Institut für Kulturpflanzenwissenschaften

Permanent URI for this collectionhttps://hohpublica.uni-hohenheim.de/handle/123456789/12

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Bayesian‐optimized experimental designs for estimating the economic optimum nitrogen rate: a model‐averaging approach
(2025) Matavel, Custódio Efraim; Meyer‐Aurich, Andreas; Piepho, Hans‐Peter
Field experiments play a crucial role in optimizing nutrient application strategies and determining the economic optimum nitrogen rate (EONR), aiding stakeholders in agricultural decision‐making. These experiments tailor agricultural input management to maximize efficiency and sustainability, ultimately improving farm economics. However, the optimal setup of field experiments remains an ongoing debate, particularly regarding economic considerations such as the selection of treatment levels (design points), their spatial arrangement, and the number of replications required for statistical validity and cost‐effectiveness. This study optimizes field experiments for estimating the EONR using a model‐averaging approach within a Bayesian framework. We employed Bayesian inference and the No‐U‐turn sampler to integrate model averaging across multiple yield response models, improving robustness in EONR estimation. Stochastic optimization, specifically simultaneous perturbation stochastic approximation, was used to optimize experimental designs, and their performance was evaluated through Monte Carlo simulations. Our results show that optimized experimental designs significantly improve the precision of EONR estimates. Designs incorporating higher number of nitrogen levels provided the best trade‐off between accuracy and efficiency, minimizing bias and mean squared error. Even with a fixed total number of plots (120), increasing the number of design points resulted in lower variance, demonstrating the efficiency of well‐structured experimental designs. This research lays the groundwork for future developments in experimental methodologies with wide‐ranging implications for agricultural economics and policymaking, ultimately supporting better‐informed decision‐making. Future work should integrate environmental constraints and account for real‐world variability in treatment replication to further refine experimental optimization strategies.
Breeding progress of disease resistance and impact of disease severity under natural infections in winter wheat variety trials
(2021) Laidig, F.; Feike, T.; Hadasch, S.; Rentel, D.; Klocke, B.; Miedaner, T.; Piepho, H. P.
Key message: Breeding progress of resistance to fungal wheat diseases and impact of disease severity on yield reduction in long-term variety trials under natural infection were estimated by mixed linear regression models. Abstract: This study aimed at quantifying breeding progress achieved in resistance breeding towards varieties with higher yield and lower susceptibility for 6 major diseases, as well as estimating decreasing yields and increasing disease susceptibility of varieties due to ageing effects during the period 1983–2019. A further aim was the prediction of disease-related yield reductions during 2005–2019 by mixed linear regression models using disease severity scores as covariates. For yield and all diseases, overall progress of the fully treated intensity (I2) was considerably higher than for the intensity without fungicides and growth regulators (I1). The disease severity level was considerably reduced during the study period for mildew (MLD), tan spot (DTR) and Septoria nodorum blotch (ear) (SNB) and to a lesser extent for brown (leaf) rust (BNR) and Septoria tritici blotch (STB), however, not for yellow/stripe rust (YLR). Ageing effects increased susceptibility of varieties strongly for BNR and MLD, but were comparatively weak for SNB and DTR. Considerable yield reductions under high disease severity were predicted for STB (−6.6%), BNR (−6.5%) and yellow rust (YLR, −5.8%), but lower reductions for the other diseases. The reduction for resistant vs. highly susceptible varieties under high severity conditions was about halved for BNR and YLR, providing evidence of resistance breeding progress. The empirical evidence on the functional relations between disease severity, variety susceptibility and yield reductions based on a large-scale multiple-disease field trial data set in German winter wheat is an important contribution to the ongoing discussion on fungicide use and its environmental impact.
Do lower nitrogen fertilization levels require breeding of different types of cultivars in triticale?
