Biology subjects

Quint, M.

Publications and source records attributed to Quint, M..

17 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↗

bioRxiv2026

Molecular and phenotypic footprints of climate in native Arabidopsis thaliana

Climate change poses a major threat to humanity by driving biodiversity loss and reducing crop yields1,2. To understand the molecular and developmental impacts of rising temperatures, plant science has relied heavily on the model organism Arabidopsis thaliana. Despite decades of research, its development under fully natural conditions remains poorly understood, and only [~]30% of genes have experimental functional annotations, largely because many functions are subtle or manifest only in specific laboratory or ecological contexts3. Here, we address this gap with a landscape transcriptomic approach that integrates intensive phenotyping and transcriptomic profiling of naturally occurring plants in their native habitats4. Across two contrasting field sites and five growing seasons (2021-2025), we phenotyped more than 3,000 A. thaliana plants and generated >1,600 matching transcriptomes. The resulting >30,000 quantitative trait measurements provide a unique opportunity to link climate fluctuations with plant traits and gene expression. Seasons characterized by extreme temperature anomalies directly influenced plant traits, and climatic variables together explained up to 17% of phenotypic variation. In situ transcriptomes carried clear temperature and local environmental signatures, closely matching temperature-response programs known from the laboratory. Leveraging paired per-plant transcriptomes and phenotypes, we applied machine learning to predict regulators of climate-relevant and other plant traits under natural conditions. The models recovered canonical thermomorphogenesis regulators, including PHYTOCHROME INTERACTING FACTOR 4 (PIF4)5,6, providing ecological evidence that temperature signaling pathways defined in controlled environments operate in the wild, and expanded this regulatory landscape by identifying hormonal receptors, signaling components, and previously uncharacterized genes, some of which we functionally validated. Together, this work demonstrates that landscape transcriptomics, by integrating natural field transcriptomes with phenotypes, and thus, capturing environmental and regulatory states, enables the predictive identification of genetic regulators of temperature responses and broader plant traits. This makes landscape transcriptomics a scalable framework for climate-aware functional genomics in plants.

plant biology↗

bioRxiv2025

ELF3 controls trait heterogeneity by tuning the rate of maturation in Arabidopsis and barley

Trait heterogeneity in a population increases the likelihood that some individuals will survive an unpredictable environmental stress. Individual plants mature at different rates due to genetics, environmental factors, and random chance. All of this contributes to trait heterogeneity. EARLY FLOWERING3 (ELF3), a core circadian clock component, determines developmental timing, and here we tested the hypothesis that it would shape trait heterogeneity. We developed a model predicting that faster-developing populations exhibit greater heterogeneity during development but reduced heterogeneity at maturity, while slower-growing populations show the opposite pattern. Experiments in Arabidopsis elf3 and barley Hvelf3 mutants supported this prediction. In Arabidopsis, ELF3 controlled hypocotyl elongation variability via maturation rate rather than direct regulation. Bolting time heterogeneity also decreased in faster-growing plants. In barley, Hvelf3 altered growth heterogeneity, but this was initially masked by germination timing differences. Finally, smaller barley plants were found to be more resilient to osmotic stress, suggesting that ELF3-driven trait heterogeneity may contribute to bet hedging. These findings highlight how modifying developmental rates influences population-level trait distributions and stress resilience.

plant biology↗

bioRxiv2024

Hypocotyl Development in Arabidopsis and other Brassicaceae Displays Evidence of Photoperiodic Memory

Sensing and responding to photoperiod changes is essential for plants to adapt to seasonal progression. Most of our understanding of how plants sense photoperiodic changes is through studies on flowering time. However, other aspects of plant development are regulated by the photoperiod, including hypocotyl elongation. Unlike flowering, hypocotyl elongation displays a greater plasticity to changes in the photoperiod with increases in daylength causing greater inhibition of growth until a threshold is met. Previous studies have only looked at hypocotyl development in the context of a stationary photoperiod. It is unknown if changes in the photoperiod during development influence hypocotyl elongation. Here, we developed a physiological assay to investigate this question. We have discovered that hypocotyl elongation is influenced by a memory of past photoperiod exposure in Arabidopsis and Brassicaceae cultivars used for microgreen agriculture. Photoperiodic memory persisted for multiple days, although it weakened over time, and the strength of the memory was dependent on the genetic background. We identified that phyB and ELF3, key regulators of hypocotyl development, were required for photoperiodic memory. Finally, we identified that the circadian clock is unlikely to function as a repository for photoperiodic memory as circadian rhythms quickly re-aligned with the new photoperiod. In summary, our work highlights for the first-time evidence of a photoperiodic memory that can control plant development.

