Julius Kühn-Institut

We used domestication as an in vivo replicated experiment to investigate how divergent selection has shaped the evolution of multivariate phenotypic spaces. We measured 11-57 qualitative and quantitative traits in 13 species, either unique or shared between species, and established a framework for cross-species comparisons. Our results revealed significant convergence that translated into a cross-species domestication syndrome. Most species exhibited a reduction of the multivariate phenotypic space during domestication. We brought evidence that Near-Infrared spectra measured on leaves reflect phenotypic evolution unrelated to domestication, enabling its use as a control for sampling effects across species. Building on this, we developed a multivariate phenotypic divergence index (mPDI) to rank species by the extent of phenotypic divergence under domestication. We found a high disjunction of wild and domestic phenotypic spaces in all species. Neither the mPDI nor the relative size of wild vs domestic multivariate phenotypic spaces was influenced by the domestication timing or mating system. Lastly, we observed a progressive decoupling of trait correlations with increasing time since domestication. In addition to introducing a new index that can be applied for cross-species comparisons, our study uncovers recurring patterns shared among species, pointing to general principles underlying plant domestication.

Hi-C data is commonly used for reference-free de novo scaffolding. However, with the rapid increase in high-quality reference genomes, reference-guided workflows are now more practical for assembling large numbers of target genomes without relying on costly and labor-intensive Hi-C sequencing. Recently, a pangenome graph-based haplotype sampling algorithm was introduced to generate personalized graphs for target genomes. Such graphs have strong potential as references for reference-guided contig scaffolding. Here, we present noHiC, a reference-guided scaffolding pipeline supporting key steps of plant contig scaffolding. A distinctive feature of noHiC is the nohic-refpick script, generating a best-fit synthetic reference (synref) from a pangenome graph that is genetically close to the target contigs. This enables the integration of genetic information from many references (up to 48 in our tests) without using them separately during scaffolding. Synrefs showed advantages over highly contiguous conventional references in reducing false contig breaking during reference-based correction. Additionally, nohic-refpick can be combined with fast scaffolders (ntJoin) to rapidly produce highly contiguous assemblies using synrefs derived from pangenome graphs. The noHiC pipeline, used alone or in combination with ntJoin, can generally produce assemblies that are structurally consistent with public Hi-C-based or manually curated genomes. The pipeline is publicly available at https://github.com/andyngh/noHiC.

Nitrous oxide (N2O) is one of the most relevant anthropogenic greenhouse gases, mainly produced in agricultural soils. Understanding the mechanisms responsible for N2O production and consumption is crucial for developing N2O mitigation strategies in croplands but field studies combining N2O flux measurements with isotopocule signatures and metagenomic analysis are very rare.With the aim to clarify how isotopic signatures and functional genes can help explaining N2O fluxes in a cropland, we conducted a two years study, from February 2023 to January 2025, at the Reinshof experimental farm of the University of Göttingen in Germany (51.49° N, 9.93° E). The crop sequence was sugar beet, winter wheat and winter barley.We measured N2O fluxes with eight manually-operated static chambers and gas chromatography and additionally collected samples for analysis of N2O isotopocule signatures. We applied FRAME, a three-dimensional model based on 15N site preference, bulk 15N and 18O isotopic signatures to distinguish between the source processes (bacterial denitrification, nitrifier denitrification, fungal denitrification, nitrification) and to estimate the reduction of N2O to N2.We regularly monitored soil water content, mineral nitrogen (Nmin) and dissolved organic carbon (DOC). Additionally, every four months we collected soil samples for real-time quantitative polymerase chain reaction (qPCR)-based quantification of bacterial and fungal DNA, as well as functional genes involved in nitrification (ammonia-oxidizing archaea and bacteria amoA genes) and denitrification (nirK, nirS, and nosZ clade I and II).We observed mean N2O fluxes of 19.8 µg N2O-N m-2 h-1. Individual chamber measurements ranged from -26.7 to 573.1 µg N2O-N m-2 h-1. The spatial variability between chambers within one day showed a high coefficient of variation of 123%. N2O fluxes increased after fertilization, rewetting and harvest while highest fluxes occurred after a freeze-thawing event. Cumulative fluxes showed that 0.97% of applied fertilizer N was emitted as N2O-N. We observed a significant positive effect of soil moisture on N2O fluxes, no significant effect of Nmin and a significant negative effect of DOC.Preliminary results showed that bacterial denitrification was the dominant process responsible for N2O production. As N2O fluxes increased, the proportion of bacterial denitrification increased while the proportion of nitrification decreased. Following freeze-thawing, there was more bacterial denitrification than after the fertilization events and very little fungal denitrification. Overall, the residual N2O fraction of 45.9 ± 15.0% suggested extensive nitrogen loss as N2 via denitrification. The dominance of nosZ over nirK and nirS further implied substantial conversion of nitrogen to N₂.In addition, bacterial DNA was more abundant than fungal DNA, and denitrifiers were more abundant than nitrifiers. No clear differences in processes or gene copy numbers were observed between chambers. Seasonally, gene copy numbers of most functional genes were higher during the growing season and lower in winter, consistent with higher N₂O fluxes during the growing season and lower fluxes in winter.In future analysis, we will show how soil characteristics, isotopic signatures, and functional genes jointly shape the spatial and temporal variation of the measured N2O fluxes.