(2022) Neuweiler, Jan E.; Trini, Johannes; Maurer, Hans Peter; Würschum, Tobias
Breeding high-yielding, nitrogen-efficient crops is of utmost importance to achieve greater agricultural sustainability. The aim of this study was to evaluate nitrogen use efficiency (NUE) of triticale, investigate long-term genetic trends and the genetic architecture, and develop strategies for NUE improvement by breeding. For this, we evaluated 450 different triticale genotypes under four nitrogen fertilization levels in multi-environment field trials for grain yield, protein content, starch content and derived indices. Analysis of temporal trends revealed that modern cultivars are better in exploiting the available nitrogen. Genome-wide association mapping revealed a complex genetic architecture with many small-effect QTL and a high level of pleiotropy for NUE-related traits, in line with phenotypic correlations. Furthermore, the effect of some QTL was dependent on the nitrogen fertilization level. High correlations of each trait between N levels and the rather low genotype-by-N-level interaction variance showed that generally the same genotypes perform well over different N levels. Nevertheless, the best performing genotype was always a different one. Thus, selection in early generations can be done under high nitrogen fertilizer conditions as these provide a stronger differentiation, but the final selection in later generations should be conducted with a nitrogen fertilization as in the target environment.
Drought impacts on plant–soil carbon allocation - integrating future mean climatic conditions
(2025) Leyrer, Vinzent; Blum, Juliette; Marhan, Sven; Kandeler, Ellen; Zimmermann, Telse; Berauer, Bernd J.; Schweiger, Andreas H.; Canarini, Alberto; Richter, Andreas; Poll, Christian
Droughts affect soil microbial abundance and functions—key parameters of plant–soil carbon (C) allocation dynamics. However, the impact of drought may be modified by the mean climatic conditions to which the soil microbiome has previously been exposed. In a future warmer and drier world, effects of drought may therefore differ from those observed in studies that simulate drought under current climatic conditions. To investigate this, we used the field experiment ‘Hohenheim Climate Change,’ an arable field where predicted drier and warmer mean climatic conditions had been simulated for 12 years. In April 2021, we exposed this agroecosystem to 8 weeks of drought with subsequent rewetting. Before drought, at peak drought, and after rewetting, we pulse‐labelled winter wheat in situ with 13CO2 to trace recently assimilated C from plants to soil microorganisms and back to the atmosphere. Severe drought decreased soil respiration (−35%) and abundance of gram‐positive bacteria (−15%) but had no effect on gram‐negative bacteria, fungi, and total microbial biomass C. This pattern was not affected by the mean precipitation regime to which the microbes had been pre‐exposed. Reduced mean precipitation had, however, a legacy effect by decreasing the proportion of recently assimilated C allocated to the microbial biomass C pool (−50%). Apart from that, continuous soil warming was an important driver of C fluxes throughout our experiment, increasing plant biomass, root sugar concentration, labile C, and respiration. Warming also shifted microorganisms toward utilizing soil organic matter as a C source instead of recently assimilated compounds. Our study found that moderate shifts in mean precipitation patterns can impose a legacy on how plant‐derived C is allocated in the microbial biomass of a temperate agroecosystem during drought. The overarching effect of soil warming, however, suggests that how temperate agroecosystems respond to drought will mainly be affected by future temperature increases.
Early prediction of biomass in hybrid rye based on hyperspectral data surpasses genomic predictability in less-related breeding material
(2021) Galán, Rodrigo José; Bernal-Vasquez, Angela-Maria; Jebsen, Christian; Piepho, Hans-Peter; Thorwarth, Patrick; Steffan, Philipp; Gordillo, Andres; Miedaner, Thomas
Key message: Hyperspectral data is a promising complement to genomic data to predict biomass under scenarios of low genetic relatedness. Sufficient environmental connectivity between data used for model training and validation is required. Abstract: The demand for sustainable sources of biomass is increasing worldwide. The early prediction of biomass via indirect selection of dry matter yield (DMY) based on hyperspectral and/or genomic prediction is crucial to affordably untap the potential of winter rye (Secale cereale L.) as a dual-purpose crop. However, this estimation involves multiple genetic backgrounds and genetic relatedness is a crucial factor in genomic selection (GS). To assess the prospect of prediction using reflectance data as a suitable complement to GS for biomass breeding, the influence of trait heritability ( ) and genetic relatedness were compared. Models were based on genomic (GBLUP) and hyperspectral reflectance-derived (HBLUP) relationship matrices to predict DMY and other biomass-related traits such as dry matter content (DMC) and fresh matter yield (FMY). For this, 270 elite rye lines from nine interconnected bi-parental families were genotyped using a 10 k-SNP array and phenotyped as testcrosses at four locations in two years (eight environments). From 400 discrete narrow bands (410 nm–993 nm) collected by an uncrewed aerial vehicle (UAV) on two dates in each environment, 32 hyperspectral bands previously selected by Lasso were incorporated into a prediction model. HBLUP showed higher prediction abilities (0.41 – 0.61) than GBLUP (0.14 – 0.28) under a decreased genetic relationship, especially for mid-heritable traits (FMY and DMY), suggesting that HBLUP is much less affected by relatedness and . However, the predictive power of both models was largely affected by environmental variances. Prediction abilities for DMY were further enhanced (up to 20%) by integrating both matrices and plant height into a bivariate model. Thus, data derived from high-throughput phenotyping emerges as a suitable strategy to efficiently leverage selection gains in biomass rye breeding; however, sufficient environmental connectivity is needed.