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↗

bioRxiv2023

Complex epistatic interactions between ELF3, PRR9, and PRR7 regulates the circadian clock and plant physiology

Circadian clocks are endogenous timekeeping mechanisms that coordinate internal physiological responses with the external environment. EARLY FLOWERING3 (ELF3), PSEUDO RESPONSE REGULATOR (PRR9), and PRR7 are essential components of the plant circadian clock and facilitate entrainment of the clock to internal and external stimuli. Previous studies have highlighted a critical role for ELF3 in repressing the expression of PRR9 and PRR7. However, the functional significance of activity in regulating circadian clock dynamics and plant development is unknown. To explore this regulatory dynamic further, we firstly employed mathematical modelling to simulate the effect of the prr9/prr7 mutation on the elf3 circadian phenotype. These simulations suggested that simultaneous mutations in prr9/prr7 could rescue the elf3 circadian arrythmia. Following these simulations, we generated all Arabidopsis elf3/prr9/prr7 mutant combinations and investigated their circadian and developmental phenotypes. Although these assays could not replicate the results from the mathematical modelling, our results have revealed a complex epistatic relationship between ELF3 and PRR9/7 in regulating different aspects of plant development. ELF3 was essential for hypocotyl development under ambient and warm temperatures, while PRR9 was critical for root thermomorphogenesis. Finally, mutations in prr9 and prr7 rescued the photoperiod insensitive flowering phenotype of the elf3 mutant. Together, our results highlight the importance of investigating the genetic relationship amongst plant circadian genes.

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↗

bioRxiv2022

Exotic alleles of EARLY FLOWERING 3 determine plant development and grain yield in barley

EARLY FLOWERING 3 (ELF3) is an important regulator of various physiological and developmental processes and hence may serve to improve plant adaptation which will be substantial for future plant breeding. To expand the limited knowledge on barley ELF3 in determining agronomic traits, we conducted field studies with heterogeneous inbred families (HIFs) derived from selected lines of the wild barley nested association mapping population HEB-25. During two growing seasons, phenotypes of nearly isogenic HIF sister lines, segregating for exotic and cultivated alleles at the ELF3 locus, were compared for ten developmental and yield-related traits. We determine novel exotic ELF3 alleles and show that HIF lines, carrying the exotic ELF3 allele, accelerated plant development compared to the cultivated ELF3 allele, depending on the genetic background. Remarkably, the most extreme phenotypic effects could be attributed to one exotic ELF3 allele, differing in only one SNP from the cultivated Barke ELF3 allele. This SNP causes an amino acid change, which predictively has an impact on the protein structure of ELF3, thereby possibly affecting phase separation behaviour and nano-compartment formation of ELF3 and, potentially, also affecting its local cellular interactions causing significant trait differences between HIF sister lines.

genetics↗

bioRxiv2022

Auxin-dependent acceleration of cell division rates regulates root growth at elevated temperature

Roots are highly plastic organs enabling plants to acclimate to a changing below-ground environment. In addition to abiotic factors like nutrients or mechanical resistance, plant roots also respond to temperature variation. Below the heat stress threshold, Arabidopsis thaliana seedlings react to elevated temperature by promoting primary root growth, possibly to reach deeper soil regions with potentially better water saturation. While above-ground thermomorphogenesis is enabled by thermo-sensitive cell elongation, it was unknown how temperature modulates root growth. We here show that roots are able to sense and respond to elevated temperature independent of shoot-derived signals. A yet unknown root thermosensor seems to employ auxin as a messenger to promote primary root growth. Growth is primarily achieved by accelerating cell division rates in the root apical meristem, likely maintained via temperature-sensitive organization of the polar auxin transport system. Hence, the primary cellular target of elevated ambient temperature differs fundamentally between root and shoot tissues, while the messenger auxin that relays temperature information to elongating or dividing cells, respectively, remains the same.

plant biology↗

bioRxiv2021

High temperature perception in leaves promotes vascular regeneration in distant tissues

Cellular regeneration in response to wounding is fundamental to maintain tissue integrity. Various internal factors including hormones and developmental pathways affect wound healing but little is known about how external factors influence regeneration. To better understand how the environment affects regeneration, we investigated the effects of temperature using the horticulturally relevant process of plant grafting. We found that elevated temperatures accelerated vascular regeneration of Arabidopsis thaliana and tomato (Solanum lycopersicum) grafts. Leaves were critical for this effect since blocking auxin transport or mutating PHYTOCHROME INTERACTING FACTOR4 (PIF4) or YUCCA2/5/8/9 in the cotyledons abolished the temperature enhancement. However, these perturbations had no effect upon graft healing at ambient temperatures and mutations in PIF4 did not affect the temperature enhancement of callus formation or tissue adhesion, suggesting that leaf-derived auxin was specific for enhancing vascular regeneration in response to elevated temperatures. Tissue-specific perturbations of auxin response using a BODENLOS (BDL) mutant revealed an asymmetric effect of temperature upon regeneration: the presence of bdl above the cut prevented temperature enhancement whereas the presence of bdl below the cut prevented graft healing regardless of temperature. Promotion of tissue regeneration by elevated temperatures was not specific for graft healing and we found that elevated temperatures accelerated xylem formation between the parasite Phtheirospermum japonicum and host Arabidopsis thaliana, and this effect required shoot-derived auxin from the parasite. Taken together, our results identify a pathway by which elevated temperatures accelerate vascular development which could be of relevance for improving regeneration and better understanding inter-plant vascular connections.

