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This document summarizes a study that used ensemble modeling to predict the suitable habitat for Quercus oblongata, a species of oak tree found in the western Himalayan region. The study used environmental variables and occurrence records to build the model, which included four algorithms. The study identified the most important environmental variables and determined the suitable habitat areas for Q. oblongata. The findings have implications for future exploration and conservation efforts. The document also provides additional resources for further reading on related topics. [Extracted from the article]

Sequoiadendron giganteum (giant sequoia) has a fragmented distribution of 75 groves found along the western slope of the Sierra Nevada Mountains, California, USA. Outplanting and range expansion or assisted migration of this iconic species for the objectives of genetic conservation and timber production would be supported by information on growth and morphology to guide seed-collection decisions. We measured and assessed giant sequoia planted as seedlings and clonal stock originating from 22 groves in two common-garden experiments at Foresthill, California, north of the current species range, after 29 growing seasons. Traits examined were tree-size parameters, fluting and asymmetry of the lower stem, basal swelling, fullness of the live crown, epicormic sprouting, and heartwood decay resistance in cut stumps. Performance in terms of tree size after 29 years varied widely among genotypes with different grove origins. Morphology and decay resistance also exhibited some variation according to grove origins. The seedling stock outperformed the clonal stock of the same grove origins in terms of size and is therefore recommended when faster early growth is desired to outcompete other trees or for other management objectives. However, more fluting was exhibited by the larger fast-growing giant sequoia, while fewer seedlings had epicormic sprouts than the clonal stock of the same grove origins. At our warm low-elevation study site, giant sequoia from Mountain Home, Giant Forest, and Converse Basin consistently exhibited above-average growth among other giant sequoia in a pure planting and in an intimate mixture with five common conifer associates. Therefore, seed collected from these three groves should perform relatively well at other locations with a similar climate. When conservation of the species and its genetic diversity is the primary objective, we recommend collecting from a wide range of groves and undertaking assisted migration by planting at multiple locations inside and outside giant sequoia’s range as a hedge against the loss of native groves.

Sweet osmanthus (Osmanthus fragrans) is a having general approval aromatic tree in China that is widely applied to landscaping and gardening. However, the evergreen tree adaptability is limited by many environmental stresses. Currently, limited information is available regarding the genetic analysis and functional identification of expansin genes in response to abiotic stress in sweet osmanthus. In this study, a total of 29 expansin genes were identified and divided into four groups by genome-wide analysis from the sweet osmanthus genome. Transcriptome and quantitative Real-time PCR analysis showed that the cell wall-localized protein expansin-like A (OfEXLA1) gene was significantly induced by salt and drought treatment. Histochemical GUS staining of transgenic Arabidopsis lines in which GUS activity was driven with the OfEXLA1 promoter, GUS activity was significantly induced by salt, drought, and exogenous abscisic acid (ABA). In yeast, we found OfEXLA1 overexpression significantly improved the population of cells compared with wild-type strains after NaCl and polyethylene glycol (PEG) treatment. Additionally, OfEXLA1 overexpression not only promoted plant growth, but also improved the salt and drought tolerance in Arabidopsis. To gain insight into the role of ABA signaling in the regulation of OfEXLA1 improving abiotic tolerance in sweet osmanthus, four differentially expressed ABA Insensitive 5 (ABI5)-like genes (OfABL4, OfABL5, OfABL7, and OfABL8) were identified from transcriptome, and dualluciferase (dual-LUC) and yeast one hybrid (Y1H) assay showed that OfABL4 and OfABL5 might bind to OfEXLA1 promoter to accumulate the OfEXLA1 expression by responding to ABA signaling to improve abiotic tolerance in sweet osmanthus. These results provide the information for understanding the molecular functions of expansin-like A gene and molecular breeding of sweet osmanthus in future. [ABSTRACT FROM AUTHOR]

The Amazonian native tree species Parkia multijuga has potential silvicultural characteristics that can be utilized to productive plantations. Understanding its mating system is necessary to delineate the methods for the breeding of the species, the collection of seeds for conservation, and the use of seedlings for production plantations. The aim of this study is to evaluate the mating system and population genetic diversity of P. multijuga, using molecular markers. The DNA of 221 plants was extracted and genotyped with nine microsatellite loci using capillary electrophoresis in an automated DNA sequencer. The estimates for single and multilocus crossing rates were 0.998 and 1.0, respectively. The paternity correlation was low ( r ^ p (m) = 0.307). The fixation index (f) showed values below zero, indicating an excess of heterozygotes. The cluster number K = 2 shows a better grouping among families for genetic structure. P. multijuga families consist mainly of half-sibs, and the reproductive strategy of the species is allogamy. [ABSTRACT FROM AUTHOR]

Sequoiadendron giganteum (giant sequoia) has a fragmented distribution of 75 groves found along the western slope of the Sierra Nevada Mountains, California, USA. Outplanting and range expansion or assisted migration of this iconic species for the objectives of genetic conservation and timber production would be supported by information on growth and morphology to guide seed-collection decisions. We measured and assessed giant sequoia planted as seedlings and clonal stock originating from 22 groves in two common-garden experiments at Foresthill, California, north of the current species range, after 29 growing seasons. Traits examined were tree-size parameters, fluting and asymmetry of the lower stem, basal swelling, fullness of the live crown, epicormic sprouting, and heartwood decay resistance in cut stumps. Performance in terms of tree size after 29 years varied widely among genotypes with different grove origins. Morphology and decay resistance also exhibited some variation according to grove origins. The seedling stock outperformed the clonal stock of the same grove origins in terms of size and is therefore recommended when faster early growth is desired to outcompete other trees or for other management objectives. However, more fluting was exhibited by the larger fast-growing giant sequoia, while fewer seedlings had epicormic sprouts than the clonal stock of the same grove origins. At our warm low-elevation study site, giant sequoia from Mountain Home, Giant Forest, and Converse Basin consistently exhibited above-average growth among other giant sequoia in a pure planting and in an intimate mixture with five common conifer associates. Therefore, seed collected from these three groves should perform relatively well at other locations with a similar climate. When conservation of the species and its genetic diversity is the primary objective, we recommend collecting from a wide range of groves and undertaking assisted migration by planting at multiple locations inside and outside giant sequoia's range as a hedge against the loss of native groves. [ABSTRACT FROM AUTHOR]