Improving cover crop mixtures to increase soil carbon inputs and weed suppression as a tool to promote yield potential
(2024) Groß, Jonas; Müller, Torsten
Arable cropping systems are facing challenges imposed by climate change and are, at the same time, a tool to mitigate climate change. Soils are essential in securing yield potential and acting as a carbon sink. Recognizing small-scale site-specific differences in crop management and integrating cover crops, which provide ecosystem services such as carbon sequestration and weed suppression, are two approaches to climate-smart agriculture. To investigate site-specific soil heterogeneity, soil properties were analyzed in a field trial, measuring at three soil depths in 42 plots to determine their influence on yield measures. Soil organic carbon, silt, and clay contents in both topsoil and subsoil explained 45-46% of the variability in grain yield. Additionally, a positive correlation was found between increasing clay content in the topsoil and grain yield and tiller density. A higher clay content in the subsoil resulted in a decrease in grain yield. Soil organic carbon was identified as a soil property that positively influences yield and yield formation at any soil depth through multiple regressions and cluster analysis. Soil organic carbon is a critical soil measure that can significantly improve yield potential and can be manipulated by crop management practices like cover cropping. In a second field experiment, the impacts of increasing plant diversity of cover crop mixtures on rhizosphere carbon input and microbial utilization were investigated. A comparison was made between Mustard (Sinapis alba L.) planted as a sole crop and diversified cover crop mixtures of four (Mix4) or twelve (Mix12) species. A 13C-pulse labeling field experiment traced C transfer from shoots to roots to the soil microbial community. Mix 4 doubled the net CO2-C removal from the atmosphere, while Mix 12 more than tripled it, indicating that plant diversity positively impacts carbon cycling. This is reflected in higher atmospheric C uptake, higher transport rates to the rhizosphere, higher microbial incorporation, and longer residence time in the soil environment, improving the efficiency of C cycling in cropping systems. Root C-transfer could be identified as a fast pathway for C to reach soil C-compartments, but a substantial share of atmospheric C-catch comes from shoot biomass. In a third field experiment, the influence of species combination on shoot biomass formation was systematically assessed by investigating species interactions in dual cover crop mixtures and their competitiveness to suppress weeds before winter under different growing conditions. The shoot biomass share of a cover crop species in a dual-species mixture was found to be directly linked to its shoot biomass in a pure stand. Mustard and phacelia had similar effects on the shoot biomass production of the second species added to the mixture. Cruciferous species were more competitive against weeds than other cover crop species and could suppress weeds even when mixed with a less competitive partner. Weed suppression in mixtures with phacelia depended on the second component. Our results indicate that dual mixtures containing one competitive species reduce weed shoot biomass before winter, comparable to competitive pure stands. The research in this thesis shows that C content in the soil plays a crucial role in yield formation in arable cropping systems in Germany. Finally, the study has demonstrated that implementing cover crop mixtures can enhance soil C input and represent a valuable method for preserving yield potential. It was also shown that an intelligent combination of cover crop species can determine successful development and weed suppression.
