, whose expression levels and function underpin natural resistance to SBW in mature white spruce ( Picea glauca) trees. In phenotypically resistant trees, Pgβglu-1 transcripts were up to 1000 times more abundant than in non-resistant trees and were highly enriched in foliage. The encoded Pgβ GLU-1 enzyme catalysed the cleavage of acetophenone sugar conjugates to release the aglycons piceol and pungenol. These aglycons were previously shown to be active against SBW. Levels of Pgβglu-1 transcripts and biologically active acetophenone aglycons were substantially different between resistant and non-resistant trees over time, were positively correlated with each other and were highly variable in a natural white spruce population. These results suggest that expression of Pgβglu-1 and accumulation of acetophenone aglycons is a constitutive defence mechanism in white spruce. The progeny of resistant trees had higher Pgβglu-1 gene expression than non-resistant progeny, indicating that the trait is heritable. With reported increases in the intensity of SBW outbreaks, influenced by climate, variation of Pgβglu-1 transcript expression, Pgβ GLU-1 enzyme activity and acetophenone accumulation may serve as resistance markers to better predict impacts of SBW in both managed and wild spruce populations. [ABSTRACT FROM AUTHOR]

Exponential fertilization has been shown to be a useful technique for improving seedling quality during nursery production. In this study, we evaluated ( i) the impact of exponential vs. conventional fertilization on trembling aspen ( Populus tremuloides Michx.) and white spruce ( Picea glauca (Moench) Voss) seedlings during nursery production and ( ii) the growth performance and nitrogen (N) utilization of those seedlings in response to foxtail barley ( Hordeum jubatum L.) competition after the transplantation of seedlings in a greenhouse experiment. Exponential fertilization with an application rate higher than the conventional fertilization increased the internal N reserve in trembling aspen and white spruce seedlings during nursery production and also increased new leaf, new stem, and old stem biomass and N retranslocation rates in trembling aspen seedlings but not in white spruce seedlings after transplantation. Foxtail barley competition decreased N concentrations in seedlings and soil N uptake by the seedlings; however, increased N retranslocation rates with foxtail barley competition were observed in white spruce seedlings but not in trembling aspen seedlings. Our results suggest that the growth performance of seedlings was improved by N loading, whereas the impact of vegetation management was species specific. [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 Genomic selection (GS) may improve selection response over conventional pedigree-based selection if markers capture more detailed information than pedigrees in recently domesticated tree species and/or make it more cost effective. Genomic prediction accuracies using 1748 trees and 6932 SNPs representative of as many distinct gene loci were determined for growth and wood traits in white spruce, within and between environments and breeding groups (BG), each with an effective size of Ne ≈ 20. Marker subsets were also tested. Results Model fits and/or cross-validation (CV) prediction accuracies for ridge regression (RR) and the least absolute shrinkage and selection operator models approached those of pedigreebased models. With strong relatedness between CV sets, prediction accuracies for RR within environment and BG were high for wood (r = 0.71-0.79) and moderately high for growth (r = 0.52-0.69) traits, in line with trends in heritabilities. For both classes of traits, these accuracies achieved between 83% and 92% of those obtained with phenotypes and pedigree information. Prediction into untested environments remained moderately high for wood (r ⩾ 0.61) but dropped significantly for growth (r ⩾ 0.24) traits, emphasizing the need to phenotype in all test environments and model genotype-by-environment interactions for growth traits. Removing relatedness between CV sets sharply decreased prediction accuracies for all traits and subpopulations, falling near zero between BGs with no known shared ancestry. For marker subsets, similar patterns were observed but with lower prediction accuracies. Conclusions Given the need for high relatedness between CV sets to obtain good prediction accuracies, we recommend to build GS models for prediction within the same breeding population only. Breeding groups could be merged to build genomic prediction models as long as the total effective population size does not exceed 50 individuals in order to obtain high prediction accuracy such as that obtained in the present study. A number of markers limited to a few hundred would not negatively impact prediction accuracies, but these could decrease more rapidly over generations. The most promising short-term approach for genomic selection would likely be the selection of superior individuals within large full-sib families vegetatively propagated to implement multiclonal forestry. [ABSTRACT FROM AUTHOR]