This study reviews the impacts of climate change on Greek forests, analysing factors such as climate trends, forest management, biodiversity, genetics, insects, and wildfires, using data from the Scopus and Mendeley databases and official reports. By utilising our current understanding and allocating necessary efforts and resources, we actively address climate change consequences on forests. This study focuses on climate change and extreme weather outcomes on forests. Greek mountain forests at 520–1310 m experience decreasing annual mean and minimum temperatures (−0.015 and −0.027 °C yr–1) but increasing maximum temperatures (+0.014 °C yr–1), especially in Southern Greece (+0.047 °C yr–1). Recent findings reveal forests migrating to higher altitudes with favourable conditions, correlating with water availability, temperature, and tree growth, necessitating further research on forest productivity. A decline in fir tree-ring growth (Average Tree Ring Width Index < 0.6) is observed in mainland Greece, indicating temperature's effect on growth. Effective forest tree conservation requires prioritising biodiversity monitoring, considering climate change impacts on phenology and addressing the absence of strategies to protect and enhance genetic diversity. Climate change influenced 70 forestry pests' ranges, notably among Greek insect pests. Annual burned areas from forest fires data indicate a consistent long-term increasing trend, underscoring fire prevention prioritization and exploring fire risk, behaviour, and climate change. The study highlights two to four significant knowledge gaps, and one to three key challenges pertaining to the six research areas. Finally, it promotes partnerships for informed decision-making and better outcomes by integrating Indigenous knowledge, scientific understanding, and collaboration among research, policy, and local management. [ABSTRACT FROM AUTHOR]

The quantitative, accurate and efficient acquisition of tree phenotypes is the basis for forest "gene-phenotype-environment" studies. It also offers significant support for clarifying the genetic control mechanisms of tree traits. The application of unmanned aerial vehicle (UAV) remote sensing technology to the collection of phenotypic traits at an individual tree level quantitatively analyses tree phenology and directionally evaluates tree growth, as well as accelerating the process of forest genetics and breeding. In this study, with the help of high-resolution, high-overlap, multispectral images obtained by an UAV, combined with digital elevation models (DEMs) extracted from point clouds acquired by a backpack LiDAR, a high-throughput tree structure and spectral phenotypic traits extraction and a genetic selection were conducted in a trial of Eucalyptus clones in the State-owned Dongmen Forest Farm in the Guangxi Zhuang Autonomous Region. Firstly, we validated the accuracy of extracting the phenotypic parameters of individual tree growth based on aerial stereo photogrammetry point clouds. Secondly, on this basis, the repeatability of the tree growth traits and vegetation indices (VIs), the genetic correlation coefficients between the traits were calculated. Finally, the eucalypt clones were ranked by integrating a selection index of traits, and the superior genotypes were selected and their genetic gain predicted. The results showed a high accuracy of the tree height (H) extracted from the digital aerial photogrammetry (DAP) point cloud based on UAV images (R2 = 0.91, and RMSE = 0.56 m), and the accuracy of estimating the diameter at breast height (DBH) was R2 = 0.71, and RMSE = 0.75 cm. All the extracted traits were significantly different within the tree species and among the clones. Except for the crown width (CW), the clonal repeatability ( R c) of the traits were all above 0.9, and the individual repeatability values ( R i) were all above 0.5. The genetic correlation coefficient between the tree growth traits and VIs fluctuated from 0.3 to 0.5, while the best clones were EA14-15, EA14-09, EC184, and EC183 when the selection proportion was 10%. The purpose of this study was to construct a technical framework for phenotypic traits extraction and genetic analysis of trees based on unmanned aerial stereo photography point clouds and high-resolution multispectral images, while also exploring the application potential of this approach in the selective breeding of eucalypt clones. [ABSTRACT FROM AUTHOR]

He passed away twenty years ago, but the memory of Prof. Ezio Magini is alive in Italian forest scientists. He was a distinguished professor of Silviculture at the University of Florence, pionieer of quantitative Forest Genetics and Forest Tree Breeding in Italy. Of high intellectual honesty and lovable personality, always willing to teach with patience to young people, he was a great example of methodological rigor, in terms of setting up clear hypotheses, sound experimental planning and data collection, in depth statistical analysis: a great guide for all of us. Thanks once again, Prof. Magini!

He passed away twenty years ago, but the memory of Prof. Ezio Magini is alive in Italian forest scientists. He was a distinguished professor of Silviculture at the University of Florence, pionieer of quantitative Forest Genetics and Forest Tree Breeding in Italy. Of high intellectual honesty and lovable personality, always willing to teach with patience to young people, he was a great example of methodological rigor, in terms of setting up clear hypotheses, sound experimental planning and data collection, in depth statistical analysis: a great guide for all of us. Thanks once again, Prof. Magini! [ABSTRACT FROM AUTHOR]

