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Abiotic stresses such as drought change plant-pathogen interactions by affecting both hosts and pathogens. Here, we aimed to unravel the molecular mechanisms underlying forest tree-pathogen interactions under drought stress and subsequent rewatering. We conducted glasshouse experiments involving infection by the stem canker-causing fungal pathogen Chrysoporthe austroafricana under drought stress and rewatering in Eucalyptus grandis and investigated host and pathogen transcriptomic changes using RNA-seq data from our current combined stress experiment as well as previous single stress studies. We found that mild drought stress enhances disease progression while, upon rewatering, pathogen infection delays recovery of leaf stomatal conductance. Transcriptomic changes in the host support increased susceptibility to the pathogen while the in planta fungal transcriptome suggests prioritization of survival in the drought-stressed host. Upon rewatering, changes in the host transcriptome suggest allocation of resources to stress responses at the expense of growth and carbohydrate storage while that of the pathogen indicate downregulation of some fungal metabolic pathways potentially because the pathogen takes advantage of changes in the host. Our study identified key molecular processes and genes that provide mechanistic insights into tree-pathogen interactions under abiotic stresses. This enables prediction of tree resilience under a changing climate and contributes towards future tree health improvement endeavours.

Wood is the water conducting tissue of tree stems. Like most angiosperm trees, poplar wood contains water-conducting vessel elements whose functional properties affect water transport and growth rates, as well as susceptibility to embolism and hydraulic failure during water stress and drought. Here we used a unique hybrid poplar pedigree carrying genomically characterized chromosomal insertions and deletions to undertake a systems genomics analysis of vessel traits. We assayed gene expression in wood forming tissues from clonal replicates of genotypes covering dosage quantitative trait loci with insertions and deletions, genotypes with extreme vessel trait phenotypes, and control genotypes. A gene co-expression analysis was used to assign genes to modules, which were then used in integrative analyses to identify modules associated with traits, to identify putative molecular and cellular processes associatedwith eachmodule, and finally to identify candidate genes using multiple criteria including dosage responsiveness. These analyses identified known processes associated with vessel traits including stress response, abscisic acid and cell wall biosynthesis, and in addition identified previously unexplored processes including cell cycle and protein ubiquitination. We discuss our findings relative to component processes contributing to vessel trait variation including signaling, cell cycle, cell expansion, and cell differentiation. [ABSTRACT FROM AUTHOR]

In the Mediterranean region, reforestation programs record failures following successive drought periods. The use of different plant-growth-promoting amendments and the understanding of drought-induced physiological and biochemical responses of carob will contribute to the reforestation program's success. In this study, the effects of arbuscular-mycorrhizal-fungi (AMF), vermicompost (VC), and rock phosphate (RP) on carob seedlings under drought stress (DS) and recovery (REC) conditions were evaluated. A greenhouse experiment was conducted with carob seedlings grown in the presence of AMF, VC, and RP, applied alone or in combination under well-watered (WW), DS (by stopping irrigation for 12 days), and recovery (REC) conditions. The obtained results indicated that the triple combination (AMF + VC + RP) presented the highest improvement in water potential, photosynthetic pigment content, stomatal conductance, and chlorophyll fluorescence compared to the controls under DS and after REC. In addition, this combination resulted in improved tolerance of carob seedlings to DS and a high potential for rapid recovery after rehydration due to a high accumulation of sugars, proteins, and antioxidant enzymes. In summary, the results underline the importance of inoculating carob with AMF in combination with (in)-organic amendments in improving its tolerance to DS and its recovery performances. [ABSTRACT FROM AUTHOR]

Robinia pseudoacacia L. is a deciduous tree planted almost all around the world for a wide variety of uses such as ornamental in urban ecosystems and forest trees in afforestation. This study aims to evaluate the genetic diversity and phylogenetic relations of R. pseudoacacia using some selected populations in Istanbul and Kocaeli cities. For this aim, molecular marker-assisted and DNA sequence-based analyses were performed. According to the results, nine of 15 inter simple sequence repeats (ISSR) primers gave clear and distinguishable bands with a total of 100 loci. The percentage of polymorphic loci (PPL) was calculated as 100% for multi-populations and ranged from 46% to 76% for single populations. Nei's gene diversity value was calculated between 0.165 and 0.251. The lowest and highest PPL were found in populations of Barbaros Boulevard and Dilovasi District, respectively. Population structure analysis showed seven different genetic structures for five populations. Internal transcribed spacer 1 region (ITS1) and trnL-F intergenic spacer region were used to examine the phylogenetic relationships of R. pseudoacacia, and both regions showed a high discriminative power at the family level. Based on the findings, R. pseudoacacia, as a forest tree residing in the urban ecosystem, may face the risk of population decline in the upcoming years due to its moderate/low genetic diversity and susceptibility to environmental pressures.

Abstract Background Local adaptation is a key evolutionary process that enhances the growth of plants in their native habitat compared to non-native habitats, resulting in patterns of adaptive genetic variation across the entire geographic range of the species. The study of population adaptation to local environments and predicting their response to future climate change is important because of climate change. Results Here, we explored the genetic diversity of candidate genes associated with bud burst in pedunculate oak individuals sampled from 6 populations in Poland. Single nucleotide polymorphism (SNP) diversity was assessed in 720 candidate genes using the sequence capture technique, yielding 18,799 SNPs. Using landscape genomic approaches, we identified 8 F ST outliers and 781 unique SNPs in 389 genes associated with geography, climate, and phenotypic variables (individual/family spring and autumn phenology, family diameter at breast height (DBH), height, and survival) that are potentially involved in local adaptation. Then, using a nonlinear multivariate model, Gradient Forests, we identified vulnerable areas of the pedunculate oak distribution in Poland that are at risk from climate change. Conclusions The model revealed that pedunculate oak populations in the eastern part of the analyzed geographical region are the most sensitive to climate change. Our results might offer an initial evaluation of a potential management strategy for preserving the genetic diversity of pedunculate oak.