We reared saproxylic beetles from 54 white spruce [ Picea glauca ( Moench) Voss] logs collected in northwestern Alberta, Canada. Logs represented six decay classes, ranging from freshly dead to well decayed., Beetle assemblages were indicated mainly by phloeophagous and predaceous species in early decay stages, although indicator species were mainly predaceous in later stages of decay. No indicator species were identified for intermediate decay stages., Larvae from rearings were disproportionately predaceous. Thus, movement of juveniles within and among coarse woody debris ( CWD) substrates is likely an important aspect of the life history for these species., Beetle assemblages changed progressively with increasing stages of decomposition. Assemblages of adjacent decay classes were highly similar, although similarity decreased with increasing difference in decay classes. Therefore, the retention of all decay classes of white spruce downed CWD on post-harvest landscapes is necessary to conserve the associated saproxylic beetle fauna., Retention of CWD in advanced decay stages, which contains species not found in earlier decay classes, presents a particular challenge in forest management because of the long times required to develop CWD in the later stages of decomposition. [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]

There is a growing interest in improving knowledge on wood quality of forest resources to allow for an end-product oriented supply for the wood-processing industry. We investigated the differences of white spruce ( Picea glauca (Moench) Voss) wood traits from 13 ecological regions of the eastern Canadian province of Quebec and identified climatic and geographic variables and tree characteristics that may help predict wood traits in novel approaches to forest inventories. One hundred and eleven wood disks were used to determine wood traits that are related to wood anatomy and to mechanical use of wood. Our results indicate significant differences between ecological regions for most of the investigated wood traits. Samples from several coastal regions showed, for example, wood anatomy that is advantageous for some pulp and paper grades, but they offer comparatively weak estimates for mechanical applications. Ordination and projection to latent structures allowed us to identify maximum temperature, degree days, geographic location, tree height, and tree diameter as important predictor variables for wood traits. The quality of models was variable and R2 values ranged from 0.13 to 0.59. Prediction errors in an independent sample were mostly below 10%, and bias was below 5%. Although the prediction of wood mechanics was less precise, the presented results are an encouraging step toward obtaining a wood trait signature for different environments. [ABSTRACT FROM AUTHOR]

Genomic selection (GS) is of interest in breeding because of its potential for predicting the genetic value of individuals and increasing genetic gains per unit of time. To date, very few studies have reported empirical results of GS potential in the context of large population sizes and long breeding cycles such as for boreal trees. In this study, we assessed the effectiveness of marker-aided selection in an undomesticated white spruce (Picea glauca (Moench) Voss) population of large effective size using a GS approach. A discovery population of 1694 trees representative of 214 open-pollinated families from 43 natural populations was phenotyped for 12 wood and growth traits and genotyped for 6385 single-nucleotide polymorphisms (SNPs) mined in 2660 gene sequences. GS models were built to predict estimated breeding values using all the available SNPs or SNP subsets of the largest absolute effects, and they were validated using various cross-validation schemes. The accuracy of genomic estimated breeding values (GEBVs) varied from 0.327 to 0.435 when the training and the validation data sets shared half-sibs that were on average 90% of the accuracies achieved through traditionally estimated breeding values. The trend was also the same for validation across sites. As expected, the accuracy of GEBVs obtained after cross-validation with individuals of unknown relatedness was lower with about half of the accuracy achieved when half-sibs were present. We showed that with the marker densities used in the current study, predictions with low to moderate accuracy could be obtained within a large undomesticated population of related individuals, potentially resulting in larger gains per unit of time with GS than with the traditional approach. [ABSTRACT FROM AUTHOR]