Uncovering the genetic basis of local adaptation is a major goal of evolutionary biology and conservation science alike. In an era of climate change, an understanding of how environmental factors shape adaptive diversity is crucial to predicting species response and directing management. Here, we investigate patterns of genomic variation in giant sequoia, an iconic and ecologically important tree species, using 1,364 bi‐allelic single nucleotide polymorphisms (SNPs). We use an FST outlier test and two genotype–environment association methods, latent factor mixed models (LFMMs) and redundancy analysis (RDA), to detect complex signatures of local adaptation. Results indicate 79 genomic regions of potential adaptive importance, with limited overlap between the detection methods. Of the 58 loci detected by LFMM, 51 showed strong correlations to a precipitation‐driven composite variable and seven to a temperature‐related variable. RDA revealed 24 outlier loci with association to climate variables, all of which showed strongest relationship to summer precipitation. Nine candidate loci were indicated by two methods. After correcting for geographic distance, RDA models using climate predictors accounted for 49% of the explained variance and showed significant correlations between SNPs and climatic factors. Here, we present evidence of local adaptation in giant sequoia along gradients of precipitation and provide a first step toward identifying genomic regions of adaptive significance. The results of this study will provide information to guide management strategies that seek to maximize adaptive potential in the face of climate change. [ABSTRACT FROM AUTHOR]

Improving wood growth rate and wood quality are worthy goals in forest genetics and breeding research. The ARK1 gene is one member of the ARBORKNOX family in all plants, which play an essential role in the process of plant growth and development, but the mechanism associated with its gene network regulation is poorly investigated. In order to generate over-expression transgenic hybrid poplar, the agrobacterium-mediated transformation was used to obtain transgenic hybrid poplar '717' plants to provide insight into the function of the ARK1 gene in poplar. Moreover, the morphology of transgenic plants was observed, and transcriptome analysis was performed to explore the ARK1 gene function. The results showed that there were significant differences in pitch, stem diameter, petiole length, leaf width, leaf length and seedling height between ARK1 transgenic seedlings and non-transgenic seedlings. The transgenic seedlings usually had multiple branches and slender leaves, with some leaves not being fully developed. The results of transcriptome analysis showed that the differentially expressed genes were involved in the growth of poplars, including proteins, transcription factors and protein kinases. Genes related to the positive regulation in plant hormone signal transduction pathways were up-regulated, and the genes related to lignin synthesis were down-regulated. The RT-qPCR analysis confirmed the expression levels of the genes involved in the plant hormone signal transduction pathways and phenylpropanoid pathway. In conclusion, the ARK1 gene had a positive regulatory effect on plant growth, and the gene's coding enzymes related to lignin synthesis were down-regulated. [ABSTRACT FROM AUTHOR]

The history of the development of forest genetics in Russia has been poorly studied, although the information obtained in this field is of great importance for research, both in general genetics and in forest science. Practically the first attempt was made to present materials on this topic. The review of publications of Russian researchers in such sections of forest genetics as population genetics (isoenzyme and DNA polymorphism analysis), karyology and cytogenetics, phenetics, genetics of quantitative features, induced mutagenesis, and genomics is presented. The applied methods are analyzed, and the main results of the studies obtained in each of these directions are summarized. In most detail, with the involvement of a large number of literature sources, studies in the field of population genetics, karyology and cytogenetics have been examined. It was noted that a limited amount of publication did not allow reflection of studies in a number of other areas of forest genetics, for example, in the development of the genetic basis for the resistance of forest woody plants to pathogens and insect pests. The review focuses on the genetics of forest-forming coniferous species that grow in Russia: Scots pine, Siberian stone pine, larch and spruce species, Siberian fir, and some other species. The importance of the conducted studies not only for the genetic analysis of the species reviewed, but also for the identification of other features of their biology is shown. An outstanding role of L. F. Pravdin and Yu. P. Altukhov in the development of Russian forest geneticists was noted. The emergence of new trends in genetics, in particular, epigenetics, poses new difficult but promising tasks for forest geneticists.

We recognize in this note a mistake in the reconstruction of a tragic episode during the Second World War, reported in the article “Remembering a leading forest scientist: Ezio Magini” (https://doi.org/10.3832/efor0060-017).

Localadaptationtoclimateallowsplantstocopewithtemporallyandspatiallyheterogeneousenvironments,andparallelphenotypic clines provide a natural experiment to uncover the genomic architecture of adaptation. Though extensive effort has been made to investigate the genomic basis of local adaptation to climate across the latitudinal range of tree species, less is known for altitudinal clines. We used exome capture to genotype 451 Populus trichocarpa genotypes across altitudinal and latitudinal gradients spanning the natural species range, and phenotyped these trees for a variety of adaptive traits in two common gardens. We observed clinal variation in phenotypic traits across the two transects, which indicates climate-driven selection, and coupled gene-based genotype- phenotype and genotype-environment association scans to identify imprints of climatic adaptation on the genome. Although many ofthephenotype-andclimate-associatedgeneswereuniquetoonetransect,wefoundevidenceofparallelismbetweenlatitudeand altitude,aswellassignificantconvergencewhenwecomparedouroutliergeneswiththoseputativelyinvolvedinclimaticadaptation in two gymnosperm species. These results suggest that not only genomic constraint during adaptation to similar environmental gradients in poplar but also different environmental contexts, spatial scale, and perhaps redundant function among potentially adaptive genes and polymorphisms lead to divergent adaptive architectures. [ABSTRACT FROM AUTHOR]

Summary: Dissecting the genetic and genomic architecture of complex traits is essential to understand the forces maintaining the variation in phenotypic traits of ecological and economical importance.Whole‐genome resequencing data were used to generate high‐resolution polymorphic single nucleotide polymorphism (SNP) markers and genotype individuals from common gardens across the loblolly pine (Pinus taeda) natural range. Genome‐wide associations were tested with a large phenotypic dataset comprising 409 variables including morphological traits (height, diameter, carbon isotope discrimination, pitch canker resistance), and molecular traits such as metabolites and expression of xylem development genes.Our study identified 2335 new SNP × trait associations for the species, with many SNPs located in physical clusters in the genome of the species; and the genomic location of hotspots for metabolic × genotype associations.We found a highly polygenic basis of quantitative inheritance, with significant differences in number, effects size, genomic location and frequency of alleles contributing to variation in phenotypes in the different traits. While mutation‐selection balance might be shaping the genetic variation in metabolic traits, balancing selection is more likely to shape the variation in expression of xylem development genes. Our work contributes to the study of complex traits in nonmodel plant species by identifying associations at a whole‐genome level. See also the Commentary on this article by Casola, 221: 1669–1671. [ABSTRACT FROM AUTHOR]

