Biology subjects

Trenner, J.

Publications and source records attributed to Trenner, J..

6 recordsLinked to original sources

bioRxiv2026

SNPstar: A Web Server Linking Allelic Variation to Protein Structure and Function in Arabidopsis thaliana

Understanding how natural genetic variants affect protein structure and function is central to plant biology. The 1001 Genomes Project has catalogued millions of single nucleotide polymorphisms (SNPs) across more than a thousand Arabidopsis thaliana accessions, offering an unprecedented opportunity to relate sequence variation to three-dimensional protein structure and population context. Yet, realizing it requires tools that integrate these scales in one accessible framework. Here we present SNPstar, a web server that links allelic variation in A. thaliana to AlphaFold3-predicted structures through a gene-centric, interactive interface. SNPstar annotates each variant with descriptive features, thermodynamic stability estimates, protein domain context, and genome-wide association results, and computes haplotypes and proteotypes that group accessions by shared DNA or protein sequence. Researchers can characterize variants, visualize their structural context, map their geographic distribution, and prioritize accessions for experimental validation without local computational infrastructure. We demonstrate SNPstar with two case studies. The first recapitulates known loss-of-function variation in the cadmium transporter HMA3, validating that SNPstar prioritizes functionally consequential alleles. The second uses SNPstar-defined proteotypes to identify an N-terminal SNP combination in ARGONAUTE 2 that distinguishes accessions differing in in vitro siRNA-directed target cleavage, linking protein-coding variation to a measurable molecular phenotype. SNPstar thus helps translate natural variation into mechanistic insight.

plant biology↗

bioRxiv2026

Fungal community composition links rhizosphere microbiome organization to plant phenotype in response to moderate warming

BackgroundGlobal warming increasingly challenges plant performance and ecosystem function, and plant responses to elevated temperature are shaped not only by intrinsic plasticity, but also by interactions with rhizosphere microbial communities. However, it remains unclear how warming-induced microbiome reorganization relates to plant performance, whether microbiome community composition predicts plant phenotypic responses to elevated temperature better than simple host-microbiome origin matching, and which bacterial or fungal community features contribute most strongly to this prediction. ResultsWe implemented a full factorial design manipulating plant genotype (P), microbial inoculum (M), and temperature (T) using natural Arabidopsis thaliana ecotypes and their corresponding rhizosphere microbiomes from contrasting climatic regions. By integrating high-throughput plant phenotyping, microbial community profiling, microbiome-phenotype coupling analyses, and predictive modeling, we found that elevated temperature induced a coherent thermomorphogenic shift in plant architecture, while plant phenotypic variation remained determined primarily by genotype over the 14-day vegetative growth period covered in this study. Overall, cold-origin genotypes showed larger temperature-induced trait shifts than warm-origin genotypes. Rhizosphere microbial communities were structured predominantly by inoculum origin, but were also affected by warming. Evidence for a increased thermomorphogenic growth when genotypes were combined with inoculum from their home site was limited. Instead, microbiome-phenotype associations were better captured by community composition than by matching status, with fungal community variation showing stronger and more consistent associations with plant phenotype than bacterial variation and providing more robust predictions of plant phenotypes across models. ConclusionsWarming reorganized plant-rhizosphere systems within persistent host- and inoculum-associated baselines. Plant phenotypic variation during vegetative development under elevated temperature was linked more closely to microbiome composition, especially in fungi, than to simple host-microbiome matching of origins. These findings provide a framework for identifying microbiome features associated with plant performance under climate warming.

plant biology↗

bioRxiv2026

EcoCore; An ecologically diverse panel of Arabidopsis thaliana accessions for studying plant-environment interactions

Arabidopsis thaliana naturally occurs across a wide geographic range and displays extensive natural variation in several traits including adaptive responses to the abiotic environment (e.g. temperature, drought, salt). Quantitative techniques like Genome Wide Association Studies (GWAS) enable mapping the genetic basis of such environmental responses and benefits from extensive genetic variation, but the size of the chosen diversity panel is often limited by phenotyping capacity. Most studies therefore use subpanels, often based on maximization of genetic diversity. However, this type of selection may overrepresent cosmopolitan alleles and underrepresent rare environment-specific alleles. Here, we demonstrate that the genetic variation in a GWAS subpanel of Arabidopsis thaliana accessions depends almost entirely on the number of accessions in the panel and very little on the composition of the panel. We present the EcoCore panel designed by grouping accessions of the 1001 genomes (1001G; 1135 accessions) collection, based on their native collection environment and selecting an equal number of accessions from each environment. We assessed hypocotyl lengths of plants grown at control and ambient high temperatures (20{degrees}C and 28{degrees}C) for 913 accessions of the 1001G and mapped these traits with the full 1001G panel versus the EcoCore panel. The EcoCore panel revealed novel genetic associations with hypocotyl length which is attributed to enrichment of alleles from rare environments. We present the EcoCore panel as a manageable resource for studying phenotypic plasticity and the genetic basis of plant-environment interactions.

