Biology subjects

Gailing, O.

Publications and source records attributed to Gailing, O..

10 recordsLinked to original sources

bioRxiv2026

Genomic Prediction Enables Provenance-Aware Selection in 1 Sessile Oak (Quercus petraea) using Foliar Physiological Traits

Climate change is reshaping the adaptive landscape of forest ecosystems, demanding more efficient strategies to identify and deploy resilient tree genotypes. Genomic prediction offers a powerful framework to accelerate selection for complex physiological traits underlying climate adaptability in long-lived species such as sessile oak (Quercus petraea (Matt.) Liebl.). Here, we conducted genomic prediction for three key physiological traits carbon isotope composition, nitrogen isotope composition, and the carbon-to-nitrogen content ratio (C/N ratio) measured in 746 trees genotyped with dense genome-wide markers ([~]580,000 SNPs). High genomic heritabilities were estimated across traits, with within-year prediction accuracies (Pearsons r between genomic estimated values and observed phenotypes) reaching 0.77. Notably, across-year and across-provenance predictions remained substantial (0.41 < r < 0.82), with predictability declining with increasing genetic distance (FST) between training and test provenances for nitrogen isotope composition and C/N ratio. In addition, GWAS-guided SNP preselection increased heritability capture by [~]15% relative to random SNP subsets. And, the pronounced provenance-by-environment interactions observed indicated substantial phenotypic plasticity in these traits. These results demonstrate the strong potential of applying genomic prediction to foliar physiological traits as polygenic predictors for climate adaptation in plants, support provenance-aware breeding to improve forest establishment, and provide practical strategies for deploying genomic prediction in long-lived species.

genetics↗

bioRxiv2025

Assessing the adaptative potential to temperature and precipitation along a steep environmental gradient in populations of European beech

Climate change poses a significant threat to European beech. These concerns highlight the need to assess the adaptive potential of European beech populations to climate change. Landscape genomics, also known as environmental association analysis, is a powerful tool for identifying gene loci that contribute to local adaptation to environmental pressures. Genotypic data was collected from [~]100 adult beech trees per stand in five locations in the South-Eastern Romanian Carpathians along an altitudinal gradient associated with precipitation and temperature. In total, 53 environmental variables, comprising frost frequency change, temperature and precipitation, were extracted from the climatology data base CHELSA. Based on these variables the Ellenberg-Quotient (EQ) was calculated. We performed environmental association analysis using LFMM (latent factor mixed models) to identify Single Nucleotide Polymorphism (SNP) markers associated with environmental variables and with the principal components calculated based on these. We identified 446 SNP markers significantly associated with the first principal component (PC). These were overlapping with the SNP markers significantly associated with all environmental variables except precipitation accumulated during the growing season. The first PC was correlated with all temperature-based variables and elevation at |r| [~]0.989 to [~]0.997 and with all precipitation-based and Ellenberg-Quotient variables at |r| [~]0.945 to 0.950, except precipitation accumulated during the growing season. A high peak region on chromosome 2 from [~]4.56 to [~]16.27 Mb appeared in all results. This region was [~]3.47 Mb downstream from a region for local adaptation identified by Lazic et al. (2024). In this peak, 273 markers located in the coding region of 22 genes were found. Ten out these 22 were described based on a literature review. Among these ten genes, two may be involved in local adaptation based on our literature review. These two genes are polygalacturonase QRT3-like and NRT1/PTR_FAMILY 5.4-like. The gene polygalacturonase QRT3-like plays a role in pollen development in Arabidopsis thaliana L. and Brassica rapa L. We observed at the corresponding SNP markers, a correlation of the minor allele frequency and temperature-based environmental variables.

genetics↗

bioRxiv2025

Genome-wide association study in European beech (Fagus sylvatica L.) for drought stress traits

Forest tree breeding is an extremely long and tedious process. To study the genetic architecture of polygenic traits in long-lived species such as forest trees, costly field experiments are implemented. Phenotypic data on traits, that are measured at maturity, are only available after a long time and juvenile-mature correlations are often unknown. Genome-wide association studies (GWAS) aim to identify loci associated with drought stress, tree physiology, growth or wood quality traits, which could be prioritized in breeding programs. Genotypic and phenotypic data were collected from approximately 100 adult beech trees per stand in five locations in the South-Eastern Romanian Carpathians along an altitudinal gradient associated with precipitation and temperature. We performed GWAS using PLINK to identify SNP markers associated with traits related to drought stress. A total of 121 markers on eight chromosomes were identified as being associated with stomatal density. Sixty-four markers are located on chromosome 10 in a region spreading from [~]4.89 to 13.67 Mb. There are five genes in this region that are thought to play a role in controlling stomatal density. All markers within this region exhibit similar allele frequencies, which are correlated with stomatal density and the altitudinal gradient of the stands. We assume this entire region is jointly involved in local adaptation to drought stress. We identified one interesting candidate SNP associated with leaf nitrogen content. Two SNP markers were identified as being significantly associated with {delta}13C as measure of intrinsic water use efficiency. Additionally, signals of significant polygenic selection for {delta}13C were observed.