Climatic stresses limit plant growth and productivity. In the past decade, tree improvement programs were mainly focused on yield but it is obvious that enhanced stress resistance is also required. In this review we highlight important drought avoidance and tolerance mechanisms in forest trees. Genomes of economically important trees species with divergent resistance mechanisms can now be exploited to uncover the mechanistic basis of long-term drought adaptation at the whole plant level. Molecular tree physiology indicates that osmotic adjustment, antioxidative defense and increased water use efficiency are important targets for enhanced drought tolerance at the cellular and tissue level. Recent biotechnological approaches focused on overexpression of genes involved in stress sensing and signaling, such as the abscisic acid core pathway, and down-stream transcription factors. By this strategy, a suite of defense systems was recruited, generally enhancing drought and salt stress tolerance under laboratory conditions. However, field studies are still scarce. Under field conditions trees are exposed to combinations of stresses that vary in duration and magnitude. Variable stresses may overrule the positive effect achieved by engineering an individual defense pathway. To assess the usability of distinct modifications, large-scale experimental field studies in different environments are necessary. To optimize the balance between growth and defense, the use of stress-inducible promoters may be useful. Future improvement programs for drought resistance will benefit from a better understanding of the intricate networks that ameliorate molecular and ecological traits of forest trees. [ABSTRACT FROM AUTHOR]

Forest tree breeding has been successful at delivering genetically improved material for multiple traits based on recurrent cycles of selection, mating, and testing. However, long breeding cycles, late flowering, variable juvenile-mature correlations, emerging pests and diseases, climate, and market changes, all pose formidable challenges. Genetic dissection approaches such as quantitative trait mapping and association genetics have been fruitless to effectively drive operational marker-assisted selection (MAS) in forest trees, largely because of the complex multifactorial inheritance of most, if not all traits of interest. The convergence of high-throughput genomics and quantitative genetics has established two new paradigms that are changing contemporary tree breeding dogmas. Genomic selection (GS) uses large number of genome-wide markers to predict complex phenotypes. It has the potential to accelerate breeding cycles, increase selection intensity and improve the accuracy of breeding values. Realized genomic relationships matrices, on the other hand, provide innovations in genetic parameters' estimation and breeding approaches by tracking the variation arising from random Mendelian segregation in pedigrees. In light of a recent flow of promising experimental results, here we briefly review the main concepts, analytical tools and remaining challenges that currently underlie the application of genomics data to tree breeding. With easy and cost-effective genotyping, we are now at the brink of extensive adoption of GS in tree breeding. Areas for future GS research include optimizing strategies for updating prediction models, adding validated functional genomics data to improve prediction accuracy, and integrating genomic and multi-environment data for forecasting the performance of genetic material in untested sites or under changing climate scenarios. The buildup of phenotypic and genome-wide data across large-scale breeding populations and advances in computational prediction of discrete genomic features should also provide opportunities to enhance the application of genomics to tree breeding. [ABSTRACT FROM AUTHOR]

The CRISPR technology continues to diversify with a broadening array of applications that touch all kingdoms of life. The simplicity, versatility and species-independent nature of the CRISPR system offers researchers a previously unattainable level of precision and control over genomic modifications. Successful applications in forest, fruit and nut trees have demonstrated the efficacy of CRISPR technology at generating null mutations in the first generation. This eliminates the lengthy process of multigenerational crosses to obtain homozygous knockouts (KO). The high degree of genome heterozygosity in outcrossing trees is both a challenge and an opportunity for genome editing: a challenge because sequence polymorphisms at the target site can render CRISPR editing ineffective; yet an opportunity because the power and specificity of CRISPR can be harnessed for allele-specific editing. Examination of CRISPR/Cas9-induced mutational profiles from published tree studies reveals the potential involvement of multiple DNA repair pathways, suggesting that the influence of sequence context at or near the target sites can define mutagenesis outcomes. For commercial production of elite trees that rely on vegetative propagation, available data suggest an excellent outlook for stable CRISPR-induced mutations and associated phenotypes over multiple clonal generations. [ABSTRACT FROM AUTHOR]

The genetic diversity and growth dynamics of fifty-three half-sib families of eleven provenance sources and one bulk seed mixed population of fast growing forest tree species i.e. Melia azedarach were studied at two stand ages viz., fourth year (mid-rotation) and eighth year (end-rotation) to determine the selection stage in northern India. Significant variations were reported between and within seed provenances in all growth characters at both rotational ages. The broad sense heritability was higher at mid-rotational age. This revealed the growth is genetically controlled but with the time environmental effects escort the growth pattern. Growth pattern was different at each stand age. Growth is diameter dependent and the pattern was crown growth type. Families maintained their superiority over the time for tree height, basal diameter and diameter at breast height, which indicated a strong potential to identify good performing families for future plantation program. This study concluded that early stage selection is appropriate that later stage selection for all parameters studied except clear bole height that is much influenced by management practice and environment factors also. Neighbor-joining clustering with similarity index revealed that it is not necessary that the families, originated in one region were distributed in one cluster, indicating that families with same geographic origin could have undergone changes for different characters under selection. [ABSTRACT FROM AUTHOR]