Leaf life span is an important plant trait associated with interspecific variation in leaf, organismal, and ecosystem processes. We hypothesized that intraspecific variation in gymnosperm needle traits with latitude reflects both selection and acclimation for traits adaptive to the associated temperature and moisture gradient. This hypothesis was supported, because across 127 sites along a 2,160-km gradient in North America individuals of Picea glauca Picea mariana, Pinus banksiana, and Abies balsamea had longer needle life span and lower tissue nitrogen concentration with decreasing mean annual temperature. Similar patterns were noted for Pinus syivestris across a north-south gradient in Europe. These differences highlight needle longevity as an adaptive feature important to ecological success of boreal conifers across broad climatic ranges. Additionally, differences in leaf life span directly affect annual foliage turnover rate, which along with needle physiology partially regulates carbon cycling through effects on gross primary production and net canopy carbon export. However, most, if not all, global land surface models parameterize needle longevity of boreal evergreen forests as if it were a constant. We incorporated temperature-dependent needle longevity and %nitrogen, and bio-mass allocation, into a land surface model. Community Atmosphere Biosphere Land Exchange, to assess their impacts on carbon cycling processes. Incorporating realistic parameterization of these variables improved predictions of canopy leaf area index and gross primary production compared with observations from flux sites. Finally, increasingly low foliage turnover and biomass fraction toward the cold far north indicate that a surprisingly small fraction of new biomass is allocated to foliage under such conditions. [ABSTRACT FROM AUTHOR]

The forest-tundra ecotone is expected to experience some of the initial effects of climate change. At the forefront of this transition zone, we find clonal growth forms of stunted and deformed trees with and without taller erect trees, called tree islands and krummholz, respectively. We sought to assess the potential effects of expansion of these growth forms on tundra plant species at two Canadian locations, one in the Mealy Mountains of Labrador and the other near Churchill, Manitoba. Our objectives were 1) to analyze the structure (height distribution and shape) of these clonal growth forms to determine whether they are expanding; 2) to compare tree cover on the leeward and windward sides of these growth forms and 3) to assess patterns in individual plant species across these growth forms. Cover of trees and other plant species was measured at both locations, while tree stems were mapped near Churchill only. The presence of seedlings and symmetric patterns of tree height suggest that half of the tree islands near Churchill may be expanding. The edges of tree islands and krummholz may harbour safe sites for tundra plant species, as shown by peaks in cover of individual species at these edges. Our results suggest that expansion of tree islands and krummholz would affect the abundance of tundra plant species, which could lead to changes in species composition and biodiversity. [ABSTRACT FROM AUTHOR]

Numerous models are available in northeastern North America to estimate aboveground tree biomass, yet most have focused on trees ≥12.5 cm diameter, and these models are often poor predictors of small tree biomass (<12.5 cm diameter). Additionally, models available to estimate small tree biomass often lack independent evaluation with field data. We developed a new set of additive biomass component (foliage, branch, and bole) models for five naturally regenerated hardwood species, four hybrid poplar (Populus sp.) clones and white spruce (Picea glauca (Moench.), from trees in eastern Maine. Biomass measurements were used to evaluate national and regional models for naturally regenerated species, and species specific models for planted stock. Results showed that the regional and national models provided similar fits for total biomass across all species. Moreover, the small tree biomass models currently used to predict woody biomass substantially underestimated biomass from 19.0% to 36.6% for all of the naturally regenerated hardwood species at our site. This substantial underestimation of small tree biomass may have contributed to the recent 34% decrease in estimated sapling woody biomass, and 15% decrease in aboveground biomass of all living trees in Maine, where nearly one-quarter of the 70,000 km2 forestlands are dominated by saplings. This problem may exist in other regions of the United States if substantial proportions of forestlands are dominated by small trees. Further model evaluation is warranted to assess the performance of the current models. [ABSTRACT FROM AUTHOR]

Phialocephala scopiformis Kowalski & Kehr is a foliar fungal endophyte of white spruce ( Picea glauca (Moench) Voss) that produces the anti-insect compound rugulosin and other compounds in lower amounts. Seedlings inoculated with this and other toxigenic endophytes have increased tolerance to the spruce budworm Choristoneura fumiferana (Clemens, 1865). The presence of rugulosin in the diet and in needles infected by P. scopiformis reduces the growth rate of the insect. One of 300 white spruce trees inoculated as a seedling in 2001 was chosen to investigate the distribution of P. scopiformis and its principal toxin rugulosin throughout the crown. To facilitate the detection of the fungus in small samples, a qPCR assay was developed based on the ITS region of fungal ribosomal DNA targeting a genetic polymorphism unique to P. scopiformis. The assay was specific, with a method limit of detection 100 ng mycelium per gram needle sample with high reproducibility and accuracy. We found that 11 years after inoculation, P. scopiformis DAOM 229536 and its toxin were detectable in needle samples distributed throughout the crown. Of the 109 samples tested, 100% of the rugulosin-positive samples also tested positive for P. scopiformis DAOM 229536 DNA in the qPCR assay. The mean and median needle rugulosin concentrations were >2 times that required to reduce the growth of spruce budworm. [ABSTRACT FROM AUTHOR]

Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change., By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we used de novo transcriptome assembly and RNAseq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime treatments in lodgepole pine ( Pinus contorta) and interior spruce (a natural hybrid population of Picea glauca and Picea engelmannii)., We found wide evidence for an effect of treatment on expression within each species, with 6413 and 11 658 differentially expressed genes identified in spruce and pine, respectively. Comparing patterns of expression among these species, we found that 74% of all orthologs with differential expression had a pattern that was conserved in both species, despite 140 million yr of evolution. We also found that the specific treatments driving expression patterns differed between genes with conserved versus diverged patterns of expression., We conclude that natural selection has probably played a role in shaping plastic responses to environment in these species. [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]

In conifers, somatic embryogenesis is uniquely initiated from immature embryos in a narrow time window, which is considerably hindered by the difficulty to induce embryogenic tissue (ET) from other tissues, including mature somatic embryos. In this study, the embryogenic ability of newly induced ET and DNA methylation levels was detected, and whole-transcriptome sequencing analyses were carried out. The results showed that ultra-low temperature treatment significantly enhanced ET induction from mature somatic embryos, with the induction rate from 0.4% to 15.5%, but the underlying mechanisms remain unclear. The newly induced ET showed higher capability in generating mature embryos than the original ET. DNA methylation levels fluctuated during the ET induction process. Here, WGCNA analysis revealed that OPT4, TIP1-1, Chi I, GASA5, GST, LAX3, WRKY7, MYBS3, LRR-RLK, PBL7, and WIN1 genes are involved in stress response and auxin signal transduction. Through co-expression analysis, lncRNAs MSTRG.505746.1, MSTRG.1070680.1, and MSTRG.33602.1 might bind to pre-novel_miR_339 to promote the expression of WRKY7 genes for stress response; LAX3 could be protected by lncRNAs MSTRG.1070680.1 and MSTRG.33602.1 via serving as sponges for novel_miR_495 to initiate auxin signal transduction; lncRNAs MSTRG.505746.1, MSTRG.1070680.1, and MSTRG.33602.1 might serve as sponges for novel_miR_527 to enhance the expression of Chi I for early somatic embryo development. This study provides new insight into the area of stress-enhanced early somatic embryogenesis in conifers, which is also attributable to practical applications. [ABSTRACT FROM AUTHOR]

Improving the accuracy of fire behavior prediction requires better understanding of live fuel, the dominant component of tree crowns, which dictates the consumption and energy release of the crown fire flame-front. Live fuel flammability is not well represented by existing evaluation methods. High-flammability live fuel, e.g., in conifers, may maintain or increase the energy release of the advancing crown fire flame-front, while low-flammability live fuel, e.g., in boreal deciduous stands, may reduce or eventually suppress flame-front energy release. To better characterize these fuel–flame-front interactions, we propose a method for quantifying flammability as the fuel's net effect on (contribution to) the frontal flame energy release, in which the frontal flame is simulated using a methane diffusion flame. The fuel's energy release contribution to the methane flame was measured using oxygen consumption calorimetry as the difference in energy release between the methane flame interacting with live fuel and the methane flame alone. In-flame testing resulted in fuel ignition and consumption comparable to those in wildfires. The energy release contribution of live fuel was significantly lower than its energy content measured using standard methods, suggesting better sensitivity of the proposed metric to water content- and oxygen deficiency-associated energy release reductions within the combustion zone. [ABSTRACT FROM AUTHOR]