genetics↗

bioRxiv2025

Phylogenetic and taxonomic insights into Betula: low-coverage whole genome sequencing and plastome analysis with focus on the rare Ukrainian endemic species Betula klokovii Zaverucha

Betula klokovii Zaverucha is a rare endemic species of Ukraine that is still not well taxonomically studied. In the current pilot study, we performed low-coverage whole genome sequencing for B. klokovii, related species (B. pendula Roth and B. pubescens Ehrh.) and the assumed hybrid B. klokovii x B. pendula, assessed the genomic structure of taxa with different mapping settings using UMAP non-linear dimension reduction algorithm, extracted and assembled whole plastomes. Single Nucleotide Polymorphism (SNP) analysis based on low-coverage whole genome sequencing (LC-WGS) followed by UMAP visualization reveals the separation of B. klokovii from the other analysed taxa. The best taxonomic resolution was achieved with reads filtered for contamination. In contrast, the best result in obtaining complete plastome assemblies was achieved via NOVOPlasty pipeline and raw reads. The size for the eight newly assembled plastid genomes ranges between 160,535 and 160,625bp, GC content is 36,1%. We annotated 130 genes (113 unique) for all eight assemblies. In addition, we investigated B. klokoviis relationships with 20 other birch species and two intraspecific taxa by reconstructing plastome-based Bayesian inference and maximum likelihood phylogenies. Overall, plastome phylogeny provides a better resolution in comparison to phylogenies based on a few plastid or nuclear molecular markers. However, it could be affected by chloroplast capture, and some other factors like quality of sequencing and assembly, and is not suitable to detect hybrids when used alone. In particular, we found that B. klokovii is likely a separate taxon that is closely related to B. pubescens but morphologically and genetically distinct. The study shows that genome-wide SNP data and plastome phylogenies have a certain potential for addressing issues with specific taxa within the genus Betula L. However, to fully leverage the potential of this approach, we suggest collecting a much larger number of birch plastome sequences to be sequenced and assembled. For a better understanding of birch phylogeny there is a need for reference-grade chromosome scale genome assemblies for polyploid species.

plant biology↗

bioRxiv2024

Land-use changes impact root-fungal network connectivity in a global biodiversity hotspot

O_LICross-kingdom associations play a fundamental role in ecological processes. Yet our understanding of plant-fungal co-occurrences in tropical rainforests and the potential impacts of land-use change shaping species connections remains limited. C_LIO_LIBy using amplicon sequencing on DNA from roots and their associated fungal communities, we aim to understand the impact of rainforest transformation on the composition and structure of root-fungal ecological networks in human-modified landscapes in Sumatra, Indonesia. C_LIO_LIEach land-use type supports a distinctive set of indicator species, which are organisms that reflect specific environmental conditions and can signal changes in ecosystem health. We observed a decline in the richness of plant species indicators and plant-fungal associations with increasing land-use intensification. Additionally, there is a turnover in root communities, shifting from native and endemic species in rainforests to non-native, generalist herbaceous species in rubber and oil palm plantations. C_LIO_LIPlant-fungal connectivity significantly declined with increasing land-use intensification, suggesting that managed ecosystems may have weakened root-fungal interactions. Network analysis highlights the distinct responses of various fungal groups. For instance, arbuscular mycorrhizal fungi (AMF) showed fewer connections with modules linked to oil palm and rubber roots, indicating weakened root-fungal associations in monocultures. This aligns with the observed reduction in AMF diversity in converted land-use areas compared to forests, further reinforcing the negative impact of land-use practices in oil palm and rubber monocultures on AMF diversity. C_LIO_LISynthesis. Dimensioning the impacts of rainforest transformations belowground is constrained by our understanding of fungal functional guilds. Highly modified systems exhibited fewer connections, suggesting a dynamic restructuring of root-fungal relationships in response to land-use changes. Understanding the intricate interplay between plants and fungi in the face of land-use change can provide valuable information for conservation efforts, agricultural practices, and ecosystem management strategies aimed at promoting biodiversity, soil health, and ecosystem resilience in the context of changing environmental conditions. Moreover, it underscores the importance of communities networks in land-use planning and management decisions to support plant and fungal diversity in terrestrial ecosystems. C_LI

ecology↗

bioRxiv2023

Planting diversity begets multifaceted tree diversity in oil palm landscapes

Optimizing restoration outcomes is crucial for enhancing multifaceted diversity, resilience, and ecosystem functioning in monoculture-dominated landscapes globally. Here, we experimentally tested the performance of passive and active restoration strategies to recover taxonomic, phylogenetic, and functional diversity by establishing 52 tree islands in an oil palm landscape. Tree diversity via natural regeneration was shaped by local rather than landscape properties, with the diversity of planted tree species and tree island size driving higher multifaceted diversity. We show that large tree islands with higher initial planted diversity catalyze the recovery of multifaceted diversity at both the local and landscape level, including forest-associated species. Our results demonstrate that planted diversity begets regenerating diversity, overcoming major limitations of natural regeneration in highly modified landscapes. By elucidating the contribution of experimental, local, and landscape drivers to natural regeneration, these findings provide practical insights to make oil palm landscapes more biodiversity-friendly by enhancing functional and phylogenetic diversity within plantations.