Robinia pseudoacacia L. is a deciduous tree planted almost all around the world for a wide variety of uses such as ornamental in urban ecosystems and forest trees in afforestation. This study aims to evaluate the genetic diversity and phylogenetic relations of R. pseudoacacia using some selected populations in Istanbul and Kocaeli cities. For this aim, molecular marker-assisted and DNA sequence-based analyses were performed. According to the results, nine of 15 inter simple sequence repeats (ISSR) primers gave clear and distinguishable bands with a total of 100 loci. The percentage of polymorphic loci (PPL) was calculated as 100% for multi-populations and ranged from 46% to 76% for single populations. Nei's gene diversity value was calculated between 0.165 and 0.251. The lowest and highest PPL were found in populations of Barbaros Boulevard and Dilovası District, respectively. Population structure analysis showed seven different genetic structures for five populations. Internal transcribed spacer 1 region (ITS1) and trnL-F intergenic spacer region were used to examine the phylogenetic relationships of R. pseudoacacia, and both regions showed a high discriminative power at the family level. Based on the findings, R. pseudoacacia, as a forest tree residing in the urban ecosystem, may face the risk of population decline in the upcoming years due to its moderate/low genetic diversity and susceptibility to environmental pressures. [ABSTRACT FROM AUTHOR]

Wood is the water conducting tissue of tree stems. Like most angiosperm trees, poplar wood contains water-conducting vessel elements whose functional properties affect water transport and growth rates, as well as susceptibility to embolism and hydraulic failure during water stress and drought. Here we used a unique hybrid poplar pedigree carrying genomically characterized chromosomal insertions and deletions to undertake a systems genomics analysis of vessel traits. We assayed gene expression in wood forming tissues from clonal replicates of genotypes covering dosage quantitative trait loci with insertions and deletions, genotypes with extreme vessel trait phenotypes, and control genotypes. A gene co-expression analysis was used to assign genes to modules, which were then used in integrative analyses to identify modules associated with traits, to identify putative molecular and cellular processes associated with each module, and finally to identify candidate genes using multiple criteria including dosage responsiveness. These analyses identified known processes associated with vessel traits including stress response, abscisic acid and cell wall biosynthesis, and in addition identified previously unexplored processes including cell cycle and protein ubiquitination. We discuss our findings relative to component processes contributing to vessel trait variation including signaling, cell cycle, cell expansion, and cell differentiation.

AbstractDirect seeding, a planting technique that has long been applied in restoring degraded land and forest, is often doubted to be successful due to many constrains, both biotic and abiotic. This study aims to increase the success of direct seeding through the application of seed briquettes, aquasorb treatment and determining the right sowing time for three forest tree species, i.e. Ceiba pentandra, Enterolobium cyclocarpum, Calophyllum inophyllum. This study used a randomized block design with two factorials (seed treatments and sowing dates) in each species. Seeds were sown in three blocks in the field according to the sowing time treatments. Each treatment consisted of 10 sowing plots in one block and 5 seeds or seed briquettes in each sowing plot. The results showed that direct seeding when the rain starts to stabilize (ST-2) supported by the use of seed briquettes and the addition of aquasorb was able to increase seedling survival, height and root collar diameter of all tested tree species. In general, seed briquettes and the addition of aquasorb provided better seedling survival and growth compared to direct seeding using untreated seeds. C. inophyllum gave higher seedling survival compared to the other two species indicating that this species is very prospective for direct seeding applications due to its high adaptability.

In the Mediterranean region, reforestation programs record failures following successive drought periods. The use of different plant-growth-promoting amendments and the understanding of drought-induced physiological and biochemical responses of carob will contribute to the reforestation program’s success. In this study, the effects of arbuscular-mycorrhizal-fungi (AMF), vermicompost (VC), and rock phosphate (RP) on carob seedlings under drought stress (DS) and recovery (REC) conditions were evaluated. A greenhouse experiment was conducted with carob seedlings grown in the presence of AMF, VC, and RP, applied alone or in combination under well-watered (WW), DS (by stopping irrigation for 12 days), and recovery (REC) conditions. The obtained results indicated that the triple combination (AMF + VC + RP) presented the highest improvement in water potential, photosynthetic pigment content, stomatal conductance, and chlorophyll fluorescence compared to the controls under DS and after REC. In addition, this combination resulted in improved tolerance of carob seedlings to DS and a high potential for rapid recovery after rehydration due to a high accumulation of sugars, proteins, and antioxidant enzymes. In summary, the results underline the importance of inoculating carob with AMF in combination with (in)-organic amendments in improving its tolerance to DS and its recovery performances.

The transition from the vegetative juvenile phase to the adult phase is a crucial event in the life cycle of flowering plants, with flowering being the most important milestone. While the regulatory pathways of flowering have been well established in model plants such as Arabidopsis and a few crops, the flowering regulation pathways in perennial forest trees remain poorly understood. This paper summarizes the regulation of flowering time by miR156 and miR172, which are the main members of the aging pathway, and also presents new information on the role of miR159 and miR169. These two microRNAs interact with miR156 and miR172 to jointly regulate flowering time in forest trees. Overall, this review sheds light on the complex regulatory mechanisms underlying flowering time in forest trees and provides insights into potential targets for manipulating the flowering time of these economically and ecologically important species.

The importance of drought as a constraint to agriculture and forestry is increasing with climate change. Genetic improvement of plants' resilience is one of the mitigation strategies to curb this threat. Although recovery from drought stress is important to long-term drought adaptation and has been considered as an indicator of dehydration tolerance in annual crops, this has not been well explored in forest trees. Thus, we aimed to investigate the physiological and transcriptional changes during drought stress and rewatering in Eucalyptus grandis W. Hill ex Maiden. We set up a greenhouse experiment where we imposed drought stress on 2-year-old seedlings and rewatered the recovery group after 17 days of drought. Our measurement of leaf stomatal conductance (gs) showed that, while gs was reduced by drought stress, it fully recovered after 5 days of rewatering. The RNA-seq analysis from stem samples revealed that genes related to known stress responses such as phytohormone and reactive oxygen species signaling were upregulated, while genes involved in metabolism and growth were downregulated due to drought stress. We observed reprogramming of signal transduction pathways and metabolic processes at 1 day of rewatering, indicating a quick response to rewatering. Our results suggest that recovery from drought stress may entail alterations in the jasmonic acid, salicylic acid, ethylene and brassinosteroid signaling pathways. Using co-expression network analysis, we identified hub genes, including the putative orthologs of ABI1 , ABF2 , ABF3 , HAI2 , BAM1 , GolS2 and SIP1 during drought and CAT2 , G6PD1 , ADG1 and FD-1 during recovery. Taken together, by highlighting the molecular processes and identifying key genes, this study gives an overview of the mechanisms underlying the response of E. grandis to drought stress and recovery that trees may face repeatedly throughout their long life cycle. This provides a useful reference to the identification and further investigation of signaling pathways and target genes for future tree improvement. [ABSTRACT FROM AUTHOR]