Abstract Stripe rust, caused by Puccinia striiformis f. sp. tritici , significantly reduces wheat ( Triticum aestivum L.) yields when uncontrolled. This study developed predictive models for stripe rust severity using weather variables. Field experiments were conducted from 2017 to 2019 at the Research Farm, Chatha, using susceptible wheat variety PBW 343 in a randomized block design with four replications. Disease severity was assessed weekly using the modified Cobb scale. Additional historical weather and disease data from 2005 to 2017 were incorporated to develop comprehensive forecasting models. Strong positive correlations were observed between disease severity and maximum temperature ( r = 0.89–0.91) and minimum temperature ( r = 0.75–0.91), while morning relative humidity showed negative correlation ( r = −0.80). Rainfall exhibited no significant correlation with disease progression. Two multiple linear regression models were developed: for 2005–2017, Y = −502.14 + 0.64 X 1 + 8.57 X 2 + 3.04 X 3 + 1.42 X 4 + 0.58 X 5 ; and for 2017–2019, Y = 322.57 + 9.41 X 1 − 4.14 X 2 − 2.56 X 3 − 0.71 X 4 + 0.26 X 5 , where Y represents disease severity and X 1 – X 5 represent weather parameters. Both models explained approximately 89%–91% of variation in disease severity. Spore concentration increased 84% from 51st to seventh standard meteorological week during 2017–2019. These models provide quantitative tools for predicting stripe rust severity using readily available weather data, enabling timely disease management decisions and supporting sustainable wheat production.

Viruses transmitted by the obligate biotrophic parasite Polymyxa graminis cause substantial losses in agriculture worldwide. A better knowledge of the infection process may lead to the identification of novel strategies for virus control. The coat protein readthrough (CP-RT) protein or its homologs, present in all P. graminis-transmitted viruses, are transmission factors of the viruses. To better characterize CP-RT function, we modified an infectious Japanese soil-borne wheat mosaic virus (JSBWMV) cDNA clone to express fluorescent protein-tagged CP-RT and analyzed the protein during infection in the model host plant Nicotiana benthamiana. We found that JSBWMV CP-RT localized to and self-interacted at the endoplasmic reticulum (ER) network and in small cortical particles during infection. The particles moved along the ER network and associated with sub-ER sites, most likely ER import sites, as indicated by co-localization with Sar1-GTP:GFP and AtSYP72:GFP. Particles were still present after reabsorption of the Golgi into the ER network after Brefeldin A treatment, thus they were not an intrinsic part of the Golgi-ER compartment. In natural CP-RT deletion mutants, the localization to the ER network was lost, while localization to the particles was maintained. Consistent with earlier data our findings from transmission experiments in hydroponic barley culture indicate that an intact JSBWMV CP-RT may be important for virus transmission by the vector, as more wild type CP-RT forms compared to mutant CP-RT forms accumulated in newly infected plants. ER-association of CP-RT may thus be important for virus transmission and early infection processes.

