Tolerance to multiple climate stressors: a case study of Douglas-fir drought and cold hardiness

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.

Testing the chilling- before drought-tolerance hypothesis in Pooideae grasses

Temperate Pooideae are a large clade of economically important grasses distributed in some of the Earth's coldest and driest terrestrial environments. Previous studies have inferred that Pooideae diversified from their tropical ancestors in a cold montane habitat, suggesting that above-freezing cold (chilling) tolerance evolved early in the subfamily. By contrast, drought tolerance is hypothesized to have evolved multiple times independently in response to global aridification that occurred after the split of Pooideae tribes. To independently test predictions of the chilling-before-drought hypothesis in Pooideae, we assessed conservation of whole plant and gene expression traits in response to chilling vs. drought. We demonstrated that both trait responses are more similar across tribes in cold as compared to drought, suggesting that chilling responses evolved before, and drought responses after, tribe diversification. Moreover, we found significantly more overlap between drought and chilling responsive genes within a species than between drought responsive genes across species, providing evidence that chilling tolerance genes acted as precursors for the novel acquisition of increased drought tolerance multiple times independently, partially through the cooption of chilling responsive genes.

Differences in heat tolerance, water use efficiency and growth among Douglas-fir families and varieties evidenced by GWAS and common garden studies

Severe and frequent heat and drought events challenge the survival and development of long-generation trees. In this study, we investigated the genomic basis of heat tolerance, water use efficiency and growth by performing genome-wide association studies in coastal Douglas-fir (Pseudotsuga menziesii) and intervarietal (menziesii × glauca) hybrid seedlings. GWAS results identified 32 candidate genes involved in primary and secondary metabolism, abiotic stress and signaling, among other functions. Water use efficiency (inferred from carbon isotope discrimination), photosynthetic capacity (inferred from %N), height and heat tolerance (inferred from electrolyte leakage in a heat stress experiment) were significantly different among Douglas-fir families and varieties. High-elevation seed sources had increased water use efficiency, which could be a result of higher photosynthetic capacity. Similarly, families with greater heat tolerance also had higher water use efficiency and slower growth, suggesting a conservative growth strategy. Intervarietal hybrids showed increased heat tolerance (lower electrolyte leakage at 50 and 55 °C) and higher water use efficiency compared with coastal families, suggesting that hybridization might be a source of pre-adapted alleles to warming climates and should be considered for large-scale reforestation projects under increasingly arid conditions.

Tree resistance and recovery from drought mediated by multiple abiotic and biotic processes across a large geographic gradient

Worldwide, increasing severity of droughts threatens to change forest ecosystem functioning and community structure. Understanding how forest resilience is determined by its two underlying components, resistance and recovery, will help elucidate the mechanisms of drought responses and help inform management strategies. However, drought responses are shaped by complex processes across different scales, including species-specific drought strategies, tree size, competition, local environmental conditions, and the intensity of the drought event. Here, we quantified the reduction in tree growth during drought (an inverse measure of drought resistance) and post-drought recovery for three montane conifers (Abies concolor, Pinus jeffreyi, and Pinus lambertiana) in California. We used tree ring analysis to quantify responses to drought events of varying intensity between 1895 and 2018 across a geographic climatic gradient, to examine the roles of tree size (DBH) and competition (tree density) in mediating drought responses. We found that years of more intense drought corresponded with larger growth reductions and recovery rates were lower following drought years where trees suffered larger reductions. We found little variation among species in their growth reductions during drought events, but significant differences among species in their recovery post-drought. Across the geographic gradient, trees in the driest locations were susceptible to large growth reductions, signaling either strong sensitivity to drought intensity or exposure to the most extreme drought conditions. These growth reductions were not always compensated for by higher recovery rates. We also found that larger trees were more susceptible to drought due to a steeper negative relationship between recovery rates and the intensity of growth reduction during the drought. Contrary to expectations, recovery rates following the most detrimental drought years were higher in denser forests. Our results demonstrate the importance of considering how factors at various spatial and temporal scales affect the different components of drought responses.