A new species of Neotropical Camerobiidae from Peru, Neophyllobius (Neophyllobius) unpensissp. nov. is described from the leaves of a native forest tree of Neltuma piurensis (Fabaceae), based on females and protonymphs. The new stilt-legged mite was found in the spring, summer, and autumn, but were more frequently observed during summer. [ABSTRACT FROM AUTHOR]

Introduction-- The masaguaro (Pseudomanea Guachapele) was used in reforestation by the" Fundación Orinoquia Biodiversa" in Arauca, and it presented an unknown wilting. Objective-- Characterize the disease and its causal agent, and evaluate the possibilities of chemical and biological control of the disease. Methodology-- The research was carried out in Campo Alegre Arauquita neighborhood (Arauca, Colombia). The samples were analyzed in the microbiology laboratory of the University of Pamplona. The disease and its causal agent were characterized, the incidence and severity of the disease were determined and the monetary losses considering the dead plants, were estimated. A wilting control experiment using benomyl and Bacillus subtilis was carried out, comparing them to a control without treatment. Fusarium oxysposum was determined as the causal agent. Results-- Fusarium oxysporum was identified as causal agent of the disease. Wilting reached between 13% and 54% of incidence. The economic losses were estimated at more than 19 million pesos/ha. Conclusion-- The preventive and eradicative action of benomyl and only preventive action of B. subtilis were verified. [ABSTRACT FROM AUTHOR]

The genetic system represents the genetic pathway of organisms for organizing and transmitting genetic material that determines the balance between coherence, gene recombination, and control over the amount and type of gene combinations. The objective of this paper is to present the main characteristics of the genetic system of several species of forest trees, namely: Picea abies, Abies alba, Larix decidua, Pinus sylvestris and Quercus robur. The main characteristics of the genetic system taken into account refer to: the mode of reproduction; population dynamics type; chromosomal cycle; recombination index; presence or absence of chromosomal genetic polymorphism, etc. The used methods included searching of the various databases with the latest publications in the field and identification of some relevant results. In the case of forest trees, the genetic systems present a special situation, compared to other higher plants; is about a particular configuration of the systems components. An optimal genetic system of long-lived species, such as forest trees, is characterized by a high recombination index and cross-pollination; however it is possible to change the rate of genetic recombination through selection. [ABSTRACT FROM AUTHOR]

Abstract Background Needle rust caused by the fungus Chrysomyxa rhododendri causes significant growth decline and increased mortality of young Norway spruce trees in subalpine forests. Extremely rare trees with enhanced resistance represent promising candidates for practice-oriented reproduction approaches. They also enable the investigation of tree molecular defence and resistance mechanisms against this fungal disease. Here, we combined RNA-Seq, RT-qPCR and secondary metabolite analyses during a period of 38 days following natural infection to investigate differences in constitutive and infection-induced defence between the resistant genotype PRA-R and three susceptible genotypes. Results Gene expression and secondary metabolites significantly differed among genotypes from day 7 on and revealed already known, but also novel candidate genes involved in spruce molecular defence against this pathogen. Several key genes related to (here and previously identified) spruce defence pathways to needle rust were differentially expressed in PRA-R compared to susceptible genotypes, both constitutively (in non-symptomatic needles) and infection-induced (in symptomatic needles). These genes encoded both new and well-known antifungal proteins such as endochitinases and chitinases. Specific genetic characteristics concurred with varying phenolic, terpene, and hormone needle contents in the resistant genotype, among them higher accumulation of several flavonoids (mainly kaempferol and taxifolin), stilbenes, geranyl acetone, α-ionone, abscisic acid and salicylic acid. Conclusions Combined transcriptional and metabolic profiling of the Norway spruce defence response to infection by C. rhododendri in adult trees under subalpine conditions confirmed the results previously gained on artificially infected young clones in the greenhouse, both regarding timing and development of infection, and providing new insights into genes and metabolic pathways involved. The comparison of genotypes with different degrees of susceptibility proved that several of the identified key genes are differently regulated in PRA-R, and that the resistant genotype combines a strong constitutive defence with an induced response in infected symptomatic needles following fungal invasion. Genetic and metabolic differences between the resistant and susceptible genotypes indicated a more effective hypersensitive response (HR) in needles of PRA-R that prevents penetration and spread of the rust fungus and leads to a lower proportion of symptomatic needles as well as reduced symptom development on the few affected needles.

With the advent of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) system, plant genome editing has entered a new era of robust and precise editing for any genes of interest. The development of various CRISPR/Cas toolkits has enabled new genome editing outcomes that not only target indel mutations but also enable base editing and prime editing. The application of the CRISPR/Cas toolkits has rapidly advanced breeding and crop improvement of economically important species. CRISPR/Cas toolkits have also been applied to a wide variety of tree species, including apple, bamboo, Cannabaceae, cassava, citrus, cacao tree, coffee tree, grapevine, kiwifruit, pear, pomegranate, poplar, ratanjoyt, and rubber tree. The application of editing to these species has resulted in significant discoveries related to critical genes associated with growth, secondary metabolism, and stress and disease resistance. However, most studies on tree species have involved only preliminary optimization of editing techniques, and a more in-depth study of editing techniques for CRISPR/Cas-based editing of tree species has the potential to rapidly accelerate tree breeding and trait improvements. Moreover, tree genome editing still relies mostly on Cas9-based indel mutation and Agrobacterium-mediated stable transformation. Transient transformation for transgene-free genome editing is preferred, but it typically has very low efficiency in tree species, substantially limiting its potential utility. In this work, we summarize the current status of tree genome editing practices using the CRISPR/Cas system and discuss limitations that impede the efficient application of CRISPR/Cas toolkits for tree genome editing, as well as future prospects.