Pollinators are a diverse group of organisms – insects, mammals, birds and, to a lesser extent, amphibians, reptiles and even snails – that support plant communities and are the foundation of global food systems. Scientific research over the past 10-20 years has clearly shown that in some parts of the world they are declining, leading to significant changes in ecosystem functioning. Despite the great interest of a large number of scientific teams around the world in studying various aspects of pollinators and pollination processes, there are still not enough specialised academic journals whose main focus is this. The journal “Advances in Pollinator Research” (APR) was founded to transform the way pollinator science is published and shared, and consequently translated into real action. APR offers the scientific community an opportunity to publish in a state-of-the-art way biological, ecological, socio-economic and management aspects of pollinator health. The journal bridges basic and applied science, linking molecular biology, ecology, evolution, conservation, agroecology, ecosystem services, behavioural, economic, and social sciences with policy development, agricultural management, commercial pollinator management practices, and community-based conservation.

In course of investigating the endophytic and nematode-associated fungus Polydomus karssenii for the production of secondary metabolites, seven previously undescribed natural products were isolated from liquid and solid-state fermentations. 1D and 2D NMR spectroscopy, together with HR-ESI–MS data, enabled the elucidation of the planar structures of 3-decalinoyltetramic acids polydosetins A–E (1–5) and cyclodepsipeptides pullularins G and H (6 and 7). The relative configurations of the decalin moiety of 1–5 were determined based on ROESY correlations and 1H–1H coupling constants. The configuration of the side chains was established through a detailed J-resolved analysis (Murata’s method) in combination with chemical shift comparison to model compounds. Absolute stereochemistry of 1–5 was assigned based on ECD data, and confirmed by Mosher’s method utilizing 3. Finally, the absolute configuration of amino acid residues in 6 and 7 was determined through advanced Marfey’s method. Bioassays revealed that compounds 1, 3, 5, and 7 were active against Gram-positive bacteria, 3 and 5 exhibited antifungal activity, and 1 and 2 showed nematicidal effects. These results underscore the untapped chemical potential of P. karssenii and highlight the importance of exploring nematode-associated fungi as sources of new natural products with potential antimicrobial and nematicidal properties.Supplementary InformationThe online version contains supplementary material available at 10.1007/s13659-025-00579-8.

The box tree pyralid moth ( Cydalima perspectalis ), which originates from Asia and has been introduced to Europe in 2006, has now infested several countries and continents outside its natural distribution. This herbivore is specialized on Buxus spp. and has destroyed not only many ornamental plantings, which are often of historical value, but also boxwood in its natural range, where it is often part of certain forest types. To date, no effective natural enemies are known, and plantings can only be saved by frequent insecticide applications, while natural boxwoods are threatened or have already gone extinct after massive outbreaks of this pest. During a monitoring in 2025, we discovered a parasitoid population in one of the first infested natural Buxus spp. stands in Europe, the boxwood forest near Grenzach-Wyhlen, Germany. According to our data, this Campoplegine larval parasitoid, Eriborus sp., is not native, but may have been accidentally introduced in the years after the introduction of its host nearby.

<title>Abstract</title> The emergence of a new corn ear rot was recently described in Germany and has since received increased attention following detections in several European and Asian countries. All reports consistently identify <italic>Trichoderma afroharzianum</italic> as the causal agent. The potential impact on maize production, combined with the risk of misdiagnosis as other ear rot diseases, highlights the need for a rapid and accurate diagnostic method for the reliable detection of <italic>T. afroharzianum</italic> . In this study, we developed PCR-based diagnostic tools including an endpoint PCR and a real-time TaqMan assay targeting the TEF1α and RPB2 loci, respectively. Both assays were validated using a broad panel of <italic>Trichoderma</italic> isolates and other fungal species obtained from maize plants, additional host species from diverse geographic origins, and soils collected from German maize fields. All performance criteria required to demonstrate assay reliability were met. The assays showed high accuracy and sensitivity, with limits of detection of 1 pg for the endpoint PCR and 1 fg per reaction for the real-time PCR. The real-time assay exhibited amplification efficiencies of 105% (R² = 0.98) for pure cultures and 118% (R² = 0.998) for infected maize kernels. Furthermore, both assays reliably detected <italic>T. afroharzianum</italic> in asymptomatic maize cobs following artificial inoculation with pathogenic strains. These methods therefore enable early and reliable detection of <italic>T. afroharzianum</italic> ear rot and allow its discrimination from other maize ear rot diseases. This capability is essential for the development of targeted management strategies to address this emerging threat to maize production.