Intraspecific assisted migration ( ISAM) through seed transfer during artificial forest regeneration has been suggested as an adaptation strategy to enhance forest resilience and productivity under future climate. In this study, we assessed the risks and benefits of ISAM in white spruce based on long-term and multilocation, rangewide provenance test data. Our results indicate that the adaptive capacity and growth potential of white spruce varied considerably among 245 range-wide provenances sampled across North America; however, the results revealed that local populations could be outperformed by nonlocal ones. Provenances originating from south-central Ontario and southwestern Québec, Canada, close to the southern edge of the species' natural distribution, demonstrated superior growth in more northerly environments compared with local populations and performed much better than populations from western Canada and Alaska, United States. During the 19-28 years between planting and measurement, the southern provenances have not been more susceptible to freezing damage compared with local populations, indicating they have the potential to be used now for the reforestation of more northerly planting sites; based on changing temperature, these seed sources potentially could maintain or increase white spruce productivity at or above historical levels at northern sites. A universal response function ( URF), which uses climatic variables to predict provenance performance across field trials, indicated a relatively weak relationship between provenance performance and the climate at provenance origin. Consequently, the URF from this study did not provide information useful to ISAM. The ecological and economic importance of conserving white spruce genetic resources in south-central Ontario and southwestern Québec for use in ISAM is discussed. [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]

Mast-seeding conifers such as Picea glauca exhibit synchronous production of large seed crops over wide areas, suggesting climate factors as possible triggers for episodic high seed production. Rapidly changing climatic conditions may thus alter the tempo and spatial pattern of masting of dominant species with potentially far-reaching ecological consequences. Understanding the future reproductive dynamics of ecosystems including boreal forests, which may be dominated by mast-seeding species, requires identifying the specific cues that drive variation in reproductive output across landscape gradients and among years. Here we used annual data collected at three sites spanning an elevation gradient in interior Alaska, USA between 1986 and 2011 to produce the first quantitative models for climate controls over both seedfall and seed viability in P. glauca, a dominant boreal conifer. We identified positive associations between seedfall and increased summer precipitation and decreased summer warmth in all years except for the year prior to seedfall. Seed viability showed a contrasting response, with positive correlations to summer warmth in all years analyzed except for one, and an especially positive response to warm and wet conditions in the seedfall year. Finally, we found substantial reductions in reproductive potential of P. glauca at high elevation due to significantly reduced seed viability there. Our results indicate that major variation in the reproductive potential of this species may occur in different landscape positions in response to warming, with decreasing reproductive success in areas prone to drought stress contrasted with increasing success in higher elevation areas currently limited by cool summer temperatures. [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]

Radial patterns of modulus of elasticity (MOE) were examined for white spruce ( Picea glauca (Moench) Voss) and trembling aspen ( Populus tremuoides Michx.) from 19 mature, uneven-aged stands in the boreal mixedwood region of northern Alberta, Canada. The main objectives were to (1) evaluate the relationship between pith-to-bark changes in MOE and cambial age or distance from pith; (2) develop species-specific models to predict pith-to-bark changes in MOE; and (3) to test the influences of radial growth, relative vertical height, and tree slenderness (tree height/DBH) on MOE. For both species, cambial age was selected as the best explanatory variable with which to build pith-to-bark models of MOE. For white spruce and trembling aspen, the final nonlinear mixed-effect models indicated that an augmented rate of increase in MOE occurred with increasing vertical position within the tree. For white spruce trees, radial growth and slenderness were found to positively influence maximum estimated MOE. For trembling aspen, there was no apparent effect of vertical position or radial growth on maximum MOE. The results shed light on potential drivers of radial patterns of MOE and will be useful in guiding silvicultural prescriptions. [ABSTRACT FROM AUTHOR]

Mixed models combining random coefficient effect and covariance patterns were used to investigate mechanical property variations in jack pine ( Pinus banksiana Lamb.) and white spruce ( Picea glauca (Moench) Voss) trees. Modulus of elasticity (MOE) and modulus of rupture (MOR) were measured by conducting three-point bending tests on small defect-free samples selected from different radial positions and at a height of 2.5 m above ground within the stems. The objective of the paper was to build statistical predictive models describing the radial variations in stems for wood mechanical properties using easily measurable explanatory variables that are typically available in the wood manufacturing industry: distance from pith, tree height and diameter, and spacing. The explanatory variables integrated into the models explained MOE adequately, whereas MOR appeared harder to predict with only these variables and at this resolution. For white spruce, the best mixed-effects models explained 80% and 61% of the variation in MOE and MOR, respectively. For jack pine, it was 51% and 33% for the same response variables. These results are a step toward models that could be used in sawing simulation software designed to estimate the internal properties of sawlogs and, as a result, better predict lumber and pulp chip quality. [ABSTRACT FROM AUTHOR]