An increase in the frequency and magnitude of drought events threatens the health of forests and the economic, ecological, and societal services they provide. It has been widely demonstrated that trees undergoing a succession of stresses may accumulate lesions that in turn lead to a decrease in their vigor and eventually to death. However, recent studies have shown that a nonlethal stress should also initiate a stress memory, which triggers a faster and stronger plant defensive response when a new stress occurs. Although this mechanism is well understood in many herbaceous plants, a better understanding in trees is needed. The aim of our study was to explore the capacity of two forest tree species to develop a stress memory. A greenhouse experiment was conducted to evaluate the tree seedlings' vigor after one or two consecutive droughts separate from a rehydration period during the same growing season. No stress memory pattern was observed for the two tree species as, on the contrary, we even observed a stress accumulation pattern in sugar maple. It remains possible that some individuals in our study developed stress memory, but that we were not able to detect it. The fine‐tuning of experimental parameters and the conducting of longitudinal studies would be helpful to detect individual capacity in stress memory activation. [ABSTRACT FROM AUTHOR]

The present study provides comprehensive detail about forest species composition and structural diversity of Shahoor Sheringal and Kandao valley at Sheringal forest subdivision Dir upper, Khyber Pakhtunkhwa, Pakistan. The whole area was divided into four sites, Shahoor Bala, Shahoor Payen, Kandao, and Janas. Sampling was started from the bed of the stream and continues up to the top of the mountain. Different stations were established. Quadrat size of 30m ×30 m was taken for studying and measuring trees. A total of 15 tree species belonging to nine families were identified in the study area. Different sampling sites were marked at different elevations. The different quantitative parameters i.e. density, relative frequency, cover, relative density, relative cover, and frequency were calculated for each tree in each study site; and importance value indexes were recorded from different blocks. SDR values were then used for identifying the dominant community in each study site. Cedrus deodara was observed as the highest average SDR value of 28.9. It is dominant species and found in all sites; however, it was more dominant in Janas site where its SDR value is noted as 40.18. The second highest dominant species is Quercus baloth having a 19.9 SDR value. Tree species diversity was optimum at the middle of Janas site as compared to the Shahoor Payen where direct anthropogenic activities are continuous. The minimum diversity was observed at the top of Janas and Shahoor Bala due to high altitudes. It is observed that huge volumes of fuelwood and timber consumption were recorded from the area. This work will also be useful in future for assessment of climate change on vegetation along elevation. [ABSTRACT FROM AUTHOR]

Abstract An increase in the frequency and magnitude of drought events threatens the health of forests and the economic, ecological, and societal services they provide. It has been widely demonstrated that trees undergoing a succession of stresses may accumulate lesions that in turn lead to a decrease in their vigor and eventually to death. However, recent studies have shown that a nonlethal stress should also initiate a stress memory, which triggers a faster and stronger plant defensive response when a new stress occurs. Although this mechanism is well understood in many herbaceous plants, a better understanding in trees is needed. The aim of our study was to explore the capacity of two forest tree species to develop a stress memory. A greenhouse experiment was conducted to evaluate the tree seedlings' vigor after one or two consecutive droughts separate from a rehydration period during the same growing season. No stress memory pattern was observed for the two tree species as, on the contrary, we even observed a stress accumulation pattern in sugar maple. It remains possible that some individuals in our study developed stress memory, but that we were not able to detect it. The fine‐tuning of experimental parameters and the conducting of longitudinal studies would be helpful to detect individual capacity in stress memory activation.

Abstract Background Diversity among phenology-related genes is predicted to be a contributing factor in local adaptations seen in widely distributed plant species that grow in climatically variable geographic areas, such as forest trees. European beech (Fagus sylvatica L.) is widespread, and is one of the most important broadleaved tree species in Europe; however, its potential for adaptation to climate change is a matter of uncertainty, and little is known about the molecular basis of climate change-relevant traits like bud burst. Results We explored single nucleotide polymorphisms (SNP) at candidate genes related to bud burst in beech individuals sampled across 47 populations from Europe. SNP diversity was monitored for 380 candidate genes using a sequence capture approach, providing 2909 unlinked SNP loci. We used two complementary analytical methods to find loci significantly associated with geographic variables, climatic variables (expressed as principal components), or phenotypic variables (spring and autumn phenology, height, survival). Redundancy analysis (RDA) was used to detect candidate markers across two spatial scales (entire study area and within subregions). We revealed 201 candidate SNPs at the broadest scale, 53.2% of which were associated with phenotypic variables. Additive polygenic scores, which provide a measure of the cumulative signal across significant candidate SNPs, were correlated with a climate variable (first principal component, PC1) related to temperature and precipitation availability, and spring phenology. However, different genotype-environment associations were identified within Southeastern Europe as compared to the entire geographic range of European beech. Conclusions Environmental conditions play important roles as drivers of genetic diversity of phenology-related genes that could influence local adaptation in European beech. Selection in beech favors genotypes with earlier bud burst under warmer and wetter habitats within its range; however, selection pressures may differ across spatial scales.