Abstract Growth, stability, and genotype x environment (GxE) interaction were investigated for 69 clones after five years at six sites in Minnesota. Fifty-three clones were Populus deltoides x Populus nigra (DxN) crosses, nine were P. deltoides x P. maximowiczi , ten other crosses. Most clones were previously screened for growth and disease resistance in Minnesota. Five-year diameter (DBH) and basal area (BA) at 1.38 m averaged 93.5 mm and 72.11 cm2, respectively, over the six sites. DBH site means varied from 109.0 to 79.4 mm. The fastest-growing clone BA was 64% and 49% larger than the mean of the two commercial standards and the mean of the population, respectively. Site, clone, and clone x site effects were highly significant in the ANOVA. The variance component for clone was over twice that of clone x site (GxE), indicating a relatively small reduction in genetic gain due to GxE. Clonal rank did not change between sites. GxE interaction was dominated by relative performance differences of clones on the different sites. Twenty-six percent of clones were stable (little change in growth between sites), 74% unstable. Stability coefficients of the unstable clones varied over a 99% range, indicating the population had high and variable phenotypic plasticity. Only 15% of clones were both stable and fast growing. Seven putatively superior clones, all DxN, were selected for future testing under near-commercial conditions. The results, if representative of other inter-specific Populus populations, suggest it will be difficult, and probably impractical, to reduce GxE with standard quantitative genetics methods in hybrid poplar tree improvement programs without sacrificing productivity gains. Highlights • The variance component for clone was over twice that of clone x site (GxE). • Clonal rank did not change between sites. • GxE interaction was dominated by relative performance differences of clones. • 74% of clones were unstable; large change in growth between sites. • Difficult to reduce GxE through selection without sacrificing productivity gain. [ABSTRACT FROM AUTHOR]

Aims Exploring species-genetic diversity correlation (SGDC) is essential for understanding spatial patterns of diversity and the underlying mechanisms. Until now, latitudinal patterns of species diversity (SD) and genetic diversity (GD) were rarely studied simultaneously. As the freezing-tolerance hypothesis predicts a decrease of SD from low to high latitudes and the central-marginal hypothesis predicts a unimodal pattern of GD along latitude, we hypothesized that SD and GD are uncorrelated. We also tested how climatic and edaphic factors affect the correlation between the two levels of biodiversity. Methods We measured (i) SD (species richness and Simpson's diversity index) and community dissimilarity of woody plants (63 plots), (ii) GD (allelic richness and expected heterozygosity) and genetic differentiation of a dominant tree species (Euptelea pleiospermum ; 678 individuals from 21 populations) using nuclear microsatellite data, and (iii) climatic (annual mean precipitation, annual mean temperature, minimum temperature, maximum temperature, annual relative moisture, solar radiation, photosynthetically active radiation) and edaphic (total C, total N, total P, available P, K, Ca, Mg, Al, Fe, Mn, Ni, Zn, B, Mo, Cu, pH) variables of 21 sites. We conducted both linear and quadratic regression analyses of diversity parameters against latitude. Relationships between SD and GD were tested using Pearson's correlation. Pearson's and Spearman's ρ correlation coefficients were calculated between diversity parameters and environmental variables. We used stepwise multiple regression analysis to identify the significant environmental predictors of SD and GD. Important Findings We observed no significant correlation between measures of SD and GD. SD decreases with increasing latitude, which can be partly explained by the freezing-tolerance hypothesis, whereas GD presents a unimodal pattern along the latitudinal gradient, which is consistent with the prediction of the central-marginal hypothesis. The contrasting latitudinal patterns of SD and GD indicate that the two levels of biodiversity do not co-vary in space. Based on both correlation analysis and stepwise multiple regression analysis, SD is only related to climatic variables, whereas GD is mainly related to edaphic variables. Our results show that different geographical and environmental factors affect SD and GD, driving the non-significant correlation between the two fundamental levels of biodiversity. Furthermore, a significantly positive correlation was observed between genetic distance and community dissimilarity, both of which were significantly correlated with geographical distance. [ABSTRACT FROM AUTHOR]

Poplar is an important research organism, and species in sections Tacamahaca and Aigeiros, have advantages in terms of stress resistance, ease of propagation, and fast growth. Poplar species are widely distributed and well-adapted in the world, presenting a large potential for genetic improvement. Hybridization between different species allows us to generate offspring with a unique combinations of traits. This approach has a huge potential for breeding new poplar varieties that could aid in controlling desertification in the arid and semi-arid zones of the "Three-North" in China. In this study, we carried out a cross test scheme with nine female and thirteen male poplar trees. A total of 105,401 seeds were collected from 117 crosses. Flowering phenology and seed maturation differences of the hybrid progeny were monitored in greenhouses. For male trees, Populus deltoides had the longest flowering time. For female trees, Populus pseudo-simonii showed the longest seed maturity time. The number of carpals and ovules were not the same in different females. Meanwhile, three carpals were found in P. pseudo-simonii. A highly significant positive correlation was found between the seed size and the Thousand Kernel Weight, as well as the seedling cotyledon length. During seed germination, non-radicle and non-hypocotyl seedlings were observed. We also observed a number of cotyledon variants, including single and fused cotyledons, two cotyledons with one cotyledon cracking into two parts, three cotyledons, as well as four cotyledons. These results lay a favorable foundation for combining the research between the sections Tacamahaca and Aigeiros in future work. [ABSTRACT FROM AUTHOR]

Gene flow is one of the main factors shaping genetic diversity within and among tree populations, and occurs through pollen and seed dispersal. Recent findings of pollen-release asynchronies in distant populations of Scots pine (Pinus sylvestris L.) within Scotland suggest that gene dispersal among more distant populations might be less effective than previously thought. Limited gene dispersal is one of the major factors causing genetic structure for neutral markers, and pollen-release asynchrony could have driven isolation by distance (IBD) among Scottish populations. Previous studies of neutral markers found little differentiation among Scottish populations of Scots pine, however they did not consider IBD over the full Scottish range. We analysed data from 6 nuclear simple sequence repeats (SSR) and 5 chloroplast SSR loci in a total of 540 individuals of Scots pine from 18 populations across Scotland. Our aim was to assess contemporary levels and distribution of genetic variation and to test if the distribution of genetic diversity was consistent with IBD. We also analysed patterns of gene flow that could have contributed to the observed patterns of variation. Levels of genetic diversity were high, for both nuclear and chloroplast markers within populations, and there was no significant differentiation among populations. A weak signal of IBD was present. We found an increase in nuclear diversity towards the East along with greater gene flow in a West-East direction commensurate with the prevailing winds. Our findings suggest that this wind-driven gene flow is dominant over genetic drift and prevents differentiation among the Scottish populations. It may also counteract any pollen-release asynchronies among populations. [ABSTRACT FROM AUTHOR]

