Biology subjects

Wildhagen, H.

Publications and source records attributed to Wildhagen, H..

6 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↗

bioRxiv2024

Site-specific metabolic labeling reveals proteome-wide phospho-dynamics

Protein phosphorylation is a critical post-translational modification that orchestrates cellular signaling. Here, we introduce PulsPhos, a method combining metabolic labeling with phosphoproteomics, spectral analysis and modeling, to quantify site-specific phosphorylation lifetimes in living cells. Phosphosite lifetimes vary over multiple orders of magnitude and are influenced by factors such as amino acid composition and subcellular localization. PulsPhos was readily applied to pharmacological perturbations revealing fundamental mechanisms governing protein phosphorylation dynamics.

molecular biology↗

bioRxiv2017

X10 Expansion Microscopy Enables 25 nm Resolution on Conventional Microscopes

Expansion microscopy is a recently introduced imaging technique that achieves super-resolution through physically expanding the specimen by ~4x, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately 4-fold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20-30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10x in each dimension, which corresponds to an expansion of the sample volume by more than 1000-fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25-30 nm on conventional epifluorescence microscopes. X10 provides multi-color images similar or even superior to those produced with more challenging methods, such as STED, STORM and iterative expansion microscopy (iExM), in both cell cultures and tissues.

cell biology↗

bioRxiv2017

Ageing synaptic vesicles are inactivated by contamination with SNAP25

Old organelles can become a hazard to cellular function, by accumulating molecular damage. Mechanisms that identify aged organelles, and prevent them from participating in cellular reactions, are therefore necessary. We describe here one such mechanism for the synaptic vesicle recycling pathway. Using cultured hippocampal neurons, we found that newly synthesized vesicle proteins were incorporated in the active (recycling) pool, and were preferentially employed in neurotransmitter release. They remained in use for up to ~24 hours, during which they recycled up to a few hundred times. We could only detect one change in the molecular composition of the vesicles, an apparent accumulation of SNAP25 in the aged synaptic vesicles. Overexpression of SNAP25, both in wild-type form or in vesicle-bound form, inhibited exocytosis and promoted the co-localization of the vesicle molecules with a recycling endosome marker. This is in line with the hypothesis that the SNAP25 contamination causes the inactivation of the aged vesicles. The SNAP25 overexpression effect could be alleviated by co-expressing the vesicle-associated molecule CSP, which has been previously shown to be involved in chaperoning SNAP25 in the vesicle priming process. Overall, these results suggest that newly synthesized vesicle molecules are preferred in vesicle recycling, probably through a mechanism that renders their priming more efficient than that of aged vesicles.

neuroscience↗