Looking for the needle in a downsized haystack: Whole-exome sequencing unravels genomic signals of climatic adaptation in Douglas-fir (Pseudotsuga menziesii)

Conifers often occur along steep gradients of diverse climates throughout their natural ranges, which is expected to result in spatially varying selection to local climate conditions. However, signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Consequently, our understanding of how selection and gene flow have shaped phenotypic and genotypic differentiation in trees is still limited.A 40-year-old common garden experiment comprising 16 Douglas-fir (Pseudotsuga menziesii) provenances from a north-to-south gradient of approx. 1,000 km was analyzed, and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach, which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency, and deviations from Hardy-Weinberg proportions). We used four conceptually different genome scan methods based on FST outlier detection and gene-environment association in order to disentangle truly adaptive SNPs from neutral SNPs.We found that a relatively small proportion of the exome showed a truly adaptive signal (0.01%-0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationships with climate at provenance origins, which strongly suggests that they have featured adaptation in Douglas-fir along a climatic gradient. Two SNPs were independently found by three of the employed algorithms, and one of them is in close proximity to an annotated gene involved in circadian clock control and photoperiodism as was similarly found in Populus balsamifera. Synthesis. We conclude that despite neutral evolutionary processes, phenotypic and genomic signals of adaptation to climate are responsible for differentiation, which in particular explain disparity between the well-known coastal and interior varieties of Douglas-fir.

Clair JB, Crepeau MW, Salzberg SL, Langley CH, Allen B, Neale DB. Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir

Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (Pseudotsuga menziesii). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes. Newly discovered associations for cold adaptation in Douglas-fir included 130 genes involved in many important biological functions such as primary and secondary metabolism, growth and reproductive development, transcription regulation, stress and signaling, and DNA processes. These genes were related to growth, phenology and cold hardiness and strongly depend on variation in environmental variables such degree days below 0c, precipitation, elevation and distance from the coast. This study is a step forward in our understanding of the complex interconnection between environment and genomics and their role in cold-associated trait variation in boreal tree species, providing a baseline for the species' predictions under climate change.

A method for experimental warming of developing tree seeds with a common garden demonstration of seedling responses

BACKGROUND

Forest dieback driven by rapid climate warming threatens ecosystems worldwide. The health of forested ecosystems depends on how tree species respond to warming during all life history stages. While it is known that seed development is temperature-sensitive, little is known about possible effects of climate warming on seed development and subsequent seedling performance. Exposure of seeds to high air temperatures may influence subsequent seedling performance negatively, though conversely, warming during seed development may aid acclimation of seedlings to subsequent thermal stress. Technical challenges associated with in-situ warming of developing tree seeds limit understanding of how tree species may respond to seed development in a warmer climate.

RESULTS

We developed and validated a simple method for passively warming seeds as they develop in tree canopies to enable controlled study of climate warming on seedling performance. We quantified thermal effects of the cone-warming method across individual pine trees and stands by measuring the air temperature surrounding seed cones using thermal loggers and the temperature of seed cone tissue using thermocouples. We then investigated seedling phenotypes in relation to the warming method through a common garden study. We assessed seedling morphology, physiology, and mycorrhizal nodulation in response to experimental cone-warming in 20 seed-source-tree canopies on the San Francisco Peaks in northern Arizona, USA. The warming method increased air temperature surrounding developing seed cones by 2.1 °C, a plausible increase in mean air temperature by 2050 under current climate projections. Notable effect sizes of cone-warming were detected for seedling root length, shoot length, and diameter at root collar using Cohen's Local f². Root length was affected most by cone-warming, but effect sizes of cone-warming on root length and diameter at root collar became negligible after the first year of growth. Cone-warming had small but significant effects on mycorrhizal fungal richness and seedling multispectral near-infrared indices indicative of plant health.

CONCLUSIONS

The method was shown to reliably elevate the temperature surrounding seed cones and thereby facilitate experimental in-situ climate warming research on forest trees. The method was furthermore shown to influence plant traits that may affect seedling performance under climate warming.