Introduction : Since the population increases and the industry develops, the demand for fossil fuels continues to increase, creating problems of energy resource depletions and accelerating global warming. Thus, many countries are making active efforts to replace fossil fuels with bioenergy as a renewable energy. In particular, trees managed and produced by forest industry have a high potential as energy sources for biofuel industry, because they have a conceptual characteristic of carbon neutrality. Recently, energy plan and policy are being developed to cultivate trees on fallow lands, environmentally restored sites, and ground-level work places of abandoned mines; however, economic feasibility for such plans and policies cannot be readily evaluated due to insufficient information on the amount of the energy to be produced from tree cultivation. Thus, the objective of this study is to develop a methodology which can be used to estimate the potential energy amount of the bioenergy from tree cultivation based on tree species, cultivation time, and cultivation area conditions. Methodology : The methodology consists of three stages. In the first stage, the total volume of the trees per area is estimated by using the number of trees per unit area and the average stem volume of the tree, which are affected by the site index representing the environmental conditions of cultivation area. In the second stage, the total mass of biomass is calculated by using the density of wood, the biomass expansion factors for the above-ground biomass, and root-shoot ratio. In the last stage, the amount of the energy produced from the tree cultivation is estimated by taking into account the caloric value evaluated based on the carbon, hydrogen, and oxygen compositions of the tree. Case Study : A case study for conifers and broad-leaved trees is performed to demonstrate the methodology. The conifers are Jungbu local pine, Korean white pine, and Japanese larch, and the broad-leaved trees are oak, red oak, and birch. The results of the case study validate the developed methodology and clearly showed the procedure and necessity for the methodology by estimating the bioenergy productions from the trees. Conclusions : The developed methodology can be used to provide practical information needed to determine the economic feasibility of the plan, policy, and project for tree cultivations.

Background: Needle rust caused by the fungus Chrysomyxa rhododendri causes significant growth decline and increased mortality of young Norway spruce trees in subalpine forests. Extremely rare trees with enhanced resistance represent promising candidates for practice-oriented reproduction approaches. They also enable the investigation of tree molecular defence and resistance mechanisms against this fungal disease. Here, we combined RNA-Seq, RT-qPCR and secondary metabolite analyses during a period of 38 days following natural infection to investigate differences in constitutive and infection-induced defence between the resistant genotype PRA-R and three susceptible genotypes. Results: Gene expression and secondary metabolites significantly differed among genotypes from day 7 on and revealed already known, but also novel candidate genes involved in spruce molecular defence against this pathogen. Several key genes related to (here and previously identified) spruce defence pathways to needle rust were differentially expressed in PRA-R compared to susceptible genotypes, both constitutively (in non-symptomatic needles) and infection-induced (in symptomatic needles). These genes encoded both new and well-known antifungal proteins such as endochitinases and chitinases. Specific genetic characteristics concurred with varying phenolic, terpene, and hormone needle contents in the resistant genotype, among them higher accumulation of several flavonoids (mainly kaempferol and taxifolin), stilbenes, geranyl acetone, α-ionone, abscisic acid and salicylic acid. Conclusions: Combined transcriptional and metabolic profiling of the Norway spruce defence response to infection by C. rhododendri in adult trees under subalpine conditions confirmed the results previously gained on artificially infected young clones in the greenhouse, both regarding timing and development of infection, and providing new insights into genes and metabolic pathways involved. The comparison of genotypes with different degrees of susceptibility proved that several of the identified key genes are differently regulated in PRA-R, and that the resistant genotype combines a strong constitutive defence with an induced response in infected symptomatic needles following fungal invasion. Genetic and metabolic differences between the resistant and susceptible genotypes indicated a more effective hypersensitive response (HR) in needles of PRA-R that prevents penetration and spread of the rust fungus and leads to a lower proportion of symptomatic needles as well as reduced symptom development on the few affected needles. [ABSTRACT FROM AUTHOR]

Key message: The lack of efficient phenotyping capacities has been recognized as a bottleneck in forestry phenotyping and breeding. Modern phenotyping technologies use systems equipped with various imaging sensors to automatically collect high volume phenotypic data that can be used to assess trees' various attributes. Context: Efficient phenotyping has the potential to spark a new Green Revolution, and it would provide an opportunity to acquire growth parameters and dissect the genetic bases of quantitative traits. Phenotyping platforms aim to link information from several sources to derive knowledge about trees' attributes. Aims: Various tree phenotyping techniques were reviewed and analyzed along with their different applications. Methods: This article presents the definition and characteristics of forest tree phenotyping and reviews newly developed imaging-based practices in forest tree phenotyping. Results: This review addressed a wide range of forest trees phenotyping applications, including a survey of actual inter- and intra-specific variability, evaluating genotypes and species response to biotic and abiotic stresses, and phenological measurements. Conclusion: With the support of advanced phenotyping platforms, the efficiency of traits phenotyping in forest tree breeding programs is accelerated. [ABSTRACT FROM AUTHOR]

Growth is the developmental process involving important genetic components. Functional mapping (FunMap) has been used as an approach to map quantitative trait loci (QTLs) governing growth trajectories by incorporating growth equations. FunMap is based on reductionism thinking, with a power to identify a small set of significant QTLs from the whole pool of genome-wide markers. Yet, increasing evidence shows that a complex trait is controlled by all genes the organism may possibly carry. Here, we describe and demonstrate a different mapping approach that encapsulates all markers into genetic interaction networks. This approach, symbolized as FunGraph, combines functional mapping, evolutionary game theory, and prey-predator theory into mathematical graphs, allowing the observed genetic effect of a locus to be decomposed into its independent component (resulting from this locus’ intrinsic capacity) and dependent component (due to extrinsic regulation by other loci). Using FunGraph, we can visualize and trace the roadmap of how each locus interact with every other locus to impact growth. In a population-based association study of Euphrates poplar, we use FunGraph to identify the previously neglected genetic interaction effects that contribute to the genetic architecture of juvenile stem growth. FunGraph could open up a novel gateway to comprehend the global genetic control mechanisms of complex traits.