Lentils can absorb amino acids as a nitrogen source supporting early growth
(2025) Kröper, Alex A.; Zikeli, Sabine; Wimmer, Monika A.; Zörb, Christian
Background: Lentils ( Lens culinaris Medik.) are a valuable crop due to their high nutritional content, low environmental impact, and nitrogen‐fixing ability via rhizobacteria. Early in development, before this symbiosis is established, lentils require external nitrogen, typically supplied through fertilizers or already present in soils. Aim: This study explores whether lentils can utilize amino acids as a nitrogen source and how amino acid supplementation affects growth and nitrate uptake. Results: The findings show that lentils can absorb amino acids from soil, with no adverse effects on growth compared to mineral N fertilizers. The amino acid patterns show only slight changes in individual amino acids. NPF/NRT1, NRT2, AMT2, and DUR3 were expressed in all treatments in root tissue. LHT1 plays a minor role in the distribution of N in the shoots of lentil plants. Conclusion: Although amino acid uptake is less efficient than that of nitrate, it may still benefit young plants in organic farming until rhizobacterial symbiosis is established.
Local and systemic metabolic adjustments to drought in maize: hydraulic redistribution in a split‐root system
(2022) Werner, Lena Maria; Hartwig, Roman Paul; Engel, Isabelle; Franzisky, Bastian Leander; Wienkoop, Stefanie; Brenner, Martin; Preiner, Julian; Repper, Dagmar; Hartung, Jens; Zörb, Christian; Wimmer, Monika Andrea
Background: It is yet unknown how maize plants respond to a partial root drying under conditions of a limited total water supply, and which adaptation mechanisms are triggered under these conditions. Aims: The aims of this study were to assess whether partial root drying results in distinguishable local and systemic physiological and metabolic drought responses, and whether compensatory water uptake and/or alteration of root architecture occurs under these conditions. Methods: Maize plants were grown in a split-root system. When plants were 20 days old, the treatments ‘well-watered’, ‘local drought’ and ‘full drought’ were established for a period of 10 days. Shoot length and gas exchange were measured non-destructively, root exudates were collected using a filter system and biomass, relative water content, osmolality and proline content were determined destructively at final harvest. Results: Local drought triggered stress responses such as reduced biomass, shoot length, relative water content and increased osmolality. Maintained root growth was systemically achieved by hydraulic redistribution rather than by altering root architecture. Local and systemic osmolyte adjustments contributed to this hydraulic redistribution. Conclusions: Both local and systemic metabolic responses helped the plants to induce hydraulic redistribution, enhance water availability and in consequence plant water relations. This resulted in a surprisingly well-maintained root growth even in the drought stressed root compartment.
Long-term breeding progress of yield, yield-related, and disease resistance traits in five cereal crops of German variety trials
(2021) Laidig, Friedrich; Feike, T.; Klocke, B.; Macholdt, J.; Miedaner, Thomas; Rentel, D.; Piepho, Hans-Peter
Plant breeding and improved crop management generated considerable progress in cereal performance over the last decades. Climate change, as well as the political and social demand for more environmentally friendly production, require ongoing breeding progress. This study quantified long-term trends for breeding progress and ageing effects of yield, yield-related traits, and disease resistance traits from German variety trials for five cereal crops with a broad spectrum of genotypes. The varieties were grown over a wide range of environmental conditions during 1988–2019 under two intensity levels, without (I1) and with (I2) fungicides and growth regulators. Breeding progress regarding yield increase was the highest in winter barley followed by winter rye hybrid and the lowest in winter rye population varieties. Yield gaps between I2 and I1 widened for barleys, while they shrank for the other crops. A notable decrease in stem stability became apparent in I1 in most crops, while for diseases generally a decrasing susceptibility was found, especially for mildew, brown rust, scald, and dwarf leaf rust. The reduction in disease susceptibility in I2 (treated) was considerably higher than in I1. Our results revealed that yield performance and disease resistance of varieties were subject to considerable ageing effects, reducing yield and increasing disease susceptibility. Nevertheless, we quantified notable achievements in breeding progress for most disease resistances. This study indicated an urgent and continues need for new improved varieties, not only to combat ageing effects and generate higher yield potential, but also to offset future reduction in plant protection intensity.
