Uncovering epigenetic and transcriptional regulation of growth in Douglas-fir: identification of differential methylation regions in mega-sized introns.

Tree growth performance can be partly explained by genetics, while a large proportion of growth variation is thought to be controlled by environmental factors. However, to what extent DNA methylation, a stable epigenetic modification, contributes to phenotypic plasticity in the growth performance of long-lived trees remains unclear. In this study, a comparative analysis of targeted DNA genotyping, DNA methylation and mRNAseq profiling for needles of 44-year-old Douglas-fir trees (Pseudotsuga menziesii (Mirb.) Franco) having contrasting growth characteristics was performed. In total, we identified 195 differentially expressed genes (DEGs) and 115 differentially methylated loci (DML) that are associated with genes involved in fitness-related processes such as growth, stress management, plant development and energy resources. Interestingly, all four intronic DML were identified in mega-sized (between 100 and 180 kbp in length) and highly expressed genes, suggesting specialized regulation mechanisms of these long intron genes in gymnosperms. DNA repetitive sequences mainly comprising long-terminal repeats of retroelements are involved in growth-associated DNA methylation regulation (both hyper- and hypomethylation) of 99 DML (86.1% of total DML). Furthermore, nearly 14% of the DML was not tagged by single nucleotide polymorphisms, suggesting a unique contribution of the epigenetic variation in tree growth.

Weak local adaptation to drought in seedlings of a widespread conifer.

Tree seedlings from populations native to drier regions are often assumed to be more drought tolerant than those from wetter provenances. However, intraspecific variation in drought tolerance has not been well-characterized despite being critical for developing climate change mitigation and adaptation strategies, and for predicting the effects of drought on forests. We used a large-scale common garden drought-to-death experiment to assess range-wide variation in drought tolerance, measured by decline of photosynthetic efficiency, growth, and plastic responses to extreme summer drought in seedlings of 73 natural populations of the two main varieties of Douglas-fir (Pseudotsuga menziesii var. menziesii and var. glauca). Local adaptation to drought was weak in var. glauca and nearly absent in menziesii. Var. glauca showed higher tolerance to drought but slower growth than var. menziesii. Clinal variation in drought tolerance and growth species-wide was mainly associated with temperature rather than precipitation. A higher degree of plasticity for growth was observed in var. menziesii in response to extreme drought. Genetic variation for drought tolerance in seedlings within varieties is maintained primarily within populations. Selective breeding within populations may facilitate adaptation to drought more than assisted gene flow.

Genetic architecture of disease resistance and tolerance in Douglas-fir trees.

Understanding the genetic basis of how plants defend against pathogens is important to monitor and maintain resilient tree populations. Swiss needle cast (SNC) and Rhabdocline needle cast (RNC) epidemics are responsible for major damage of forest ecosystems in North America. Here we investigate the genetic architecture of tolerance and resistance to needle cast diseases in Douglas-fir (Pseudotsuga menziesii) caused by two fungal pathogens: SNC caused by Nothophaeocryptopus gaeumannii, and RNC caused by Rhabdocline pseudotsugae. We performed case-control genome-wide association analyses and found disease resistance and tolerance in Douglas-fir to be polygenic and under strong selection. We show that stomatal regulation as well as ethylene and jasmonic acid pathways are important for resisting SNC infection, and secondary metabolite pathways play a role in tolerating SNC once the plant is infected. We identify a major transcriptional regulator of plant defense, ERF1, as the top candidate for RNC resistance. Our findings shed light on the highly polygenic architectures underlying fungal disease resistance and tolerance and have important implications for forestry and conservation as the climate changes.

Ectomycorrhizal fungi of Douglas-fir retain newly assimilated carbon derived from neighboring European beech.