Abstract: Leaf litter provides an important nutrient subsidy to headwater streams, but little is known about how tree genetics influence energy pathways from litter to higher trophic levels. Despite the charge to quantify carbon (C) and nitrogen (N) pathways from decomposing litter, the relationship between litter decomposition and aquatic consumers remains unresolved. We measured litter preference (attachments to litter), C and N assimilation rates, and growth rates of a shredding caddisfly (Hesperophylax magnus, Limnephilidae) in response to leaf litter of different chemical and physical phenotypes using Populus cross types (P. fremontii, P. angustifolia, and F1 hybrids) and genotypes within P. angustifolia. We combined laboratory mesocosm studies using litter from a common garden with a field study using doubly labeled litter (13C and 15N) grown in a greenhouse and incubated in Oak Creek, Arizona, USA. We found that, in the lab, shredders initially chose relatively labile (low lignin and condensed tannin concentrations, rapidly decomposing) cross type litter, but preference changed within 4 d to relatively recalcitrant (high lignin and condensed tannin concentrations, slowly decomposing) litter types. Additionally, in the lab, shredder growth rates were higher on relatively recalcitrant compared to labile cross type litter. Over the course of a three‐week field experiment, shredders also assimilated more C and N from relatively recalcitrant compared to labile cross type litter. Finally, among P. angustifolia genotypes, N assimilation by shredders was positively related to litter lignin and C:N, but negatively related to condensed tannins and decomposition rate. C assimilation was likewise positively related to litter C:N, and also to litter %N. C assimilation was not associated with condensed tannins or lignin. Collectively, these findings suggest that relatively recalcitrant litter of Populus cross types provides more nutritional benefit, in terms of N fluxes and growth, than labile litter, but among P. angustifolia genotypes the specific trait of litter recalcitrance (lignin or tannins) determines effects on C or N assimilation. As shredders provide nutrients and energy to higher trophic levels, the influence of these genetically based plant decomposition pathways on shredder preference and performance may affect community and food web structure. [ABSTRACT FROM AUTHOR]

Background: A huge and continuous increase in the number of completely sequenced chloroplast genomes, available for evolutionary and functional studies in plants, has been observed during the past years. Consequently, it appears possible to build large-scale phylogenetic trees of plant species. However, building such a tree that is well-supported can be a difficult task, even when a subset of close plant species is considered. Usually, the difficulty raises from a few core genes disturbing the phylogenetic information, due for example from problems of homoplasy. Fortunately, a reliable phylogenetic tree can be obtained once these problematic genes are identified and removed from the analysis.Therefore, in this paper we address the problem of finding the largest subset of core genomes which allows to build the best supported tree. Results: As an exhaustive study of all core genes combination is untractable in practice, since the combinatorics of the situation made it computationally infeasible, we investigate three well-known metaheuristics to solve this optimization problem. More precisely, we design and compare distributed approaches using genetic algorithm, particle swarm optimization, and simulated annealing. The latter approach is a new contribution and therefore is described in details, whereas the two former ones have been already studied in previous works. They have been designed de novo in a new platform, and new experiments have been achieved on a larger set of chloroplasts, to compare together these three metaheuristics. Conclusions: The ways genes affect both tree topology and supports are assessed using statistical tools like Lasso or dummy logistic regression, in an hybrid approach of the genetic algorithm. By doing so, we are able to provide the most supported trees based on the largest subsets of core genes. [ABSTRACT FROM AUTHOR]

Context Peripheral populations especially those in the leading edge are isolated from rest of the areas in the species distribution range. This can make them less genetically diverse yet genetically distinct from the rest of the populations in the species distribution range. Evaluation of their genetic diversity is thus crucial in understanding the local adaptation potential of a species. Aims We investigated the genetic diversity and genotype by environment interaction at the northern parts of the distribution range of P. avium. Methods Quantitative genetic variation of growth, stem form, and spring phenology were assessed in progenies from 93 plus trees of P. avium selected from 43 locations at the north of the species distribution range in Sweden and tested at two Swedish sites and one Danish site. Results We find large quantitative genetic variation in growth and phenology at the northern part of the distribution range of P. avium. Only a limited genotype by environment interaction was observed with no clear indication of local adaptation at the northern parts of the species distribution. Conclusion We conclude that P. avium harbors a high level of genetic diversity at the north of its distribution range. Present patterns therefore reflect more likely the recent introduction of the species and dispersal dynamics rather than a long-term loss of diversity along South-North ecological clines during the Holocene. With no indications of genetic depletion in growth or phenology, the gene pool in the breeding program is considered suitable for the future propagation of the species in the tested area. [ABSTRACT FROM AUTHOR]