Champions of winter survival: cold acclimation and molecular regulation of cold hardiness in evergreen conifers

Evergreen conifers are champions of winter survival, based on their remarkable ability to acclimate to cold and develop cold hardiness. Counterintuitively, autumn cold acclimation is triggered not only by exposure to low temperature, but also by a combination of decreasing temperature, decreasing photoperiod and changes in light quality. These environmental cues control a network of signaling pathways that coordinate cold acclimation and cold hardiness in overwintering conifers, leading to cessation of growth, bud dormancy, freezing tolerance and changes in energy metabolism. Advances in genomic, transcriptomic and metabolomic tools for conifers have improved our understanding of how trees sense and respond to changes in temperature and light during cold acclimation and the development of cold hardiness, but there remain considerable gaps deserving further research in conifers. In the first section of this review, we focus on the physiological mechanisms used by evergreen conifers to adjust metabolism seasonally and to protect overwintering tissues against winter stresses. In the second section, we review how perception of low temperature and photoperiod regulate the induction of cold acclimation. Finally, we explore the evolutionary context of cold acclimation in conifers and evaluate challenges imposed on them by changing climate and discuss emerging areas of research in the field.

Phenology of Douglas-Fir Beetle (Coleoptera: Curculionidae) and Its Role in Douglas-Fir Mortality in Western Washington

Douglas-fir dominated forests are an integral part of the Pacific Northwest. In the Cedar River Municipal Watershed, Washington, these forests provide erosion control and ecosystem buffering for the Cedar River system that supplies high-quality drinking water to the Seattle area. Mortality of Douglas-fir in the watershed has been increasing in recent years. The Douglas-fir beetle, Dendroctonus pseudotsugae Hopkins, as well as fungal pathogens, are key agents of mortality in Douglas-fir dominated forests, but their contributions to the current rates of mortality are unknown. We modeled D. pseudotsugae phenology in western Washington and estimated peak flight of overwintering adults at 344.5 cumulative degree-days (base temperature threshold = 4.3°C). We extended the results from the phenology model when assuming a 1.7°C increase in temperature and estimated that D. pseudotsugae adult flight could be advanced by 21-27 d. We also conducted a field study over 2 yr to quantify the individual and interacting roles of D. pseudotsugae, root rot pathogens, and other abiotic and biotic variables as drivers of Douglas-fir mortality. Study sites with recent high rates of mortality of Douglas-fir (>30%) were generally in lower elevation stands and affected by both D. pseudotsugae and root rot pathogens. Attacks by D. pseudotsugae in 1 yr were significantly associated with the presence of root rot mycelia in the following year, but not vice versa. The development of a D. pseudotsugae phenology model for the region and the identification of variables associated with Douglas-fir mortality facilitates the development of management strategies.

Climate Response of Douglas Fir Reveals Recently Increased Sensitivity to Drought Stress in Central Europe

Research Highlights: In Central Europe, Douglas fir became more responsive to summer drought in recent years. Background and Objectives: Until now, Douglas fir has been considered a tree species resistant to drought. However, how Douglas fir will be able to cope with the increasing frequency and intensity of summer heat waves remains a question. The long-term variability in the climate response of Douglas fir in Central European conditions has not been fully explored. The aim of the study was to identify climatic factors controlling the stem radial growth of Douglas fir and Norway spruce, and to examine the temporal changes in tree responses to key climatic variables related to drought stress. Materials and Methods: We analysed the pattern of the climate–growth relationship of Douglas fir and Norway spruce, growing in mixed stands distributed between 260 and 600 m above sea level, which corresponds with the altitudinal zone of intensive spruce dieback in the Czech Republic. Nine-site tree-ring-width chronologies were developed for each tree species. Pointer year analysis and correlation analysis in combination with principal component analysis were used to identify climatic factors limiting their growth. Moving correlation function was computed to assess temporal changes of the climate–growth relationship. Results: In the entire 1961–2015 period, growth of both species was positively related to summer precipitation. The response to temperature differed between species. While spruce was negatively affected by the temperatures in summer months, the increments of Douglas fir were positively correlated with the temperatures in February and March. However, moving correlation analysis revealed recently increasing sensitivity to summer temperatures also for Douglas fir. Higher responsiveness of Douglas fir to drought was also revealed by the increasing frequency of negative pointer years in the 2003–2015 period. Conclusions: The recommendations of Douglas fir as a suitable alternative tree species for declining spruce stands at lower altitudes must be regarded with caution.