Drought stress events are becoming more frequent and intense worldwide, leading to significant yield losses in crops like barley, which is a major concern for farmers. Drought stress is a complex and strongly quantitative, influenced by factors such as the timing, severity, and duration of the stress. Therefore, identifying traits responsible for drought stress tolerance of specific barley genotypes is essential. However, traits that are advantageous for tolerance to late drought stress may not be the same as those for early drought stress and vice versa. Some traits might even have disadvantageous effects at other developmental stages. While most drought stress studies have focused on late-stage drought stress, this thesis aims to investigate physiological, metabolic, and yield-related traits in a diverse set of spring barley genotypes to identify trait inter-relationships and those most associated with early drought stress tolerance. First, eleven genotypes were screened for their root behavior under drought stress in a hydroponic system for four weeks using polyethylene glycol (PEG) as an osmotic stressor. One main result was that PEG consistently increased root diameter compared to the control treatment. When comparing PEG-treated roots with those grown in sand-filled pots where drought stress was induced by reduced watering, the drought-stressed roots had a significantly (P &lt; 0.05) smaller root diameter than those in the control treatment. Furthermore, the shoot biomass of plants grown in sand pots showed a stronger correlation with field conditions than that of PEG-treated plants. Thus, a key finding of this study was that PEG is unsuitable for screening barley root traits related to early drought stress tolerance. The second part of this work was the analysis of a diverse set of 40 spring barley genotypes for their early drought stress performance (BBCH 13 - BBCH 53) in a greenhouse experiment. Based on their trait performances, the genotypes were classified into different drought stress tolerance groups (sensitive, neutral, tolerant). Thereafter, the traits that best characterized the drought-tolerant group were identified. Thereby, drought stress tolerance was defined by a high grain biomass (i.e., yield). In addition to a higher grain biomass, the drought-tolerant genotypes were characterized by a significantly (P &lt; 0.05) higher water uptake during the recovery phase and a lower accumulation of proline and soluble sugars in the flag leaf as well as a lower osmolality compared to the neutral and sensitive genotypes. In addition to a significantly (P &lt; 0.05) increased accumulation of the aforementioned metabolites, the sensitive genotypes also showed a significant (P &lt; 0.05) higher water use efficiency (WUE) during drought stress and recovery phase. Afterwards, ten genotypes, representing each drought tolerance group, were selected for further investigations under field conditions to verify the trait performances and inter-relationships observed in the greenhouse. In this respect, significant positive correlations of the trait under drought stress between greenhouse and field conditions were observed for yield-related traits such as full ears (r = 0.58, P &lt; 0.05), grains per ear (r = 0.84, P &lt; 0.05), and grain biomass (r = 0.41, P &lt; 0.05). Surprisingly, proline content was significantly negative correlated to grain biomass under greenhouse condition and field conditions, respectively (r = -0.66, P &lt; 0.05, and r = -0.55, P &lt; 0.05), although proline is often mentioned in context with drought stress tolerance. These results emphasize the importance of continuing early drought stress experiments until maturity as a specific trait performance during the early drought stress period could only be properly assessed in this way. The third part of this work investigated a new and much-debated approach: the use of "biologicals", which are products of natural origin (e.g., microorganisms, plants) that are discussed to improve drought stress tolerance. Here, four biologicals were tested in detail regarding their effect under drought stress on molecular, physiological, yield and quality level. A first important result was that the effect of a biological highly (P &lt; 0.001) depended on the genotype in all environments. Drought stress-responsive genes Dhn1 and HvA1 associated with abscisic acid pathways were downregulated by biologicals in those genotypes, which showed a significant (P &lt; 0.05) yield increase for the same biologicals under drought stress. Interestingly, trait inter-relationships were influenced by the application of biologicals. Regarding the physiological and yield-related traits, the effect of biologicals on drought stress was strongly dependent on the environment and the biological itself. Thereby, most significant effects were observed for Cropcover and Giant knotweed. There, higher and more significant (P &lt; 0.05) effects among all genotypes on yield were observed in the greenhouse (30.5%) than under field conditions (14.1%). This work provides: 1) a deeper understanding of the effects of early drought stress in spring barley, and 2) new insights into the effects and modes of action of biologicals in improving early drought stress tolerance.