An understanding of how variation is shared within and among closely related species is important for understanding evolutionary processes and managing biological diversity. We studied genetic structure in the three species occurring in south-western Australia that form the small and distinct monophyletic section Calophyllae of the genus Corymbia. We compared diversity in nuclear microsatellites and chloroplast DNA sequences in two species with patchy distributions, namely, Corymbia haematoxylon (Maiden) K.D. Hill & L.A.S. Johnson and Corymbia ficifolia (F. Muell.) K.D. Hill & L.A.S. Johnson, with that in the widespread congener, C. calophylla (Lindl.) K.D. Hill & L.A.S. Johnson. Consistent with predictions for the influence of range and abundance on genetic structure in the Australian flora, population differentiation was higher in the two restricted patchy species than in the widespread, semicontinuous C. calophylla. Genetic diversity in C. haematoxylon was similar to that in C. calophylla , but diversity was lower in the highly localised C. ficifolia , likely owing to genetic bottlenecks. All three species were distinguished by nuclear SSR variation, but C. haematoxylon and C. ficifolia each shared chloroplast haplotypes with C. calophylla from incomplete lineage sorting of ancestral variation and introgression. Limited evidence of recent hybridisation in two populations of C. haematoxylon was also present. Understanding how genetic variation is shared between species is important for managing biological diversity. There are only three bloodwood tree species in south-western Australia and the species are closely related through shared ancestry. Genetic differentiation was higher among species with patchy distributions, whereas diversity was lower only in the species with a highly localised range, and probably indicates the impact of severe reductions in population size in species with very restricted distributions. [ABSTRACT FROM AUTHOR]

Abstract Background Norway spruce trees in subalpine forests frequently face infections by the needle rust fungus Chrysomyxa rhododendri, which causes significant growth decline and increased mortality of young trees. Yet, it is unknown whether trees actively respond to fungal attack by activating molecular defence responses and/or respective gene expression. Results Here, we report results from an infection experiment, in which the transcriptomes (via RNA-Seq analysis) and phenolic profiles (via UHPLC-MS) of control and infected trees were compared over a period of 39 days. Gene expression between infected and uninfected ramets significantly differed after 21 days of infection and revealed already known, but also novel candidate genes involved in spruce molecular defence against pathogens. Conclusions Combined RNA-Seq and biochemical data suggest that Norway spruce response to infection by C. rhododendri is restricted locally and primarily activated between 9 and 21 days after infestation, involving a potential isolation of the fungus by a hypersensitive response (HR) associated with an activation of phenolic pathways. Identified key regulatory genes represent a solid basis for further specific analyses in spruce varieties with varying susceptibility, to better characterise resistant clones and to elucidate the resistance mechanism.

Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations' resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine‐scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies alba Mill.) population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1,368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east‐west isolation‐by‐distance pattern consistent with the post‐glacial colonization history of the species. Genetic differentiation among sites (FCT = 0.148) was an order of magnitude greater than between elevations within sites (FSC = 0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modelling revealed that elevation and, to a lesser extent, post‐glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non‐spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees. [ABSTRACT FROM AUTHOR]

High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range‐wide patterns of potentially adaptive genetic variation in 64 populations of European beech (Fagus sylvatica L.) using 270 SNPs from 139 candidate genes involved either in phenology or in stress responses. We inferred neutral genetic structure and processes (drift and gene flow) and performed differentiation outlier analyses and gene‐environment association (GEA) analyses to detect signatures of divergent selection. Beech range‐wide genetic structure was consistent with the species' previously identified postglacial expansion scenario and recolonization routes. Populations showed high diversity and low differentiation along the major expansion routes. A total of 52 loci were found to be putatively under selection and 15 of them turned up in multiple GEA analyses. Temperature and precipitation related variables were equally represented in significant genotype‐climate associations. Signatures of divergent selection were detected in the same proportion for stress response and phenology‐related genes. The range‐wide adaptive genetic structure of beech appears highly integrated, suggesting a balanced contribution of phenology and stress‐related genes to local adaptation, and of temperature and precipitation regimes to genetic clines. Our results imply a best‐case scenario for the maintenance of high genetic diversity during range shifts in beech (and putatively other forest trees) with a combination of gene flow maintaining within‐population neutral diversity and selection maintaining between‐population adaptive differentiation. [ABSTRACT FROM AUTHOR]

During secondary growth, forest trees can modify the anatomy of the wood produced by the vascular cambium in response to environmental conditions. Notably, the trees of the model angiosperm genus, Populus, reduce the risk of cavitation and hydraulic failure under water stress by producing water-conducting vessel elements with narrow lumens, which are more numerous and more interconnected with each other. Here, we determined the genetic architecture of vessel traits affecting hydraulic physiology and resilience to water stress. Vessel traits were measured for clonally replicated genotypes of a unique Populus deltoides x nigra population carrying genomically defined insertions and deletions that create gene dosage variation. We found significant phenotypic variation for all traits measured (mean vessel diameter, height-corrected mean vessel diameter, vessel frequency, height-corrected vessel frequency, vessel grouping index, and mean vessel circularity), and that all traits were under genetic control and showed moderate heritability values, ranging from 0.32 to 0.53. Whole-genome scans of correlations between gene dosage and phenotypic traits identified quantitative trait loci for tree height, mean vessel diameter, height-corrected mean vessel diameter, height-corrected vessel frequency, and vessel grouping index. Our results demonstrate that vessel traits affecting hydraulic physiology are under genetic control, and both pleiotropic and trait-specific quantitative trait loci are found for these traits.

During secondary growth, forest trees can modify the anatomy of the wood produced by the vascular cambium in response to environmental conditions. Notably, the trees of the model angiosperm genus, Populus , reduce the risk of cavitation and hydraulic failure under water stress by producing water-conducting vessel elements with narrow lumens, which are more numerous and more interconnected with each other. Here, we determined the genetic architecture of vessel traits affecting hydraulic physiology and resilience to water stress. Vessel traits were measured for clonally replicated genotypes of a unique Populus deltoides x nigra population carrying genomically defined insertions and deletions that create gene dosage variation. We found significant phenotypic variation for all traits measured (mean vessel diameter, height-corrected mean vessel diameter, vessel frequency, height-corrected vessel frequency, vessel grouping index, and mean vessel circularity), and that all traits were under genetic control and showed moderate heritability values, ranging from 0.32 to 0.53. Whole-genome scans of correlations between gene dosage and phenotypic traits identified quantitative trait loci for tree height, mean vessel diameter, height-corrected mean vessel diameter, height-corrected vessel frequency, and vessel grouping index. Our results demonstrate that vessel traits affecting hydraulic physiology are under genetic control, and both pleiotropic and trait-specific quantitative trait loci are found for these traits. [ABSTRACT FROM AUTHOR]