Biomass production is traditionally an important goal in forest tree breeding programs. However, progress in classical tree breeding is limited because of long generation cycles of many forest tree species. Due to this limitation, genetic engineering, and also the quite recently developed genome editing technique, are very attractive tools to improve tree characteristics in a relatively short time. As a proof-of-concept approach, the GIBBERELLIC ACID 20 OXIDASE (GA20-OXIDASE) gene was constitutively overexpressed in poplar leading to significantly higher plants. Unfortunately, deleterious side-effects were also observed, like longer and thinner shoots leading to plants with unstable stems unable to grow without external stabilization. In the literature, polyploidization was reported to increase stem thickness relatively to plant height in several plant species. Therefore, polyploidization of GA20-OXIDASE overexpressing transgenic poplar lines was attempted. Mixoploid (ploidy chimeric: diploid and tetraploid nuclei) plants were obtained and assessed for several years for ploidy status and growth performance (stem height and diameter, bud set) in climate chamber and glasshouse. The results indicate that mixoploid GA20-OXIDASE overexpressing transgenic poplar still reveal increased growth but also showed a lower height-to-stem ratio compared to the diploid GA20-OXIDASE transgenic poplar, enabling the mixoploid transgenic plants to grow without external stabilization. [ABSTRACT FROM AUTHOR]

Like many other high elevation alpine tree species, Rocky Mountain bristlecone pine (Pinus aristata Engelm.) may be particularly vulnerable to climate change. To evaluate its potential vulnerability to shifts in climate, we defined the suitable climate space for each of four genetic lineages of bristlecone pine and for other subalpine tree species in close proximity to bristlecone pine forests. Measuring changes in the suitable climate space for lineage groups is an important step beyond models that assume species are genetically homogenous. The suitable climate space for bristlecone pine in the year 2090 is projected to decline by 74% and the proportional distribution of suitable climate space for genetic lineages shifts toward those associated with warmer and wetter conditions. The 2090 climate space for bristlecone pine exhibits a bimodal distribution along an elevation gradient, presumably due to the persistence of the climate space in the Southern Rocky Mountains and exclusion at mid-elevations by conditions that favor the climate space of other species. These shifts have implications for changes in fire regimes, vulnerability to pest and pathogens, and altered carbon dynamics across the southern Rockies, which may reduce the likelihood of bristlecone pine trees achieving exceptional longevity in the future. The persistence and expansion of climate space for southern bristlecone pine genetic lineage groups in 2090 suggests that these sources may be the least vulnerable in the future. While these lineages may be more likely to persist and therefore present opportunities for proactive management (e.g., assisted migration) to maintain subalpine forest ecosystem services in a warmer world, our findings also imply heighted conservation concern for vulnerable northern lineages facing range contractions. [ABSTRACT FROM AUTHOR]

Forest trees use various strategies to cope with drought stress and these strategies involve complex molecular mechanisms. Pinus halepensis Miller (Aleppo pine) is found throughout the Mediterranean basin and is one of the most drought-tolerant pine species. In order to decipher the molecular mechanisms that P. halepensis uses to withstand drought, we performed large-scale physiological and transcriptome analyses. We selected a mature tree from a semi-arid area with suboptimal growth conditions for clonal propagation through cuttings. We then used a high-throughput experimental system to continuously monitor whole-plant transpiration rates, stomatal conductance and the vapor pressure deficit. The transcriptomes of plants were examined at six physiological stages: pre-stomatal response, partial stomatal closure, minimum transpiration, post-irrigation, partial recovery and full recovery. At each stage, data from plants exposed to the drought treatment were compared with data collected from well-irrigated control plants. A drought-stressed P. halepensis transcriptome was created using paired-end RNA-seq. In total, ~6000 differentially expressed, non-redundant transcripts were identified between drought-treated and control trees. Cluster analysis has revealed stress-induced down-regulation of transcripts related to photosynthesis, reactive oxygen species (ROS)-scavenging through the ascorbic acid (AsA)-glutathione cycle, fatty acid and cell wall biosynthesis, stomatal activity, and the biosynthesis of flavonoids and terpenoids. Up-regulated processes included chlorophyll degradation, ROS-scavenging through AsA-independent thiol-mediated pathways, abscisic acid response and accumulation of heat shock proteins, thaumatin and exordium. Recovery from drought induced strong transcription of retrotransposons, especially the retrovirus-related transposon Tnt1-94. The drought-related transcriptome illustrates this species' dynamic response to drought and recovery and unravels novel mechanisms. [ABSTRACT FROM AUTHOR]

Wood is a renewable resource that can be employed for the production of second generation biofuels by enzymatic saccharification and subsequent fermentation. Knowledge on how the saccharification potential is affected by genotype-related variation of wood traits and drought is scarce. Here, we used three Populus nigra L. genotypes from habitats differing in water availability to (i) investigate the relationships between wood anatomy, lignin content and saccharification and (ii) identify genes and coexpressed gene clusters related to genotype and drought-induced variation in wood traits and saccharification potential. The three poplar genotypes differed in wood anatomy, lignin content and saccharification potential. Drought resulted in reduced cambial activity, decreased vessel and fiber lumina, and increased the saccharification potential. The saccharification potential was unrelated to lignin content as well as to most wood anatomical traits. RNA sequencing of the developing xylem revealed that 1.5% of the analyzed genes were differentially expressed in response to drought, while 67% differed among the genotypes. Weighted gene correlation network analysis identified modules of co-expressed genes correlated with saccharification potential. These modules were enriched in gene ontology terms related to cell wall polysaccharide biosynthesis and modification and vesicle transport, but not to lignin biosynthesis. Among the most strongly saccharification-correlated genes, those with regulatory functions, especially kinases, were prominent. We further identified transcription factors whose transcript abundances differed among genotypes, and which were co-regulated with genes for biosynthesis and modifications of hemicelluloses and pectin. Overall, our study suggests that the regulation of pectin and hemicellulose metabolism is a promising target for improving wood quality of second generation bioenergy crops. The causal relationship of the identified genes and pathways with saccharification potential needs to be validated in further experiments. [ABSTRACT FROM AUTHOR]

