Transcriptional time-course analysis during ash dieback infection revealed different responses in tolerant and susceptible Fraxinus excelsior genotypes.

Hymenoscyphus fraxineus, the causal agent of Ash Dieback (ADB), has been introduced to eastern Europe in the 1990s from where it spread causing decline in European ash populations. However, the genetic basis of the molecular response in tolerant and susceptible ash trees to this disease is still largely unknown. We performed RNA-sequencing to study the transcriptomic response to the disease in four ash genotypes (ADB-tolerant FAR3 and FS36, and ADB-susceptible UW1 and UW2), during a time-course of 7, 14, 21, and 28 days post-inoculation, including mock-inoculated trees as control samples for each sampling time point.

Diverse and larger tree islands promote native tree diversity in oil palm landscapes.

In monoculture-dominated landscapes, recovering biodiversity is a priority, but effective restoration strategies have yet to be identified. In this study, we experimentally tested passive and active restoration strategies to recover taxonomic, phylogenetic, and functional diversity of woody plants within 52 tree islands established in an oil palm landscape. Large tree islands and higher initial planted diversity catalyzed diversity recovery, particularly functional diversity at the landscape level.

Applications of CRISPR Technologies in Forestry and Molecular Wood Biotechnology.

Forests worldwide are under increasing pressure from climate change and emerging diseases, threatening their vital ecological and economic roles. Traditional breeding approaches, while valuable, are inherently slow and limited by the long generation times and existing genetic variation of trees. CRISPR technologies offer a transformative solution, enabling precise and efficient genome editing to accelerate the development of climate-resilient and productive forests.

Development of a highly polymorphic chloroplast SSR set in with transferability to other conifer species-A promising toolkit for gene flow investigations.

The genus is widely distributed across the world and is of high importance for forestry. Since chloroplasts are usually uniparentally inherited, they are an important tool for specific scientific issues like gene flow, parentage, migration and, in general, evolutionary analysis. Established genetic markers for organelles in conifers are rather limited to RFLP markers, which are more labour and time intensive, compared with SSR markers.

A genome-wide genetic association study reveals SNPs significantly associated with environmental variables and specific leaf area in European beech.

European beech is negatively affected by climate change and a further growth decline is predicted for large parts of its distribution range. Despite the importance of this species, little is known about its genetic adaptation and especially the genetic basis of its physiological traits. Here, we used genotyping by sequencing to identify SNPs in 43 German European beech populations growing under different environmental conditions.

Circadian rhythm and redox homeostasis candidate genes showed association with shallow elevation in Norway spruce.

The analysis of genetic variation underlying local adaptation in natural populations, together with the response to different external stimuli, is currently a hot topic in forest sciences, with the aim of identifying genetic markers controlling key phenotypic traits of interest for their inclusion in restoration and breeding programs. In Europe, one of the main tree species is Norway spruce (Picea abies (L.) H.

Scots pine - panmixia and the elusive signal of genetic adaptation.

Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation.

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

Tree growth performance can be partly explained by genetics, while a large proportion of growth variation is thought to be controlled by environmental factors. However, to what extent DNA methylation, a stable epigenetic modification, contributes to phenotypic plasticity in the growth performance of long-lived trees remains unclear. In this study, a comparative analysis of targeted DNA genotyping, DNA methylation and mRNAseq profiling for needles of 44-year-old Douglas-fir trees (Pseudotsuga menziesii (Mirb.

Beyond the surface: exploring the mycobiome of Norway spruce under drought stress and with Heterobasidion parviporum.

The mycobiome, comprising fungi inhabiting plants, potentially plays a crucial role in tree health and survival amidst environmental stressors like climate change and pathogenic fungi. Understanding the intricate relationships between trees and their microbial communities is essential for developing effective strategies to bolster the resilience and well-being of forest ecosystems as we adopt more sustainable forest management practices. The mycobiome can be considered an integral aspect of a tree's biology, closely linked to its genotype.

A haplotype-resolved chromosome-scale genome for Quercus rubra L. provides insights into the genetics of adaptive traits for red oak species.

Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q.

Tree islands enhance biodiversity and functioning in oil palm landscapes.

In the United Nations Decade on Ecosystem Restoration, large knowledge gaps persist on how to increase biodiversity and ecosystem functioning in cash crop-dominated tropical landscapes. Here, we present findings from a large-scale, 5-year ecosystem restoration experiment in an oil palm landscape enriched with 52 tree islands, encompassing assessments of ten indicators of biodiversity and 19 indicators of ecosystem functioning. Overall, indicators of biodiversity and ecosystem functioning, as well as multidiversity and ecosystem multifunctionality, were higher in tree islands compared to conventionally managed oil palm.

Integrative taxonomy using the plant core DNA barcodes in Sumatra's Burseraceae.

The high diversity and limited floral information in tropical forests often pose a challenge for species identification. However, over the past decade, DNA barcoding has been employed in tropical forests, including Sumatran forests, to enhance floristic surveys. This technique facilitates the discrimination of morphologically similar species and addresses the limitations of conventional species identification, which relies on short-lived reproductive structures.

Applying molecular and genetic methods to trees and their fungal communities.

Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms.

Molecular and morphological survey of Lamiaceae species in converted landscapes in Sumatra.