Ectomycorrhizal (ECM) fungi distribute tree-derived carbon (C) via belowground hyphal networks in forest ecosystems. Here, we asked the following: (1) Is C transferred belowground to a neighboring tree retained in fungal structures or transported within the recipient tree? (2) Is the overlap of ectomycorrhizal fungi in mycorrhizal networks related to the amount of belowground C transfer? We used potted sapling pairs of European beech (Fagus sylvatica) and North-American Douglas-fir (Pseudotsuga menziesii) for 13CO2 pulse-labeling. We compared 13C transfer from beech (donor) to either beech or Douglas-fir (recipient) and identified the ECM species. We measured the 13C enrichment in soil, plant tissues, and ECM fractions of fungal-containing parts and plant transport tissues. In recipients, only fungal-containing tissue of ectomycorrhizas was significantly enriched in 13C and not the plant tissue. Douglas-fir recipients shared on average one ECM species with donors and had a lower 13C enrichment than beech recipients, which shared on average three species with donors. Our results support that recently assimilated C transferred belowground is shared among fungi colonizing tree roots but not among trees. In mixed forests with beech and Douglas-fir, the links for C movement might be hampered due to low mycorrhizal overlap with consequences for soil C cycling.

How useful are genomic data for predicting maladaptation to future climate?

Methods using genomic information to forecast potential population maladaptation to climate change or new environments are becoming increasingly common, yet the lack of model validation poses serious hurdles toward their incorporation into management and policy. Here, we compare the validation of maladaptation estimates derived from two methods-Gradient Forests (GFoffset) and the risk of non-adaptedness (RONA)-using exome capture pool-seq data from 35 to 39 populations across three conifer taxa: two Douglas-fir varieties and jack pine. We evaluate sensitivity of these algorithms to the source of input loci (markers selected from genotype-environment associations [GEA] or those selected at random). We validate these methods against 2- and 52-year growth and mortality measured in independent transplant experiments. Overall, we find that both methods often better predict transplant performance than climatic or geographic distances. We also find that GFoffset and RONA models are surprisingly not improved using GEA candidates. Even with promising validation results, variation in model projections to future climates makes it difficult to identify the most maladapted populations using either method. Our work advances understanding of the sensitivity and applicability of these approaches, and we discuss recommendations for their future use.

Predictive accuracy of post-fire conifer death declines over time in models based on crown and bole injury.

A key uncertainty of empirical models of post-fire tree mortality is understanding the drivers of elevated post-fire mortality several years following fire, known as delayed mortality. Delayed mortality can represent a substantial fraction of mortality, particularly for large trees that are a conservation focus in western US coniferous forests. Current post-fire tree mortality models have undergone limited evaluation of how injury level and time since fire interact to influence model accuracy and predictor variable importance. Less severe injuries potentially serve as an indicator for vulnerability to additional stressors such as bark beetle attack or moisture stress. We used a collection of 164,293 individual tree records to examine post-fire tree mortality in eight western USA conifers: Abies concolor, Abies grandis, Calocedrus decurrens, Larix occidentalis, Pinus contorta, Pinus lambertiana, Pinus ponderosa, and Pseudotsuga menziesii. We evaluated the importance of fire injury predictors on discriminating between surviving trees versus immediate and delayed post-fire mortality. We fit balanced random forest models for each species using cumulative tree mortality from 1 to 5-years post-fire. We compared these results to multi-class random forest models using first-year mortality, 2-5-year mortality, and survival 5-years post-fire as a response variable. Crown volume scorched, diameter at breast height, and relative bark char height, were used as predictor variables. The cumulative mortality models all predicted trees that died within 1-year of fire with high accuracy but failed to predict 2-5-year mortality. The multi-class models were an improvement but had lower accuracy for predicting 2-5-year mortality. Multi-class model accuracies ranged from 85% to 95% across all species for predicting 1-year post-fire mortality, 42%-71% for predicting 2-5-year mortality, and 64%-85% for predicting trees that lived past 5-years. Our study highlights the differences in tree species tolerance to fire injury and suggests that including second-order predictors such as beetle attack or climatic water stress before and after fire will be critical to improve accuracy and better understand the mechanisms and patterns of fire-caused tree death. Random forest models have potential for management applications such as post-fire harvesting and simulating future stand dynamics.

Introduction of non-native Douglas fir reduces leaf damage on beech saplings and mature trees in European beech forests.