Background: Diversity among phenology-related genes is predicted to be a contributing factor in local adaptations seen in widely distributed plant species that grow in climatically variable geographic areas, such as forest trees. European beech (Fagus sylvatica L.) is widespread, and is one of the most important broadleaved tree species in Europe; however, its potential for adaptation to climate change is a matter of uncertainty, and little is known about the molecular basis of climate change-relevant traits like bud burst. Results: We explored single nucleotide polymorphisms (SNP) at candidate genes related to bud burst in beech individuals sampled across 47 populations from Europe. SNP diversity was monitored for 380 candidate genes using a sequence capture approach, providing 2909 unlinked SNP loci. We used two complementary analytical methods to find loci significantly associated with geographic variables, climatic variables (expressed as principal components), or phenotypic variables (spring and autumn phenology, height, survival). Redundancy analysis (RDA) was used to detect candidate markers across two spatial scales (entire study area and within subregions). We revealed 201 candidate SNPs at the broadest scale, 53.2% of which were associated with phenotypic variables. Additive polygenic scores, which provide a measure of the cumulative signal across significant candidate SNPs, were correlated with a climate variable (first principal component, PC1) related to temperature and precipitation availability, and spring phenology. However, different genotype-environment associations were identified within Southeastern Europe as compared to the entire geographic range of European beech. Conclusions: Environmental conditions play important roles as drivers of genetic diversity of phenology-related genes that could influence local adaptation in European beech. Selection in beech favors genotypes with earlier bud burst under warmer and wetter habitats within its range; however, selection pressures may differ across spatial scales. [ABSTRACT FROM AUTHOR]

In the course of global climate change, Central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) differently: even in the same stand, drought-damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance with Pool-GWAS. Contrasting the extreme phenotypes identified 106 significantly associated single-nucleotide polymorphisms (SNPs) throughout the genome. Most annotated genes with associated SNPs (>70%) were previously implicated in the drought reaction of plants. Non-synonymous substitutions led either to a functional amino acid exchange or premature termination. A non-parametric machine learning approach on 98 validation samples yielded 20 informative loci which allowed an 88% prediction probability of the drought phenotype. Drought resistance in European beech is a moderately polygenic trait that should respond well to natural selection, selective management, and breeding.

Understanding local adaptation is critical for conservation management under rapidly changing environmental conditions. Local adaptation inferred from genotype‐environment associations may show different genomic patterns depending on the spatial scale of sampling, due to differences in the slope of environmental gradients and the level of gene flow. We compared signatures of local adaptation across the genome of mountain ash (Eucalyptusregnans) at two spatial scales: A species‐wide data set and a topographically‐complex subregional data set. We genotyped 367 individual trees at over 3700 single‐nucleotide polymorphisms (SNPs), quantified patterns of spatial genetic structure among populations, and used two analytical methods to identify loci associated with at least one of three environmental variables at each spatial scale. Together, the analyses identified 549 potentially adaptive SNPs at the subregion scale, and 435 SNPs at the range‐wide scale. A total of 39 genic or near‐genic SNPs, associated with 28 genes, were identified at both spatial scales, although no SNP was identified by both methods at both scales. We observed that nongenic regions had significantly higher homozygote excess than genic regions, possibly due to selective elimination of inbred genotypes during stand development. Our results suggest that strong environmental selection occurs in mountain ash, and that the identification of putatively adaptive loci can differ substantially depending on the spatial scale of analyses. We also highlight the importance of multiple adaptive genetic architectures for understanding patterns of local adaptation across large heterogenous landscapes, with comparison of putatively adaptive loci among spatial scales providing crucial insights into the process of adaptation. [ABSTRACT FROM AUTHOR]

Trees are generally propagated from seeds and the suitability and quality of the seeds have a big effect on the success of the plantations, afforestation and reforestation programmes established from their seedlings. In view of the fact that good forestry projects start with good seeds, the quality as well as quantity of tree seeds is very important. Processing of seeds is one of the main factors that determined the quality and quantity of seeds. However, processing of forest tree seeds in Nigeria and other developing countries has mostly been carried out using traditional methods which affects the quality of the seeds especially for large quantity of seeds. This work attempts to raise awareness on the need to mechanize processing of forest tree seeds so as to increase the quantity and quality of the seeds and to reduce the drudgery, time and health hazards involved in the common traditional methods of processing the seeds. Tree seeds are often regarded as inferior to crop seeds, a misnomer (mistaken belief) that needs to be rectified to promote tree planting. [ABSTRACT FROM AUTHOR]

Tree architecture and functioning facing multispecies environments: We have gone only halfway in fruit-trees Keywords: agroecology; agroecosystem; agroforestry; biodiversity; biotic and abiotic environment; forest; forest tree; orchard EN agroecology agroecosystem agroforestry biodiversity biotic and abiotic environment forest forest tree orchard 3 7 5 02/04/21 20210101 NES 210101 Plant architecture analysis aims at deciphering the relative roles of endogenous processes and exogenous above- and belowground factors in the morphological development and functioning of a plant. GLO:ABO/01jan21:ajb21598-fig-0001.jpg PHOTO (COLOR): 1 Traditional multilayered cocoa-agroforestry system in Cameroon including from top to bottom, trees grown as shade trees for wood and medicinal products (top layer with large reiterative branches), for fruit (avocado or cola nuts; top-medium layer) that are overtopping oil palm trees, and citrus and cocoa trees (medium layer). At the system scale, the conventional way to design an orchard is to fit various pieces together considering the fruit tree itself (cultivar and rootstock if any), planting density, tree arrangement, support system, and tree and branch management over consecutive years. [Extracted from the article]

Proteome analysis of embryo and endosperm of Givotia moluccana, a promising angiosperm tree species was carried out using two-dimensional electrophoresis combined with matrix-assisted laser desorption/ionization time of flight to identify differentially abundant proteins and their possible functions. The study revealed the presence of 492 protein spots in the embryo and 432 in the endosperm, and the relative abundance of 44 spots varied significantly between the two. Of the 21 functionally characterized protein spots, 14.3% were involved in metabolism and energy, 28.6% in protein destination and storage, 14.3% in defense and stress and 19% in cell growth and division. The embryo-specific protein ATP-dependent zinc metalloprotease FtsH is predicted to be involved in chloroplast biogenesis and the endosperm-specific protein hydroxyacyl-ACP dehydratase in fatty acid synthesis. These results suggested that the seeds have proteins required for germination and for stress responses. [ABSTRACT FROM AUTHOR]