plant biology↗

bioRxiv2021

Bacterial-type plant ferroxidases tune local phosphate sensing in root development

Fluctuating bioavailability of inorganic phosphate (Pi), often caused by complex Pi-metal interactions, guide root tip growth and root system architecture for maximizing the foraged soil volume. Two interacting genes in Arabidopsis thaliana, PDR2 (P5-type ATPase) and LPR1 (multicopper oxidase), are central to external Pi monitoring by root tips, which is modified by iron (Fe) co-occurrence. Upon Pi deficiency, the PDR2-LPR1 module facilitates cell type-specific Fe accumulation and cell wall modifications in root meristems, inhibiting intercellular communication and thus root growth. LPR1 executes local Pi sensing, whereas PDR2 restricts LPR1 function. We show that native LPR1 displays specific ferroxidase activity and requires a conserved acidic triad motif for high-affinity Fe2+ binding and root growth inhibition under limiting Pi. Our data indicate that substrate availability tunes LPR1 function and implicate PDR2 in maintaining Fe homeostasis. LPR1 represents the prototype of an ancient ferroxidase family, which evolved very early upon bacterial colonization of land. During plant terrestrialization, horizontal gene transfer transmitted LPR1-type ferroxidase from soil bacteria to the common ancestor of Zygnematophyceae algae and embryophytes, a hypothesis supported by homology modeling, phylogenomics, and activity assays of bacterial LPR1-type multicopper oxidases.

plant biology↗

bioRxiv2020

EARLY FLOWERING 3 controls temperature responsiveness of the circadian clock

Predictable changes in light and temperature during a diurnal cycle are major entrainment cues that enable the circadian clock to generate internal biological rhythms that are synchronized with the external environment. With the average global temperature predicted to keep increasing, the intricate light-temperature coordination that is necessary for clock functionality is expected to be seriously affected. Hence, understanding how temperature signals are perceived by the circadian clock has become an important issue, especially in light of climate change scenarios. In Arabidopsis, the clock component EARLY FLOWERING 3 (ELF3) not only serves as an essential light Zeitnehmer, but also functions as a thermosensor participating in thermomorphogenesis. However, the role of ELF3 in temperature entrainment of the circadian clock is not fully understood. Here, we report that ELF3 is essential for delivering temperature input to the clock. We demonstrate that in the absence of ELF3, the oscillator was unable to properly respond to temperature changes, resulting in an impaired gating of thermoresponses. Consequently, clock-controlled physiological processes such as rhythmic growth and cotyledon movement were disturbed. Together, our results reveal that ELF3 is an essential Zeitnehmer for temperature sensing of the oscillator, and thereby for coordinating the rhythmic control of thermoresponsive physiological outputs.

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↗

bioRxiv2018

Photoperiod sensing of the circadian clock is controlled by ELF3 and GI

ELF3 and GI are two important components of the Arabidopsis circadian clock. They are not only essential for the oscillator function but are also pivotal in mediating light inputs to the oscillator. Lack of either results in a defective oscillator causing severely compromised output pathways, such as photoperiodic flowering and hypocotyl elongation. Although single loss of function mutants of ELF3 and GI have been well-studied, their genetic interaction remains unclear. We generated an elf3 gi double mutant to study their genetic relationship in clock-controlled growth and phase transition phenotypes. We found that ELF3 and GI repress growth differentially during the night and the day, respectively. Circadian clock assays revealed that ELF3 and GI are essential Zeitnehmers that enable the oscillator to synchronize the endogenous cellular mechanisms to external environmental signals. In their absence, the circadian oscillator fails to synchronize to the light-dark cycles even under diurnal conditions. Consequently, clock-mediated photoperiod-responsive growth and development is completely lost in plants lacking both genes, suggesting that ELF3 and GI together convey photoperiod sensing to the central oscillator. Since ELF3 and GI are conserved across flowering plants and represent important breeding and domestication targets, our data highlight the possibility of developing photoperiod-insensitive crops by adjusting the allelic combination of these two key genes.\n\nOne sentence summaryELF3 and GI are essential for circadian clock mediated photoperiod sensing.

plant biology↗

bioRxiv2017

Young Genes To The Front -- A Strategy For Future Resistance Against Powdery Mildew?

Nonhost resistance of a plant against a microbial pathogen can be the result of a long-lasting coevolutionary optimization of resource allocation in both host and pathogen. Although this has been suggested for years, coevolutionary aspects leading to nonhost resistance in plants are not fully understood yet. Instead, most studies focus on limited subsets of genes which are differentially expressed in infected plants to describe details of defense strategies and symptoms of diseases.\n\nHere, we exploit publicly available whole genome gene expression data and combine them with evolutionary characteristics of genes to uncover a mechanism of host-pathogen coevolution. Our results suggest that metabolic efficiency in gene regulation is a key aspect leading to nonhost resistance. In addition, we find that progressing host-pathogen coevolution is accompanied by subtle, but systematic overexpression of recently founded genes. In support of our plant-specific data, we observe similar effects in animal species.

evolutionary biology↗