Recent ecological research suggests that, in general, mixtures are more resistant to insect herbivores and pathogens than monocultures. However, we know little about mixtures with non-native trees, where enemy release could lead to patterns that differ from commonly observed relationships among native species. This becomes particularly relevant when considering that adaptation strategies to climate change increasingly promote a larger share of non-native tree species, such as North American Douglas fir in Central Europe. We studied leaf damage on European beech (Fagus sylvatica) saplings and mature trees across a wide range of site conditions in monocultures and mixtures with phylogenetically distant conifers native Norway spruce (Picea abies) and non-native Douglas fir (Pseudotsuga menziesii). We analyzed leaf herbivory and pathogen damage in relation to tree diversity and composition effects, as well as effects of environmental factors and plant characteristics. We observed lower sapling herbivory and tree sucking damage on beech in non-native Douglas fir mixtures than in beech monocultures, probably due to a lower herbivore diversity on Douglas fir trees, and higher pathogen damage on beech saplings in Norway spruce than Douglas fir mixtures, possibly because of higher canopy openness. Our findings suggest that for low diversity gradients, tree diversity effects on leaf damage can strongly depend on tree species composition, in addition to modifications caused by feeding guild and tree ontogeny. Moreover, we found that nutrient capacity modulated the effects of tree diversity, composition, and environmental factors, with different responses in sites with low or high nutrient capacity. The existence of contrasting diversity effects based on tree species composition provides important information on our understanding of the relationships between tree diversity and plant-herbivore interactions in light of non-native tree species introductions. Especially with recent Norway spruce die-off, the planting of Douglas fir as replacement is likely to strongly increase in Central Europe. Our findings suggest that mixtures with Douglas fir could benefit the survival or growth rates of beech saplings and mature trees due to lower leaf damage, emphasizing the need to clearly identify and compare the potential benefits and ecological trade-offs of non-native tree species in forest management under ongoing environmental change.

Metabarcoding reveals that mixed forests mitigate negative effects of non-native trees on canopy arthropod diversity.

Averting climate change-induced forest diebacks increasingly relies on tree species planted outside of their natural range and on the addition of non-native tree species to mixed-species forests. However, the consequences of such changes for associated biodiversity remain poorly understood, especially for the forest canopy as a largely understudied forest stratum. Here, we used flight interception traps and a metabarcoding approach to study the taxonomic and functional (trophic guilds) composition and taxon richness of canopy arthropods. We sampled 15 monospecific and mixed stands of native European beech, native Norway spruce-planted outside its natural range-and non-native Douglas fir in northwest Germany. We found that the diversity of arthropods was lower in non-native Douglas fir compared with native beech stands. Taxon richness of herbivores was reduced by both conifer species. Other functional guilds, however, were not affected by stand type. Arthropod composition differed strongly between native broadleaved beech and monospecific coniferous (native spruce or non-native Douglas fir) stands, with less pronounced differences between the native and non-native conifers. Beech-conifer mixtures consistently hosted intermediate arthropod diversity and community composition compared with the respective monospecific stands. Moreover, arthropod diversity had a positive relationship with the number of canopy microhabitats. Our study shows that considering arthropod taxa of multiple functional groups reveals the multifaceted impact of non-native tree species on forest canopy arthropod communities. Contrasting with previous studies that primarily focused on the forest floor, we found that native beech hosts a rich diversity of arthropods, compared with lower diversity and distinct communities in economically attractive, and especially in non-native, conifers with few canopy microhabitats. Broadleaf-conifer mixtures did not perform better than native beech stands, but mitigated the negative effects of conifers, making such mixtures a compromise to foster both forest-associated diversity and economic yield.

Forrestiacids E-K: Further [4 + 2]-Type Triterpene-Diterpene Hybrids as Potential ACL Inhibitors from the Vulnerable Conifer Pseudotsuga forrestii.

Seven [4 + 2]-type triterpene-diterpene hybrids derived from a rearranged or a normal lanostane unit (dienophile) and an abietane moiety (diene), forrestiacids E-K (1-7, respectively), were further isolated and characterized from Pseudotsuga forrestii (a vulnerable conifer endemic to China). The intriguing molecules were revealed with the guidance of an LC-MS/MS-based molecular ion networking strategy combined with conventional phytochemical procedures. Their chemical structures with absolute configurations were established by spectroscopic data, chemical transformation, electronic circular dichroism calculations, and single-crystal X-ray diffraction analysis. They all contain a rare bicyclo[2.2.2]octene motif. Both forrestiacids J (6) and K (7) represent the first examples of this unique class of [4 + 2]-type hybrids that arose from a normal lanostane-type dienophile. Some isolates remarkably inhibited ATP-citrate lyase (ACL), with IC50 values ranging from 1.8 to 11 µM. Docking studies corroborated the findings by highlighting the interactions between the bioactive compounds and the ACL enzyme (binding affinities: -9.9 to -10.7 kcal/mol). The above findings reveal the important role of protecting plant species diversity in support of chemical diversity and potential sources of new therapeutics.