Background and aims: Soil pH is among the major environmental factors affecting plant growth. Although the optimum range of soil pH for growth and the tolerance of pH extremes widely vary among plant species, the pH tolerance mechanisms in plants are still poorly understood. In this study, possible mechanisms were examined to explain the differences in tolerance of boreal plants to root zone pH. Methods: In the controlled-environment solution culture experiments, we compared growth, physiological parameters and tissue nutrient concentrations in aspen, white spruce and tamarack seedlings that were subjected to 8 weeks of root zone pH treatments ranging from 5.0 to 9.0. Results: The pH treatments had little effect on dry weights and net photosynthesis in white spruce seedlings despite reductions in transpiration rates at higher pH levels. In aspen and tamarack, both the growth and physiological parameters significantly decreased at pH higher than 6.0. The chlorosis of young tissues in aspen and tamarack was associated with the reductions in foliar concentrations of several of the examined essential nutrients including Fe and Mn. Although the plants varied in their ability to deliver essential nutrients to growing leaves, there was no direct correlation between tissue nutrient concentrations, chlorophyll concentrations and plant growth. The results also demonstrated strong inhibition of transpiration rates by high pH. Conclusions: The results suggest that high root zone pH can upset water balance in pH sensitive species including aspen. Although the uptake and assimilation of essential elements such as Fe and Mn contribute to plant tolerance of high soil pH, we did not observe a direct relationship between growth and foliar nutrient concentrations to account for the observed differences in growth. [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]

We examined the effect of competition on stem growth of Picea glauca and Populus tremuloides in boreal mixedwood stands during the stem exclusion stage. We combined traditional approaches of collecting competition data with dendrochronology to provide retrospective measurements of stem diameter growth. Several competition indices including stand basal area (BA), the sum of stem diameter at breast height (SDBH), and density (N) for the broadleaf and coniferous species, as well as similar indices considering only trees with diameters greater than each subject (BAGR, SDBHGR, and NGR), were evaluated. We used a nonlinear mixed model to characterize the basal area increment over the past 5, 10, 15, 20, 25, 30, and 35 years as a function of growth of nearby dominant trees, the size of the subject trees, deciduous and coniferous competition indices, and ecoregions. SDBHGR and BAGR were better predictors for spruce, and SDBHGR and NGR were better for aspen, respectively, than other indices. Results showed strongest correlations with long-term stem growth, as the best models integrated growth for 10–25 years for aspen and ≥25 for spruce. Our model demonstrated a remarkable capability (adjusted R2>0.67) to represent this complex variation in growth as a function of site, size and competition. [ABSTRACT FROM AUTHOR]

Despite their prevalence and importance, the genome sequences of loblolly pine, Norway spruce, and white spruce, three ecologically and economically important conifer species, are just becoming available to the research community. Following the completion of these large assemblies, annotation efforts will be undertaken to characterize the reference sequences. Accurate annotation of these ancient genomes would be aided by a comprehensive repeat library; however, few studies have generated enough sequence to fully evaluate and catalog their non-genic content. In this paper, two sets of loblolly pine genomic sequence, 103 previously assembled BACs and 90,954 newly sequenced and assembled fosmid scaffolds, were analyzed. Together, this sequence represents 280 Mbp (roughly 1% of the loblolly pine genome) and one of the most comprehensive studies of repetitive elements and genes in a gymnosperm species. A combination of homology and de novo methodologies were applied to identify both conserved and novel repeats. Similarity analysis estimated a repetitive content of 27% that included both full and partial elements. When combined with the de novo investigation, the estimate increased to almost 86%. Over 60% of the repetitive sequence consists of full or partial LTR (long terminal repeat) retrotransposons. Through de novo approaches, 6,270 novel, full-length transposable element families and 9,415 sub-families were identified. Among those 6,270 families, 82% were annotated as single-copy. Several of the novel, high-copy families are described here, with the largest, PtPiedmont, comprising 133 full-length copies. In addition to repeats, analysis of the coding region reported 23 full-length eukaryotic orthologous proteins (KOGS) and another 29 novel or orthologous genes. These discoveries, along with other genomic resources, will be used to annotate conifer genomes and address long-standing questions about gymnosperm evolution. [ABSTRACT FROM AUTHOR]