plant biology↗

bioRxiv2023

Tracing the evolutionary emergence of the temperature sensing prion-like domain in EARLY FLOWERING 3 across the plant kingdom

Plants have evolved to anticipate and adjust their growth and development in response to environmental changes. To mitigate the negative influence of global climate change on crop production, understanding the key regulators of plant performance is imperative. EARLY FLOWERING 3 (ELF3) is such a regulator involved in the circadian clock and thermomorphogenesis. Arabidopsis thaliana ELF3 contains a prion-like domain (PrLD) that functions as a thermosensor, enabling its liquid-liquid phase separation at high ambient temperatures. To understand the conservation of this function across the plant kingdom, we traced the evolutionary emergence of ELF3 with a focus on PrLD existence. We observed that the presence of the domain within ELF3, mainly contributed by the length of polyglutamine (polyQ) repeats, is most prominent Brassicales. By analyzing 319 natural Arabidopsis thaliana accessions, we detected a wide range of polyQ length variation in ELF3. However, it is only weakly associated with geographic origin, climate conditions and classic temperature-responsive phenotypes. Based on available prediction tools and limited experimental evidence, we conclude that although the emergence of PrLD is not likely to be a key driver of environmental adaptation, it adds an extra layer to ELF3s role in thermomorphogenesis.

plant biology↗

bioRxiv2022

An exotic allele of barley EARLY FLOWERING 3 contributes to developmental plasticity at elevated temperatures

Increase in ambient temperatures caused by climate change affects various morphological and developmental traits of plants, threatening crop yield stability. In the model plant Arabidopsis thaliana, EARLY FLOWERING 3 (ELF3) plays prominent roles in temperature sensing and thermomorphogenesis signal transduction. However, how crop species respond to elevated temperatures is poorly understood. Here, we show that the barley ortholog of AtELF3 interacts with high temperature to control growth and development. We used heterogeneous inbred family (HIF) pairs generated from a segregating mapping population and systematically studied the role of exotic ELF3 variants in barley temperature responses. An exotic ELF3 allele from Syrian origin promoted elongation growth in barley at elevated temperatures, whereas plant area and estimated biomass were drastically reduced, resulting in an open canopy architecture. The same allele accelerated inflorescence development at high temperature, which correlated with early transcriptional induction of MADS-box floral identity genes BM3 and BM8. Consequently, barley plants carrying the exotic ELF3 allele displayed stable total grain number and mitigated yield loss at elevated temperatures. Our findings therefore demonstrate that exotic ELF3 variants can contribute to phenotypic and developmental acclimation to elevated temperatures, providing a stimulus for breeding of climate resilient crops. HighlightWe demonstrate that an exotic allele of EARLY FLOWERING 3 (ELF3) contributes to plant architectural and developmental acclimation, and thereby improves yield stability at high ambient temperatures.

plant biology↗

bioRxiv2019

Cut and paste - Efficient cotyledon micrografting for Arabidopsis thaliana seedlings

Cotyledon micrografting represents a very useful tool for studying the central role of cotyledons during early plant development, especially their interplay with other plant organs with regard to long distance transport. While hypocotyl grafting methods are established, cotyledon grafting is still inefficient. By optimizing cotyledon micrografting, we aim for higher success rates and increased throughput in the model species Arabidopsis thaliana. We established a cut and paste cotyledon surgery procedure on a flat solid but moist surface which improved handling of small plant seedlings. Applying a specific cutting and joining pattern throughput was increased up to 40 seedlings per hour. The combination of short day conditions and low light intensities for germination and long day plus high light intensities and vertical plate positioning after grafting significantly increased ligation efficiency. Together, we achieved up to 46 % grafting success in A. thaliana. Reconnection of vasculature was shown by successful transport of a vasculature-specific dye across the grafting site. On a whole plant level, plants with grafted cotyledons match plants with intact cotyledons in biomass production and rosette development. This cut and paste cotyledon-to-petiole grafting protocol simplifies the handling of plant seedlings in surgery, increases the number of grafted plants per hour and produces higher success rates for A. thaliana seedlings. The developed cotyledon micrografting method is also suitable for other plant species of comparable size.

plant biology↗