Knotwood and Branchwood Polyphenolic Extractives of Silver Fir, Spruce and Douglas Fir and Their Antioxidant, Antifungal and Antibacterial Properties.

The extractive contents of three softwood species largely used in the wood industry, namely Abies alba (Silver fir), Picea abies (spruce) and Pseudotsuga menziesii (Douglas fir), have been determined quantitatively for knots and at different points chosen along their branches, before analysis using high-performance liquid chromatography coupled with Mass Spectrometry (HPLC-MS). The results indicated that branchwood samples located in close proximity to the stem present high contents of extractives similar to those recorded for the knots. HPLC analysis showed quite similar chemical compositions, indicating that first cm of the branches could be considered as an additional source of knotwood. The antibacterial, antifungal and antioxidant activities of knot's extractives have been investigated with the dual objective of better understanding the role of high levels of secondary metabolites present in the knot and evaluating their potential for biorefinery applications. The antioxidant activity study showed that crude extracts of Douglas fir knotwood presented higher radical scavenging activity levels than the extracts of Silver fir and spruce, which presented more or less the same activities. Silver fir and spruce knotwood extracts presented higher antibacterial activity levels than the Douglas fir knotwood extracts did, while Douglas fir knotwood extracts presented more fungal growth inhibition than the spruce and fir knotwood extracts did. The structure-activity relationships indicate that radical scavenging and antifungal activities are associated with a higher relative quantity of flavonoids in the crude extracts, while higher relative quantities of lignans are associated with antibacterial activity.

Gymnosperms of Idaho: Chemical Compositions and Enantiomeric Distributions of Essential Oils of Abies lasiocarpa, Picea engelmannii, Pinus contorta, Pseudotsuga menziesii, and Thuja plicata.

Conifers are of great economic value in terms of lumber production, important for construction and other uses such as pulp and paper. They are also important sources of essential oils. Conifer species have been vital to the ethnobotany and traditional herbal medicine of many different Native American groups. The objective of this work was to obtain and analyze the essential oils of several conifer species (Abies lasiocarpa, Picea engelmannii, Pinus contorta, Pseudotsuga menziesii, and Thuja plicata) growing in Idaho. The foliar essential oils were obtained by hydrodistillation and then analyzed by gas chromatographic methods, including GC-MS, GC-FID, and chiral GC-MS. The essential oils were obtained in varying yields from 0.66% up to 4.70%. The essential oil compositions were largely dominated by monoterpene hydrocarbons and oxygenated monoterpenoids. The chiral monoterpenoids were generally rich in the (-)-enantiomers for members of the Pinaceae, but the (+)-enantiomers predominated in the Cupressaceae. The essential oil compositions obtained in this work are qualitatively similar, but quantitatively different, to previously reported compositions and confirm and complement the previous reports. However, this is the first comprehensive analysis of the chiral terpenoid components in these conifer species. Additional research on essential oils of the Pinaceae and Cupressaceae is needed to describe the chemical profiles, chemical compositions, and enantiomeric distributions more reliably in the various species and infraspecific taxa of these two families.

Structurally diverse mono-/dimeric triterpenoids from the vulnerable conifer Pseudotsuga gaussenii and their PTP1B inhibitory effects. The role of protecting species diversity in support of chemical diversity.