The conservation and sustainable use of forests and forest genetic resources (FGR) is a challenging task for scientists and foresters. Forest management practices can affect diversity on various levels: genetic, species, and ecosystem. Understanding past natural disturbance dynamics and their level of dependence on human disturbances and management practices is essential for the conservation and management of FGR, especially in the light of climate change. In this review, forest management practices and their impact on genetic composition are reviewed, synthesized, and interpreted in the light of existing national and international forest monitoring schemes and concepts from various European projects. There is a clear need and mandate for forest genetic monitoring (FGM), while the requirements thereof lack complementarity with existing forest monitoring. Due to certain obstacles (e.g., the lack of unified FGM implementation procedures across the countries, high implementation costs, large number of indicators and verifiers for FGM proposed in the past), merging FGM with existing forest monitoring is complicated. Nevertheless, FGM is of paramount importance for forestry and the natural environment in the future, regardless of the presence or existence of other monitoring systems, as it provides information no other monitoring system can yield. FGM can provide information related to adaptive and neutral genetic diversity changes over time, on a species and/or on a population basis and can serve as an early warning system for the detection of potentially harmful changes of forest adaptability. In addition, FGM offers knowledge on the adaptive potential of forests under the changing environment, which is important for the long-term conservation of FGR. [ABSTRACT FROM AUTHOR]

A central challenge in community ecology is understanding the role that phenotypic variation among genotypes plays in structuring host-associated communities. While recent studies have investigated the relationship between plant genotype and the composition of soil microbial communities, the effect of genotype-by-environment interactions on the plant microbiome remains unclear. In this study, we assessed the influence of tree genetics (G), nitrogen (N) form and genotype-by-environment interaction (G x N) on the composition of the root microbiome. Rhizosphere communities (bacteria and fungi) and root-associated fungi (including ectomycorrhizal and saprotrophic guilds) were characterised in two genotypes of Pinus radiata with contrasting physiological responses to exogenous organic or inorganic N supply. Genotype-specific responses to N form influenced the composition of the root microbiome. Specifically, (1) diversity and composition of rhizosphere bacterial and root-associated fungal communities differed between genotypes that had distinct responses to N form, (2) shifts in the relative abundance of individual taxa were driven by the main effects of N form or host genotype and (3) the root microbiome of the P. radiata genotype with the most divergent growth responses to organic and inorganic N was most sensitive to differences in N form. Our results show that intraspecific variation in tree response to N form has significant consequences for the root microbiome of P. radiata, demonstrating the importance of genotype-by-environment interactions in shaping host-associated communities. [ABSTRACT FROM AUTHOR]

Abstract: Identifying and quantifying the importance of environmental variables in structuring population genetic variation can help inform management decisions for conservation, restoration, or reforestation purposes, in both current and future environmental conditions. Landscape genomics offers a powerful approach for understanding the environmental factors that currently associate with genetic variation, and given those associations, where populations may be most vulnerable under future environmental change. Here, we applied genotyping by sequencing to generate over 11,000 single nucleotide polymorphisms from 311 trees and then used nonlinear, multivariate environmental association methods to examine spatial genetic structure and its association with environmental variation in an ecologically and economically important tree species endemic to Hawaii, Acacia koa. Admixture and principal components analyses showed that trees from different islands are genetically distinct in general, with the exception of some genotypes that match other islands, likely as the result of recent translocations. Gradient forest and generalized dissimilarity models both revealed a strong association between genetic structure and mean annual rainfall. Utilizing a model for projected future climate on the island of Hawaii, we show that predicted changes in rainfall patterns may result in genetic offset, such that trees no longer may be genetically matched to their environment. These findings indicate that knowledge of current and future rainfall gradients can provide valuable information for the conservation of existing populations and also help refine seed transfer guidelines for reforestation or replanting of koa throughout the state. [ABSTRACT FROM AUTHOR]

Six non-thinned loblolly pine (Pinus taeda L.) culture × density study sites in the Piedmont and Upper Coastal Plain of the Southeast U.S. were used to examine the effects of two cultural intensities and three planting densities on solid wood potential as well as the proportion and position of product-defining defects (forks, crooks, broken tops). A tree quality index (TQI) was used to grade stems for solid wood potential. The results show that an operational management regime exhibited a higher proportion of trees with solid wood product potential than did a very intensive management regime. Trees subject to operational management exhibited product-defining defects higher on the stem; however, the proportion of stems with defects was not significantly different from the intensive management. Planting densities of 741, 1482, and 2223 trees per hectare (TPH) exhibited a relatively narrow range of the proportion of trees with solid wood product potential that were not significantly different. Density did not have a significant effect on the heights of the product-defining defects. These results show that management intensity and less so planting density, affect the solid wood product potential indicators evaluated and should be considered when making management decisions. [ABSTRACT FROM AUTHOR]

DNA polymorphism at nine nuclear microsatellites of nine selected naturally-regenerated Norway spruce populations growing mainly within gene conservation units in different parts of the Czech Republic was studied. To verify the genetic quality of the selected gene conservation unit, we analyzed nine Norway spruce subpopulations from gene conservation unit GZ 102-Orlické hory. Genetic parameters can be used in state administrative decision making on including stands into gene conservation units. The level of genetic diversity within 17 investigated Czech Norway spruce units was relatively high. Mean values for the number of different alleles ranged from 12.2 (population SM 08) to 16.2 (subpopulation SM T4). The values of observed heterozygosity (Ho) ranged from 0.65 to 0.80 and expected heterozygosity (He) from 0.74 to 0.81. Pairwise population FST values ranging from 0.006 to 0.027 indicated low genetic differentiation between units, and values of Nei's genetic distance among Norway spruce units ranged from 0.046 to 0.168, thus structuring of the investigated Norway spruce units was confirmed. Closer genetic similarity was seen in subpopulations from the gene conservation unit in Orlické hory than in the studied populations from other genetic conservation units. Additionally, the populations SM 01 and SM 05, both of Hurst ecotypes, were the closest to one another and the populations of mountain and alpine ecotypes were assembled into another group. [ABSTRACT FROM AUTHOR]