Background: Among the many commercial opportunities afforded by somatic embryogenesis (SE), it is the ability to clonally propagate individual plants with rare or elite traits that has some of the most significant implications. This is particularly true for many long-lived species, such as conifers, but whose long generation times pose substantive challenges, including increased recalcitrance for SE as plants age. Identification of a clonal line of somatic embryo-derived trees whose shoot primordia have remained responsive to SE induction for over a decade, provided a unique opportunity to examine the molecular aspects underpinning SE within shoot tissues of adult white spruce trees. Results: Microarray analysis was used to conduct transcriptome-wide expression profiling of shoot explants taken from this responsive genotype following one week of SE induction, which when compared with that of a nonresponsive genotype, led to the identification of four of the most differentially expressed genes within each genotype. Using absolute qPCR to expand the analysis to three weeks of induction revealed that differential expression of all eight candidate genes was maintained to the end of the induction treatment, albeit to differing degrees. Most striking was that both the magnitude and duration of candidate gene expression within the nonresponsive genotype was indicative of an intense physiological response. Examining their putative identities further revealed that all four encoded for proteins with similarity to angiosperm proteins known to play prominent roles in biotic defense, and that their high-level induction over an extended period is consistent with activation of a biotic defense response. In contrast, the more temperate response within the responsive genotype, including induction of a conifer-specific dehydrin, is more consistent with elicitation of an adaptive stress response. Conclusions: While additional evidence is required to definitively establish an association between SE responsiveness and a specific physiological response, these results suggest that biotic defense activation may be antagonistic, likely related to the massive transcriptional and metabolic reprogramming that it elicits. A major issue for future work will be to determine how and if suppressing biotic defense activation could be used to promote a physiological state more conducive to SE induction. [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]

Abstract: We present a reconstruction of June–July minimum temperatures since AD1245 for the Mackenzie Delta region based on a 29-site network of white spruce (Picea glauca) ring-width series. Most but not all trees experienced a divergent temperature–growth response, similar to the divergence that has affected other white spruce trees across Yukon and Alaska. However, divergence in the study region began as early as AD1900 and we have documented our methods to avoid including divergent signals in the reconstruction. Calibration/verification testing based on local temperature data, and multi-century coherence with nearby and large-scale temperature proxy records, confirm that our reconstruction is robust. The reconstruction shows cool conditions in the late 13th, early 18th and early 19th centuries, corresponding with solar minima and increased volcanism. These cool periods are interrupted by warm periods consistent with early to mid-20th century warmth. The late 20th century is the warmest interval, and the last decade is estimated to be 1.4°C warmer than any decade before the mid-20th century. The reconstructed climate history corroborates other proxy-based inferences and supports the notion that high-latitude regions such as the Mackenzie Delta have experienced rapid warming in recent decades that is exceptional in the last eight centuries. [Copyright &y& Elsevier]

Abstract: White spruce (Picea glauca [Moench] Voss) seedlings produced by somatic embryogenesis were grown both at the Kennedy Space Center and in weightlessness in the ISS for 30days. Plants were placed in closed environment incubators (Advanced Biological Research System) under controlled light, temperature, humidity and CO2 conditions. At the end of the experiment, the leading shoot from three plantlets of each of the three lines tested were sampled and pooled in Kennedy Space Center Fixation Tubes (KFT) containing a RNA stabilization solution. Transcript levels were determined by quantitative real-time polymerase chain reaction (RT-qPCR) for 27 candidate genes and three reference genes on the nine seedlings grown in each environment. About two-thirds of the 27 genes produced a larger number of transcript molecules in microgravity conditions. However, only three genes showed significant differences between the two environments, and all of them were up-regulated in microgravity. These genes appear to be involved in important processes such as cell propagation, plant development and response to stress, and their up-regulation has likely contributed to influencing seedling growth patterns. [Copyright &y& Elsevier]