A preliminary phytochemical investigation on the MeOH extract of the twigs and needles of Pseudotsuga gaussenii (a 'vulnerable' plant endemic to China) led to the isolation and characterization of 25 structurally diverse mono- and dimeric triterpenoids. 19 of them are previously undescribed, including eight cucurbitane-type triterpenoids (gaussenols A-H, 1-8, resp.), one serratene-type triterpene (gaussenol I, 9), and 10 triterpenic dimers (gaussenols J-S, 10-19, resp.). Their chemical structures were elucidated by means of spectroscopic data, some chemical transformations, the modified Mosher's method, and single crystal X-ray diffraction analyses. Compound 9 is the first 13R diastereoisomeric serratene-type triterpenoid derivative from nature. The unprecedented dimeric triterpenoids are constructed either through ester linkage (10-18) or via ether bond (19) among the side chains of same or different types of triterpenoid skeletons (e.g., cucurbitane-type, lanostane-type, and/or cycloartane-type). Compounds 9, 15, 21, and 25 exhibited inhibitory effects against the human protein tyrosine phosphatase 1B (PTP1B, a potential drug target for the treatment of type-II diabetes and obesity), with IC50 values of 3.1, 8.6, 9.0, and 5.6 µM, respectively. The interactions of the bioactive compounds with PTP1B were thereafter performed by employing molecular docking studies, with binding affinities ranging from - 6.9 to - 7.3 kcal/mol. The above findings could reveal the important role of protecting plant species diversity in support of chemical diversity and potential sources of new therapeutics.

Wildfires and climate change push low-elevation forests across a critical climate threshold for tree regeneration.

Climate change is increasing fire activity in the western United States, which has the potential to accelerate climate-induced shifts in vegetation communities. Wildfire can catalyze vegetation change by killing adult trees that could otherwise persist in climate conditions no longer suitable for seedling establishment and survival. Recently documented declines in postfire conifer recruitment in the western United States may be an example of this phenomenon. However, the role of annual climate variation and its interaction with long-term climate trends in driving these changes is poorly resolved. Here we examine the relationship between annual climate and postfire tree regeneration of two dominant, low-elevation conifers (ponderosa pine and Douglas-fir) using annually resolved establishment dates from 2,935 destructively sampled trees from 33 wildfires across four regions in the western United States. We show that regeneration had a nonlinear response to annual climate conditions, with distinct thresholds for recruitment based on vapor pressure deficit, soil moisture, and maximum surface temperature. At dry sites across our study region, seasonal to annual climate conditions over the past 20 years have crossed these thresholds, such that conditions have become increasingly unsuitable for regeneration. High fire severity and low seed availability further reduced the probability of postfire regeneration. Together, our results demonstrate that climate change combined with high severity fire is leading to increasingly fewer opportunities for seedlings to establish after wildfires and may lead to ecosystem transitions in low-elevation ponderosa pine and Douglas-fir forests across the western United States.

Soil spore bank communities of ectomycorrhizal fungi in Pseudotsuga japonica forests and neighboring plantations.

Ectomycorrhizal (EcM) fungal spores play an important role in seedling establishment and forest regeneration, especially in areas where compatible host tree species are absent. However, compared to other Pinaceae trees with a wide distribution, limited information is available for the interaction between the endangered Pseudotsuga trees and EcM fungi, especially the spore bank. The aim of this study was to investigate EcM fungal spore bank communities in soil in remnant patches of Japanese Douglas-fir (Pseudotsuga japonica) forest. We conducted a bioassay of 178 soil samples collected from three P. japonica forests and their neighboring arbuscular mycorrhizal artificial plantations, using the more readily available North American Douglas-fir (Pseudotsuga menziesii) as bait seedlings. EcM fungal species were identified by a combination of morphotyping and DNA sequencing of the ITS region. We found that EcM fungal spore banks were present not only in P. japonica forests but also in neighboring plantations. Among the 13 EcM fungal species detected, Rhizopogon togasawarius had the second highest frequency and was found in all plots, regardless of forest type. Species richness estimators differed significantly among forest types. The community structure of EcM fungal spore banks differed significantly between study sites but not between forest types. These results indicate that EcM fungal spore banks are not restricted to EcM forests and extend to surrounding forest dominated by arbuscular mycorrhizal trees, likely owing to the durability of EcM fungal spores in soils.

Friendly neighbours: Hydraulic redistribution accounts for one quarter of water used by neighbouring drought stressed tree saplings.