Mapping and validating stem rust resistance genes directly in self-incompatible genetic resources of winter rye
(2021) Gruner, Paul; Schmitt, Anne-Kristin; Flath, Kerstin; Piepho, Hans-Peter; Miedaner, Thomas
Key message: Individual stem rust resistance genes could be directly mapped within self-incompatible rye populations. Abstract: Genetic resources of rye (Secale cereale L.) are cross-pollinating populations that can be highly diverse and are naturally segregating. In this study, we show that this segregation could be used for mapping stem rust resistance. Populations of pre-selected donors from the Russian Federation, the USA and Austria were tested on a single-plant basis for stem rust resistance by a leaf-segment test with three rust isolates. Seventy-four plants per population were genotyped with a 10 K-SNP chip. Using cumulative logit models, significant associations between the ordinal infection score and the marker alleles could be found. Three different loci (Pgs1, Pgs2, Pgs3) in three populations were highly significant, and resistance-linked markers could be validated with field experiments of an independent seed sample from the original population and were used to fix two populations for resistance. We showed that it is possible to map monogenically inherited seedling resistance genes directly in genetic resources, thus providing a competitive alternative to linkage mapping approaches that require a tedious and time-consuming inbreeding over several generations.
Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses, and enhance maize growth at field scale
(2025) Francioli, Davide; Kampouris, Ioannis D.; Kuhl-Nagel, Theresa; Babin, Doreen; Sommermann, Loreen; Behr, Jan H.; Chowdhury, Soumitra Paul; Zrenner, Rita; Moradtalab, Narges; Schloter, Michael; Geistlinger, Joerg; Ludewig, Uwe; Neumann, Günter; Smalla, Kornelia; Grosch, Rita
Background: Field inoculation of crops with beneficial microbes is a promising sustainable strategy to enhance plant fitness and nutrient acquisition. However, effectiveness can vary due to environmental factors, microbial competition, and methodological challenges, while their precise modes of action remain uncertain. This underscores the need for further research to optimize inoculation strategies for consistent agricultural benefits. Results: Using a comprehensive, multidisciplinary approach, we investigate the effects of a consortium of beneficial microbes (BMc) ( Pseudomonas sp. RU47, Bacillus atrophaeus ABi03, Trichoderma harzianum OMG16) on maize ( Zea mays cv. Benedictio) through an inoculation experiment conducted within a long-term field trial across intensive and extensive farming practices. Additionally, an unexpected early drought stress emerged as a climatic variable, offering further insight into the effectiveness of the microbial consortium. Our findings demonstrate that BMc root inoculation primarily enhanced plant growth and fitness, particularly by increasing iron uptake, which is crucial for drought adaptation. Inoculated maize plants show improved shoot growth and fitness compared to non-inoculated plants, regardless of farming practices. Specifically, BMc modulate plant hormonal balance, enhance the detoxification of reactive oxygen species, and increase root exudation of iron-chelating metabolites. Amplicon sequencing reveals shifts in rhizosphere bacterial and fungal communities mediated by the consortium. Metagenomic shotgun sequencing indicates enrichment of genes related to antimicrobial lipopeptides and siderophores. Conclusions: Our findings highlight the multifaceted benefits of BMc inoculation on plant fitness, significantly influencing metabolism, stress responses, and the rhizosphere microbiome. These improvements are crucial for advancing sustainable agricultural practices by enhancing plant resilience and productivity.
NAC transcription factors ATAF1 and ANAC055 affect the heat stress response in Arabidopsis
(2022) Alshareef, Nouf Owdah; Otterbach, Sophie L.; Allu, Annapurna Devi; Woo, Yong H.; de Werk, Tobias; Kamranfar, Iman; Mueller-Roeber, Bernd; Tester, Mark; Balazadeh, Salma; Schmöckel, Sandra M.