Northern forest tree populations are physiologically maladapted to drought

Northern forests at the leading edge of their distributions may not show increased primary productivity under climate warming, being limited by climatic extremes such as drought. Looking beyond tree growth to underlying physiological mechanisms is fundamental for accurate predictions of forest responses to climate warming and drought stress. Within a 32-year genetic field trial, we analyze relative contributions of xylem plasticity and inferred stomatal response to drought tolerance in regional populations of a widespread conifer. Genetic adaptation leads to varying responses under drought. Trailing-edge tree populations produce fewer tracheids with thicker cell walls, characteristic of drought-tolerance. Stomatal response explains the moderate drought tolerance of tree populations in central areas of the species range. Growth loss of the northern population is linked to low stomatal responsiveness combined with the production of tracheids with thinner cell walls. Forests of the western boreal may therefore lack physiological adaptations necessary to tolerate drier conditions.

Survival, early growth and impact of damage by late-spring frost and winter desiccation on Douglas-fir seedlings in southern Sweden

Introduction of non-native species, such as Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco), can be a means of mitigating the effects of climate change by meeting the growing demand for biomass and high quality wood. The aim of this study was to investigate early growth, survival and damage from late-spring frost and winter desiccation. A provenance trial with four coastal and three interior provenances of Douglas-fir originating from British Columbia, Canada, was established in Southwest Sweden (56°43'N, 13°08'E). Seedling height, length of the leading shoot, and occurrence of frost damage, were measured after one, three, and six growing seasons. Timing of bud break in spring was also observed. The interior Douglas-fir were more frequently damaged by late-spring frost compared to the coastal Douglas-fir. The interior Douglas-fir still had a higher survival after six growing seasons compared to the coastal variety. All provenances were damaged by winter desiccation, but the provenances originating from the coastal area were more severely damaged. Choice of variety may reduce the risk for either late-spring frost or winter desiccation.

Growth gains from selective breeding in a spruce hybrid zone do not compromise local adaptation to climate

Hybrid zones contain extensive standing genetic variation that facilitates rapid responses to selection. The Picea glauca × Picea engelmannii hybrid zone in western Canada is the focus of tree breeding programs that annually produce ~90 million reforestation seedlings. Understanding the direct and indirect effects of selective breeding on adaptive variation is necessary to implement assisted gene flow (AGF) polices in Alberta and British Columbia that match these seedlings with future climates. We decomposed relationships among hybrid ancestry, adaptive traits, and climate to understand the implications of selective breeding for climate adaptations and AGF strategies. The effects of selection on associations among hybrid index estimated from ~6,500 SNPs, adaptive traits, and provenance climates were assessed for ~2,400 common garden seedlings. Hybrid index differences between natural and selected seedlings within breeding zones were small in Alberta (average +2%), but larger and more variable in BC (average −7%, range −24% to +1%), slightly favoring P. glauca ancestry. The average height growth gain of selected seedlings over natural seedlings within breeding zones was 36% (range 12%–86%). Clines in growth with temperature‐related variables were strong, but differed little between selected and natural populations. Seedling hybrid index and growth trait associations with evapotranspiration‐related climate variables were stronger in selected than in natural seedlings, indicating possible preadaptation to drier future climates. Associations among cold hardiness, hybrid ancestry, and cold‐related climate variables dominated signals of local adaptation and were preserved in breeding populations. Strong hybrid ancestry–phenotype–climate associations suggest that AGF will be necessary to match interior spruce breeding populations with shifting future climates. The absence of antagonistic selection responses among traits and maintenance of cold adaptation in selected seedlings suggests breeding populations can be safely redeployed using AGF prescriptions similar to those of natural populations.