Hydraulic redistribution (HR) can buffer drought events of tree individuals, however, its relevance for neighbouring trees remains unclear. Here, we quantified HR to neighbouring trees in single- and mixed-species combinations. We hypothesized that uptake of HR water positively correlates with root length, number of root tips and root xylem hydraulic conductivity and that neighbours in single-species combinations receive more HR water than in phylogenetic distant mixed-species combinations. In a split-root experiment, a sapling with its roots split between two pots redistributed deuterium labelled water from a moist to a dry pot with an additional tree each. We quantified HR water received by the sapling in the dry pot for six temperate tree species. After 7 days, one quarter of the water in roots (2.1 ± 0.4 ml), stems (0.8 ± 0.2 ml) and transpiration (1.0 ± 0.3 ml) of the drought stressed sapling originated from HR. The amount of HR water transpired by the receiving plant stayed constant throughout the experiment. While the uptake of HR water increased with root length, species identity did not affect HR as saplings of Picea abies ((L.) Karst) and Fagus sylvatica (L.) in single- and mixed-species combinations received the same amount of HR water.

Strobiloscyphones A-F, 6-Isopentylsphaeropsidones and Other Metabolites from Strobiloscypha sp. AZ0266, a Leaf-Associated Fungus of Douglas Fir.

Six new 6-isopentylsphaeropsidones, strobiloscyphones A-F (1-6), and a new hexadecanoic acid, (2Z,4E,6E)-8,9-dihydroxy-10-oxohexadeca-2,4,6-trienoic acid (7), together with sphaeropsidone (8) and its known synthetic analogue 5-dehydrosphaeropsidone (9) were isolated from Strobiloscypha sp. AZ0266, a fungus inhabiting the leaf litter of Douglas fir (Pseudotsuga menziesii). The structures of 1-7 were established on the basis of their high-resolution mass and 1D and 2D NMR spectroscopic data, and their relative and/or absolute configurations were determined by NOE, comparison of experimental and calculated ECD spectra, and application of the modified Mosher's ester method. Of these, strobiloscyphone F (6) contains a novel highly oxygenated tetracyclic oxireno-octahydrodibenzofuran ring system. Natural products 1, 6, and 9 and the semisynthetic analogue 12 derived from 8 exhibited cytotoxic activity, whereas 9 and 12 showed antimicrobial activity. Possible biosynthetic pathways to 1-6, 8, and 9 are proposed.

Pseudotsuga menziesii (Pinaceae): Volatile Profiles, Antimicrobial Activity and Toxicological Evaluation of Its Essential Oil.

The present article investigates the chemical composition of volatiles of essential oil (EO) and headspace (HS) fraction, as well as biological activities of EO obtained from needles with twigs of Pseudotsuga menziesii var. menziesii cultivated in Serbia. The major class of compounds was monoterpene hydrocarbons with α-terpinolene, sabinene and ß-pinene (EO), and sabinene, α-terpinolene and ß-pinene (HS) as the dominant volatiles. Tested EO exhibited mostly low antimicrobial potential against investigated strains (ATCC and respiratory isolates), where MICs ranged 1.25-20.00 mg/mL. Nevertheless, based on presented results, where antimicrobial testing was done for the first time on human respiratory system isolates, there is a potential of this EO to be used as an adjuvant in the treatment of human respiratory infections, especially those caused by Pseudomonas aeruginosa or Candida albicans strains. Regarding toxicological evaluation, EO showed moderate toxicity in Artemia salina toxicity bioassay (LC50 =347.41, after 24 h) as well as week toxicity against Drosophila melanogaster with the ability only to moderately delay larval and pupal development.

Carbon balance for biosolids use in commercial Douglas Fir plantations in the Pacific Northwest.

Municipal biosolids are commonly used to fertilize Douglas fir (Pseudotsuga menziesii) plantations in the Pacific Northwest. An intensive soil sampling was conducted to quantify the effects of long-term biosolids application on soil carbon, nitrogen and bulk density for forest soils. This information was used to calculate a carbon balance for biosolids use in commercial tree plantations. Paired control and treated sites on two soil series (Klaus and Tokul) were included with samples collected to a 30 cm depth. A significant decrease in bulk density for two depths, but no changes in total C or N were observed in the Klaus soil. In the Tokul soil, biosolids fertilization increased C storage (total C * bulk density) for three of the four measured depths, resulting in an increase in total C from 112.8 Mg C ha-1 to 172 Mg C ha-1 for the 0-30 cm depth. A comparable increase in N was observed, with significant increases in N storage for all measured depths. The C balance considered fuel use associated with transport and application as costs. The fertilizer (N and P) content of the biosolids and changes in soil C were considered as credits. The balance showed net sequestration for both soil series. Carbon benefits for the Klaus soil totaled -0.2 Mg CO2 per Mg biosolids. Benefits in the Tokul soil totaled -5.15 Mg CO2 per Mg biosolids. Based on diameter at breast height (DBH) biosolids use also resulted in increased tree growth for both soil series. However, differences in stand age and stocking rate complicated interpretation of these results.