The purpose of this study was to develop an understanding of the pattern of variation in longitudinal, radial, and tangential shrinkage in two commercially important Canadian wood species using multivariate nonlinear mixed-effects models. Shrinkage data were measured in each growth ring at different heights on trees harvested from a mixed-species Nelder tree-spacing plot located in New Brunswick, Canada. Live crown base was reconstructed based on stem analysis. Cambial age, sampling height, crown characteristics (crown length, crown ratio, and distance to live crown base), and ring width at time of wood formation were used as prediction variables. The results indicated that shrinkage magnitude and pattern were closely related to crown dimensions and stem position at time of wood formation. Trees from wider tree spacings with larger crown lengths and ratios tended to have smaller tangential and radial shrinkage. Longitudinal shrinkage decreased nonlinearly from pith outwards with slower rate changes near the bottom of the trees. The model fixed effects accounted for more variation in jack pine ( Pinus banksiana Lamb.) than in white spruce ( Picea glauca (Moench) Voss) for shrinkage in the same anatomical direction. After further validation, the model developed can be used to provide shrinkage predictions for lumber distortion models within the framework of an individual tree growth model. [ABSTRACT FROM AUTHOR]

Height and diameter of white spruce clones were measured over two growing seasons in a forest nursery and for 4 more yr at two field sites. Clonal heritability (Hc2) was moderate and stable in the nursery, but decreased with age, reaching 0.26 and 0.11 for height and 0.14 and 0.04 for diameter, respectively, at the two field sites. Height exhibited weak to moderate Hc2and strong genotypic correlations with the different growth characteristics. The strong age-age genotypic correlations (≥0.809) and nursery-plantation correlations (≥0.347) for height indicate that selection for height can be conducted at a young age thus reducing the costs of clonal tests. [ABSTRACT FROM PUBLISHER]

Pulsed resources have significant effects on population and community dynamics in terrestrial ecosystems. Mast seeding is an important resource pulse in deciduous forests; these boom and bust cycles of seed production generate strong lagged population responses by post-dispersal seed predators such as rodents, which then cascade through multiple trophic levels and regulate population dynamics of their predators and prey. However, similar interactions in another major pulsed system, coniferous forests, are inconsistent, and the effects of interannual variation in conifer seed production on many consumer populations are largely unknown., We used large-scale manipulation and intensive monitoring to examine the population dynamics of deer mice ( Peromyscus maniculatus) in relation to fall seed production by two northern conifers, white spruce ( Picea glauca) and subalpine fir ( Abies lasiocarpa). Previous studies have shown that spruce seeds are a preferred food source of mice, while fir seeds are generally avoided if other foods are available. Therefore, we expected that there would be a positive relationship between mouse demography and previous spruce seed production, but no effect of fir mast seeding., Supplementation of a mouse population using spruce seeds indicated that increased fall spruce seed availability can enhance overwinter survival and population densities in the following spring, summer, and fall. However, long-term population monitoring indicated that mouse demography was not positively affected by spruce mast seeding, likely due to strong interspecific competition with the North American red squirrel ( Tamiasciurus hudoniscus), a dominant pre-dispersal spruce seed predator., Conversely, we observed an unexpected delayed effect of fir mast seeding, where increased fall fir seed production did not influence overwinter or spring mouse demography, but instead enhanced summer survival, body masses and pregnancy rates of overwintered adults. This led to increased summer population densities and may have been mediated by population responses of invertebrate post-dispersal seed predators to increased fir seed availability., Our results indicate that rodent responses to resource pulses in coniferous forests are more complex than in deciduous environments and reveal previously unobserved direct and indirect consumer-resource dynamics that require further examination. This system is ideal for the large-scale, integrative ecosystem studies that ecologists are encouraged to pursue. [ABSTRACT FROM AUTHOR]