ecology↗

bioRxiv2023

Low genetic differentiation across an entire continent: the Scots pine paradox

O_LIScots 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. C_LIO_LITo understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2,321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species, and examined signals of genetic adaptation. C_LIO_LIWe found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expending populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of SNPs significantly linked to environmental gradients. C_LIO_LIThe results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment. C_LI

evolutionary biology↗

bioRxiv2022

Differentiation and admixture of Fagus sylvatica L. and Fagus orientalis Lipsky in a northern German forest -- learning from pioneer forest work

Tree species are suffering from changing and stressful environmental conditions worldwide. Fagus sylvatica L., one of the most common Central European deciduous tree species showed symptoms of crown damage, a reduction in growth and increased mortality following the severe recent drought years. For Germany Fagus orientalis Lipsky, a closely related species with higher drought tolerance, originating from south-eastern Europe, Turkey, the Greater Caucasus region and the Hyrcanian forest, has been proposed as an alternative with high future potential. The translocation of pre-adapted planting material has been proposed as a tool to mitigate negative effects of climate change. This approach can be beneficial but might also harbor risks. Taking advantage of F. orientalis trees planted over 100 years ago in the forest district of Memsen, Germany, we set out to study admixture between the two beech species and the direction of gene flow. Furthermore, we used a range-wide dataset of F. sylvatica and F. orientalis provenances to determine the origin of the introduced trees. Using a combination of nuclear EST-SSRs and one chloroplast SSR marker with species-specific variants, we could show that interspecific gene flow was going in both directions. In most cases, F. sylvatica was the pollen donor which is likely explained by the higher abundance of this species producing vast amounts of pollen. The planted trees originated from the Greater Caucasus region and showed strong genetic divergence from German F. sylvatica populations. In the future, gene flow patterns as well as hybrid performance from different provenances should be tested in additional stands and in comparison to F. sylvatica provenances from southern Europe to assess the suitability of Oriental beech for the mitigation of climate change impacts.

plant biology↗

bioRxiv2019

Assignment of frost tolerant coast redwood trees of unknown origin to populations within their natural range using nuclear and chloroplast microsatellite genetic markers

Considering climate change and expected changes in temperature and precipitation, some introduced timber species are prospective for growing in Germany or Europe to produce valuable wood products and support sustainable forestry. The Californian tree, coast redwood (Sequoia sempervirens [D. Don] Endl.) is one of such species due to its excellent wood properties and high growth rate. It is sensitive to the freezing temperatures, but several trees of unknown origin introduced to Germany decades ago demonstrated high frost tolerance, and their propagated cuttings were planted all over German botanic gardens and arboreta. The knowledge of their origin within the natural distribution range could help us identify the potential genetic resources of frost resistant coast redwood genotypes. Therefore, both trees of unknown origin in Germany (G) and two reference data sets representing the \"Kuser provenance test\" established in 1990 in France (F) and samples collected in California (C) with known origin were genotyped using 18 microsatellite markers including 12 nuclear and six chloroplast simple sequence repeat (cpSSR) markers. The number of haplotypes found in the data sets based on six cpSSR markers was surprisingly very high. These markers were used to assign the German frost resistant trees (G) to the two reference data sets (F and C). The genetic structure among California samples (C) based on nSSR and cpSSR markers was very weak and mainly due to northern and southern clusters separated by the San Francisco Bay as a geographic barrier between coast redwood populations confirming previously published data. It was impossible to confidently assign frost tolerant trees (G) to single native populations, but rather to either the northern or southern cluster. However, the existing frost tolerant genotypes can already be used to establish commercial coast redwood plantation for future German forestry.

genetics↗

bioRxiv2019

Genomic landscape of the global oak phylogeny

O_LIThe tree of life is highly reticulate, with the history of population divergence buried amongst phylogenies deriving from introgression and lineage sorting. In this study, we test the hypothesis that there are regions of the oak (Quercus, Fagaceae) genome that are broadly informative about phylogeny and investigate global patterns of oak diversity.\nC_LIO_LIWe utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the worlds oaks. We use reversible-jump MCMC to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20,000 RAD-seq loci back to a recently published oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.\nC_LIO_LIOak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification due to climatic transitions or ecological opportunity.\nC_LIO_LIThe support we find for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.\nC_LI

evolutionary biology↗