An Axiom SNP genotyping array for Douglas-fir.

BACKGROUND: In forest trees, genetic markers have been used to understand the genetic architecture of natural populations, identify quantitative trait loci, infer gene function, and enhance tree breeding. Recently, new, efficient technologies for genotyping thousands to millions of single nucleotide polymorphisms (SNPs) have finally made large-scale use of genetic markers widely available. These methods will be exceedingly valuable for improving tree breeding and understanding the ecological genetics of Douglas-fir, one of the most economically and ecologically important trees in the world. RESULTS: We designed SNP assays for 55,766 potential SNPs that were discovered from previous transcriptome sequencing projects. We tested the array on ~ 2300 related and unrelated coastal Douglas-fir trees (Pseudotsuga menziesii var. menziesii) from Oregon and Washington, and 13 trees of interior Douglas-fir (P. menziesii var. glauca). As many as ~ 28 K SNPs were reliably genotyped and polymorphic, depending on the selected SNP call rate. To increase the number of SNPs and improve genome coverage, we developed protocols to 'rescue' SNPs that did not pass the default Affymetrix quality control criteria (e.g., 97% SNP call rate). Lowering the SNP call rate threshold from 97 to 60% increased the number of successful SNPs from 20,669 to 28,094. We used a subset of 395 unrelated trees to calculate SNP population genetic statistics for coastal Douglas-fir. Over a range of call rate thresholds (97 to 60%), the median call rate for SNPs in Hardy-Weinberg equilibrium ranged from 99.2 to 99.7%, and the median minor allele frequency ranged from 0.198 to 0.233. The successful SNPs also worked well on interior Douglas-fir. CONCLUSIONS: Based on the original transcriptome assemblies and comparisons to version 1.0 of the Douglas-fir reference genome, we conclude that these SNPs can be used to genotype about 10 K to 15 K loci. The Axiom genotyping array will serve as an excellent foundation for studying the population genomics of Douglas-fir and for implementing genomic selection. We are currently using the array to construct a linkage map and test genomic selection in a three-generation breeding program for coastal Douglas-fir.

Continental-scale tree-ring-based projection of Douglas-fir growth: Testing the limits of space-for-time substitution.

A central challenge in global change research is the projection of the future behavior of a system based upon past observations. Tree-ring data have been used increasingly over the last decade to project tree growth and forest ecosystem vulnerability under future climate conditions. But how can the response of tree growth to past climate variation predict the future, when the future does not look like the past? Space-for-time substitution (SFTS) is one way to overcome the problem of extrapolation: the response at a given location in a warmer future is assumed to follow the response at a warmer location today. Here we evaluated an SFTS approach to projecting future growth of Douglas-fir (Pseudotsuga menziesii), a species that occupies an exceptionally large environmental space in North America. We fit a hierarchical mixed-effects model to capture ring-width variability in response to spatial and temporal variation in climate. We found opposing gradients for productivity and climate sensitivity with highest growth rates and weakest response to interannual climate variation in the mesic coastal part of Douglas-fir's range; narrower rings and stronger climate sensitivity occurred across the semi-arid interior. Ring-width response to spatial versus temporal temperature variation was opposite in sign, suggesting that spatial variation in productivity, caused by local adaptation and other slow processes, cannot be used to anticipate changes in productivity caused by rapid climate change. We thus substituted only climate sensitivities when projecting future tree growth. Growth declines were projected across much of Douglas-fir's distribution, with largest relative decreases in the semiarid U.S. Interior West and smallest in the mesic Pacific Northwest. We further highlight the strengths of mixed-effects modeling for reviving a conceptual cornerstone of dendroecology, Cook's 1987 aggregate growth model, and the great potential to use tree-ring networks and results as a calibration target for next-generation vegetation models.