Background: Norway spruce trees in subalpine forests frequently face infections by the needle rust fungus Chrysomyxa rhododendri, which causes significant growth decline and increased mortality of young trees. Yet, it is unknown whether trees actively respond to fungal attack by activating molecular defence responses and/or respective gene expression. Results: Here, we report results from an infection experiment, in which the transcriptomes (via RNA-Seq analysis) and phenolic profiles (via UHPLC-MS) of control and infected trees were compared over a period of 39 days. Gene expression between infected and uninfected ramets significantly differed after 21 days of infection and revealed already known, but also novel candidate genes involved in spruce molecular defence against pathogens. Conclusions: Combined RNA-Seq and biochemical data suggest that Norway spruce response to infection by C. rhododendri is restricted locally and primarily activated between 9 and 21 days after infestation, involving a potential isolation of the fungus by a hypersensitive response (HR) associated with an activation of phenolic pathways. Identified key regulatory genes represent a solid basis for further specific analyses in spruce varieties with varying susceptibility, to better characterise resistant clones and to elucidate the resistance mechanism. [ABSTRACT FROM AUTHOR]

Summary: Brassinosteroids have been implicated in the differentiation of vascular cell types in herbaceous plants, but their roles during secondary growth and wood formation are not well defined.Here we pharmacologically and genetically manipulated brassinosteroid levels in poplar trees and assayed the effects on secondary growth and wood formation, and on gene expression within stems.Elevated brassinosteroid levels resulted in increases in secondary growth and tension wood formation, while inhibition of brassinosteroid synthesis resulted in decreased growth and secondary vascular differentiation. Analysis of gene expression showed that brassinosteroid action is positively associated with genes involved in cell differentiation and cell‐wall biosynthesis.The results presented here show that brassinosteroids play a foundational role in the regulation of secondary growth and wood formation, in part through the regulation of cell differentiation and secondary cell wall biosynthesis. [ABSTRACT FROM AUTHOR]

Drought is a major stress impacting forest ecosystems worldwide. We utilized quantitative trait loci (QTL) analysis to study the genetic basis of variation in (a) drought resistance and recovery and (b) candidate traits that may be associated with this variation in the forest tree Eucalyptus globulus. QTL analysis was performed using a large outcrossed F2 mapping population from which 300 trees were phenotyped based on the mean performance of their open‐pollinated F3 progeny. Progenies were grown in a glasshouse in a randomized complete block design. A subset of seedlings was subjected to a drought treatment after which they were rewatered and scored for damage and growth postdrought. Nondroughted seedlings were assessed for growth traits as well as lignotuber size and resprouting following severe damage to the main stem. QTL were detected for most traits. Importantly, independent QTL were detected for (a) drought damage and plant size, (b) drought damage and growth recovery, and (c) lignotuber size and resprouting capacity. Such independence argues that trade‐offs are unlikely to be a major limitation to the response to selection and at the early life history stage studied; there are opportunities to improve resilience to drought without adverse effects on productivity. We show that the genomic regions underlying variation in plant size, drought resistance and recovery are largely independent in Eucalyptus globulus seedlings. This suggests that trade‐offs are unlikely and drought resilience may be genetically improved without negatively impacting productivity. [ABSTRACT FROM AUTHOR]

Despite tremendous advancements in high throughput sequencing, the vast majority of tree genomes, and in particular, forest trees, remain elusive. Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing pipelines. The tree databases reviewed here serve as secondary repositories for community data. They vary in their focal species, the data they curate, and the analytics provided, but they are united in moving toward a goal of centralizing both data access and analysis. They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype and phenotype data. The organism databases of today are no longer simply catalogs or containers of genetic information. These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments. These resources are striving to integrate across diverse experimental designs, sequence types, and related measures through ontologies, community standards, and web services. Efficient, simple, and robust platforms that enhance the data generated by the research community, contribute to improving forest health and productivity.

Despite tremendous advancements in high throughput sequencing, the vast majority of tree genomes, and in particular, forest trees, remain elusive. Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing pipelines. The tree databases reviewed here serve as secondary repositories for community data. They vary in their focal species, the data they curate, and the analytics provided, but they are united in moving toward a goal of centralizing both data access and analysis. They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype and phenotype data. The organism databases of today are no longer simply catalogs or containers of genetic information. These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments. These resources are striving to integrate across diverse experimental designs, sequence types, and related measures through ontologies, community standards, and web services. Efficient, simple, and robust platforms that enhance the data generated by the research community, contribute to improving forest health and productivity. [ABSTRACT FROM AUTHOR]

Summary: The extent to which spatial structuring of host resistance in wild plant populations reflects direct pathogen‐imposed selection is a subject of debate. To examine this issue, genetic susceptibilities to an exotic and a coevolved native fungal pathogen were compared using two Australian host tree species.Damage to common host germplasm of Corymbia citriodora ssp. variegata (CCV) and Eucalyptus globulus, caused by recently introduced (Austropuccinia psidii) and native (Quambalaria pitereka and Teratosphaeria sp.) pathogens was evaluated in common‐garden experiments.There was significant additive genetic variation within host species for susceptibility to both the exotic and native pathogens. However, susceptibility to A. psidii was not genetically correlated with susceptibility to either native pathogen, providing support for pathogen‐specific rather than general mechanisms of resistance.Population differentiation (QST) for susceptibility to the native pathogens was greater than neutral expectations (molecular FST), arguing for divergent selection. Coupled with lower native, but not exotic, pathogen susceptibility in host populations from areas climatically more prone to fungal proliferation, these findings suggest that pathogen‐imposed selection has contributed directly to a geographic mosaic of host resistance to native pathogens. [ABSTRACT FROM AUTHOR]