Pre-exposing (priming) plants to mild, non-lethal elevated temperature improves their tolerance to a later higher-temperature stress (triggering stimulus), which is of great ecological importance. ‘Thermomemory’ is maintaining this tolerance for an extended period of time. NAM/ATAF1/2/CUC2 (NAC) proteins are plant-specific transcription factors (TFs) that modulate responses to abiotic stresses, including heat stress (HS). Here, we investigated the potential role of NACs for thermomemory. We determined the expression of 104 Arabidopsis NAC genes after priming and triggering heat stimuli, and found ATAF1 expression is strongly induced right after priming and declines below control levels thereafter during thermorecovery. Knockout mutants of ATAF1 show better thermomemory than wild type, revealing a negative regulatory role. Differential expression analyses of RNA-seq data from ATAF1 overexpressor, ataf1 mutant and wild-type plants after heat priming revealed five genes that might be priming-associated direct targets of ATAF1: AT2G31260 (ATG9), AT2G41640 (GT61), AT3G44990 (XTH31), AT4G27720 and AT3G23540. Based on co-expression analyses applied to the aforementioned RNA-seq profiles, we identified ANAC055 to be transcriptionally co-regulated with ATAF1. Like ataf1, anac055 mutants show improved thermomemory, revealing a potential co-control of both NAC TFs over thermomemory. Our data reveals a core importance of two NAC transcription factors, ATAF1 and ANAC055, for thermomemory.
Projecting results of zoned multi-environment trials to new locations using environmental covariates with random coefficient models: accuracy and precision
(2021) Buntaran, Harimurti; Forkman, Johannes; Piepho, Hans-Peter
Multi-environment trials (MET) are conducted to assess the performance of a set of genotypes in a target population of environments. From a grower’s perspective, MET results must provide high accuracy and precision for predictions of genotype performance in new locations, i.e. the grower’s locations, which hardly ever coincide with the locations at which the trials were conducted. Linear mixed modelling can provide predictions for new locations. Moreover, the precision of the predictions is of primary concern and should be assessed. Besides, the precision can be improved when auxiliary information is available to characterize the targeted locations. Thus, in this study, we demonstrate the benefit of using environmental information (covariates) for predicting genotype performance in some new locations for Swedish winter wheat official trials. Swedish MET locations can be stratified into zones, allowing borrowing information between zones when best linear unbiased prediction (BLUP) is used. To account for correlations between zones, as well as for intercepts and slopes for the regression on covariates, we fitted random coefficient (RC) models. The results showed that the RC model with appropriate covariate scaling and model for covariate terms improved the precision of predictions of genotypic performance for new locations. The prediction accuracy of the RC model was competitive compared to the model without covariates. The RC model reduced the standard errors of predictions for individual genotypes and standard errors of predictions of genotype differences in new locations by 30–38% and 12–40%, respectively.
Testing agronomic treatments to improve the establishment of novel miscanthus hybrids on marginal land
(2025) Lewin, Eva; Clifton-Brown, John; Jensen, Elaine; Lewandowski, Iris; Krzyżak, Jacek; Pogrzeba, Marta; Hartung, Jens; Wolfmüller, Cedric; Kiesel, Andreas; Fujii, Yoshiharu
Miscanthus is considered a promising candidate for the cultivation of marginal land. This land poses unique challenges, and experiments have shown that the “establishment phase” is of paramount importance to the long-term yield performance of miscanthus. This experiment analyzes novel miscanthus hybrids and how their establishment on marginal land can be improved through agronomic interventions. Experiments took place at two sites in Germany: at Ihinger Hof, with a very shallow soil profile and high stone content, and at Reichwalde, where the soil was repurposed river sediment with low organic matter, high stone content, and a compacted lower horizon. These marginal conditions functioned as test cases for the improvement of miscanthus establishment agronomy. Four hybrids ( Miscanthus x giganteus , Gnt10, Gnt43, and Syn55) and agronomic treatments such as plastic mulch film, miscanthus mulch, inoculation with mycorrhizal fungi, and fertilization were tested in two years at both sites in 2021 and 2022. Specific weather conditions and the timing of planting were strong determinants of establishment success and no single treatment combination was found that consistently increased the establishment success. Plastic mulch films were found to hinder rather than help establishment in both these locations. Chipped miscanthus mulch caused nitrogen immobilization and stunted plant growth. At Ihinger Hof the novel seed-based miscanthus hybrid Gnt43 produced twice the biomass of other hybrids (7 t ha −1 ) in the first growing season. Gnt10 yielded well in 2021 and showed impressive tolerance to water stress in the summer of 2022. No treatment combination was found that consistently increased the establishment success of miscanthus hybrids across sites and years. Novel genotypes consistently outperformed the standard commercial miscanthus hybrid Miscanthus x giganteus . Gnt10 may be a promising candidate for the cultivation of water-stress-prone marginal lands, due to its isohydric behavior and high yield potential.

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