Molecular biodiversity surveys have been increasingly applied in hyperdiverse tropical regions as an efficient tool for rapid species assessment of partially undiscovered fauna and flora. This is done by overcoming shortfalls in knowledge or availability of reproductive structures during the sampling period, which often represents a bottleneck for accurate specimens' identification. DNA sequencing technology is intensifying species discovery, and in combination with morphological identification, has been filling gaps in taxonomic knowledge and facilitating species inventories of tropical ecosystems.

Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection.

The ecological and economic importance of forest trees is evident and their survival is necessary to provide the raw materials needed for wood and paper industries, to preserve the diversity of associated animal and plant species, to protect water and soil, and to regulate climate. Forest trees are threatened by anthropogenic factors and biotic and abiotic stresses. Various diseases, including those caused by fungal pathogens, are one of the main threats to forest trees that lead to their dieback.

Current status and trends in forest genomics.

Forests are not only the most predominant of the Earth's terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation. Forest genomics has great potential of increasing forest productivity and adaptation to the changing climate.

A Non-Destructive High-Speed Procedure to Obtain DNA Barcodes from Soft-Bodied Insect Samples with a Focus on the Dipteran Section of Schizophora.

While the need for biodiversity research is growing, paradoxically, global taxonomical expertise is decreasing as a result of the neglected funding for young academics in taxonomy. Non-destructive approaches for DNA barcoding are necessary for a more efficient use of this dwindling expertise to fill gaps, and identify incorrect entries in sequence databases like BOLD or GenBank. They are efficient because morphological re-examination of species vouchers is still possible post-DNA barcoding.

Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra.

Background: Intense conversion of tropical forests into agricultural systems contributes to habitat loss and the decline of ecosystem functions. Plant-pollinator interactions buffer the process of forest fragmentation, ensuring gene flow across isolated patches of forests by pollen transfer. In this study, we identified the composition of pollen grains stored in pot-pollen of stingless bees, Tetragonula laeviceps, via dual-locus DNA metabarcoding (ITS2 and rbcL) and light microscopy, and compared the taxonomic coverage of pollen sampled in distinct land-use systems categorized in four levels of management intensity (forest, shrub, rubber, and oil palm) for landscape characterization.

Genotyping by sequencing reveals lack of local genetic structure between two German L. populations.

The European spruce bark beetle ( L.) is a serious pest in Norway spruce stands. While usually attacking freshly fallen trees or trees with a reduced defense system, also healthy trees can be infested during massive outbreaks of that can occur after catastrophic events such as drought periods or storms.

From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees.

Due to the economic and ecological importance of forest trees, modern breeding and genetic manipulation of forest trees have become increasingly prevalent. The CRISPR-based technology provides a versatile, powerful, and widely accepted tool for analyzing gene function and precise genetic modification in virtually any species but remains largely unexplored in forest species. Rapidly accumulating genetic and genomic resources for forest trees enabled the identification of numerous genes and biological processes that are associated with important traits such as wood quality, drought, or pest resistance, facilitating the selection of suitable gene editing targets.

Identifying of Quercus vulcanica and Q. frainetto growing in different environments through deep learning analysis.

Quercus is one of the important elements of forests worldwide. But the diagnosis of the species in this genus in particular using leaves is pretty challenging due to the presence of natural hybrids and phenotypically plastic trait expression. In this sense, this study aims to classify the leaves of Q.

Foliar Application of Salicylic Acid Improves Water Stress Tolerance in L. and L. Saplings: Evidence from Morphological, Physiological, and Biochemical Changes.

Reforestation efforts are being challenged as water stress is hampering the sapling growth and survival in arid to semiarid regions. A controlled experiment was conducted to evaluate the effect of foliar application of salicylic acid (SA) on water stress tolerance of and . Saplings were watered at 90%, 60%, and 30% of field capacity (FC), and half of the saplings under 60% and 30% FC were sprayed with 1.

ITS secondary structure reconstruction to resolve taxonomy and phylogeny of the L. genus.

The taxonomy and phylogeny of the L. genus remain unresolved and are very difficult to assess due to several factors, especially because of frequent hybridization among different species. In the current study, we used nucleotide sequences of two internal transcribed spacer regions (ITS1 and ITS2), which are commonly used as phylogenetic markers.

Genetic structure of coast redwood (Sequoia sempervirens [D. Don] Endl.) populations in and outside of the natural distribution range based on nuclear and chloroplast microsatellite markers.

Coast redwood (Sequoia sempervirens) naturally growing in southern Oregon and northern California is one of the few conifer tree species that are polyploid. Despite its unique ecological and economic importance, its population genetic structure is still insufficiently studied. To obtain additional data on its population genetic structure we genotyped 317 samples collected from populations in California (data set C) and 144 trees growing in a provenance trial in France (data set F) using 12 nuclear (five random nuclear genomic nSSRs and seven expressed sequence tag EST-SSRs) and six chloroplast (cpSSRs) microsatellite or simple sequence repeat (SSR) markers, respectively.

Visual detection of based on dual-cycle signal amplification and T5 exonuclease.

A novel visual detection of species through recombinase polymerase amplification and rolling circle amplification was established. Single-stranded circle DNA was produced based on one strand of RPA product, which used as a template for rolling circle amplification.