Newest publications
Design evaluation and predictive accuracy of multi-environment trials in plant breeding
(2025) Gudata, Diriba Tadese; Piepho, Hans-Peter
In plant breeding, predictive accuracy of genotype means in the target population of environment (TPE) can be improved through proper experimental design and statistical analysis. During experimentation, blocking and randomization are expected to handle the major source of heterogeneity in the field. When heterogeneity exist in both directions, across row and column, two-way blocking is necessary to ensure homogeneity within blocks. Several trials need to be conducted in the TPE to generalize information. The TPE can be divided to form zonation that allows for borrowing information between zones when fitting genotypes as random and to allow for the zone-specific recommendation. The multi-environment trials (MET) data analysis can follow either one-stage or stage-wise analysis where in the latter case, information from individual trials is forwarded to the next stage of analysis. The linear mixed models (LMM) is commonly used in the MET data analysis. Furthermore, auxiliary information from the locations, particularly soil information and weather data can be integrated to MET data analysis to improve predictive accuracy. In general, the objective of this thesis was to improve predictive accuracy of modeling MET data based on different approaches of integrating ECs and pedigree information. Different spatial model selection and design evaluation was conducted in the second chapter using existing MET data from dry lowland sorghum breeding program of Ethiopia. Randomization based model, augmenting randomization-based model with linear variance and exponential spatial variations were compared in partially replicated and fully replicated row- column designs using Akaike information criterion (AIC). The baseline model with a two- dimensional nonlinear spatial model plus nugget improved the fitted model in many trials. In addition, the randomization-based plus two-dimensional linear variance model was also a good candidate model. According to the AIC, it is difficult to find a specific model that suits all the trials. Therefore, trying different spatial models and select the best fit model per trial could be a solution. Evaluation of the current design practice was also assessed in the same chapter through generating alternative designs by restructuring the blocking units and computing the relative efficiency. The relative efficiency results indicate most of the alternative alpha designs with block sizes of five, six, ten, fifteen, and the alternative row-column designs were more efficient when compared to the current practice. In the third chapter, a method of extracting and fitting synthetic environmental covariates (SCs) and pedigree information in multi-location trials data analysis was investigated. The main goal of this chapter was comparing predictive accuracy of LMM without pedigree information and SCs and with pedigree or/and SC to predict genotype performances in untested locations. The SCs were extracted from the actual ECs by using multivariate partial least squares (PLS) analysis. Then, subsequently we fitted in the LMM assuming the random coefficients of genotypes. An unstructured variance-covariance matrix of the random intercept and slope(s) was considered to ensure translational invariance. For the model with pedigree information, the baseline model with the independent genotype effect was modified to allow correlation between genotype through parents. For the GEI effect, the identity, the diagonal and the FA variance-covariance structures were considered. The mean squared error of prediction differences (MSEPD) and Spearman rank correlation shows that integrating the SCs in MET improve predictive accuracy of the model compared to the model without SCs. In all different variance-covariance structures of the GEI models, integrating SC was beneficial. There is also improvement with modelling pedigree information using diagonal and FA variance-covariance structures for genotype-environment effects. The diagonal variance-covariance structure of the GEI with the SC is the most accurate model in predicting genotype means to the new locations. In Chapter 4, the predictive accuracy under different approaches of fitting ECs in predicting genotypic performance in new environments was evaluated. The kinship matrix based on ECs, reduced rank regression and extended Finlay-Wilkinson approaches were evaluated and compared in predicting genotype means. Among the others, the reduced rank regression approach showed the smallest MSEPD. The limitation with this approach is that there are singularity problems when the number of ECs exceeds the number of environments. For this reason, a variable selection by using multivariate PLS was conducted to consider only the very important covariates in the subsequent modelling. Over all, there is a substantial gain in predictive accuracy in considering ECs compared to the model without ECs. In addition, we evaluated the importance of fitting the geographic zone factor, however, the result shows less improvement compared to the model without the zone factor. This result may be related to a smaller number of trials in some of the zones. One limitation with the data set when considering the zone effect is that only few trials remained in the western and northern zones after removing trials with zero genotype variances during individual trials analysis. The southern zone comprises the majority of the trials. The optimum allocation of trials to the zones was also tried based on the variance-covariances of the genotype -by-zone interactions. In chapter 3 and 4, when predicting genotype performance to new environments, the drop-out-one-environment at a time cross-validation (CV) mechanism was considered. This type of CV mimics the prediction for new environments and assesses uncertainty in model prediction. In conclusion, this study developed methods for improving the accuracy of genotypic performance prediction models in METs by improving the design efficiency in ongoing breeding programs through post-blocking mechanism, by fitting spatial models to capture spatial field trends in an experiment, and by using ECs, SCs and pedigree information.
Analyse viraler Promotoren von Phycodnaviren und deren Interaktion mit Transkriptionsfaktoren
(2025) Wahl, Benjamin; Pfitzner, Artur
Acanthocystis turfacea Chlorella Virus 1 (ATCV-1) ist ein dsDNA-Virus aus der Gattung Chloroviren, welches Chlorella heliozoae infiziert. Das Virus besitzt 860 offene Leserahmen (open reading frames, ORF), die für die Gene codieren, die für einen korrekten Virusreplikationszyklus benötigt werden. Diese Gene werden in sehr frühe/frühe/späte Gene eingeteilt. Diese Einteilung basiert auf den Zeitpunkten der Expression der Gene. Für die Expression dieser Gene nutzt ATCV-1 virale Promotoren, die eine Mischung aus eukaryotischen und prokaryotischen Bestandteilen darstellen. Die erfolgreiche Initialisierung des Replikationszyklus mit Hilfe von sehr frühen und frühen Genen ist essenziell für eine vollständige Virusreplikation. In früheren Arbeiten konnten Gene in Paramecium busaria Chlorella Virus 1 (PBCV-1) identifiziert werden, die als sehr frühe Gene klassifiziert wurden. Das Ziel dieser Arbeit beinhaltet die Untersuchung sehr früher/ früher Gene und deren Promotoren. Im zweiten Teil der Arbeit sollte die Interaktion von Proteinen, deren Promotor ein Hex-Motiv (XXXCGTGG) enthalten, mit verschiedenen Faktoren untersucht werden.
Basierend auf Sequenzvergleich-Analysen zwischen den sehr frühen Genen aus PBCV-1 und den Genen aus ATCV-1 wurden 20 Gene identifiziert. Die Promotoren dieser Gene wurden auf ihre Motive analysiert. Mit Hilfe einer RT-qPCR konnte gezeigt werden, dass diese Gene in der sehr frühen Phase der Virusreplikation (5 min p.i.) alle aktiv waren. Die Analyse in Pflanzen konnte zeigen, dass das Hex-Motiv in Verbindung mit mindestens einer TATA-Box ideal für die Expression der frühen Promotoren ist. Weitere Analysen konnten zeigen, dass für eine generelle Expression in Pflanzen mindestens zwei TATA-Box-Motiv in Verbindung mit anderen Motiven existieren müssen. In HEK293-Zellen konnte für die Promotoren mit dem Hex-Motiv ebenfalls eine Aktivität demonstriert werden. In der Arbeit konnte gezeigt werden, dass das Arg7-ASL-System zur Untersuchung der Aktivität von viralen Promotoren genutzt werden konnte. Alle frühen Promotoren zeigten eine Aktivität in Chlamydomonas reinhardtii, inklusive Promotoren anderer Viren.
Promotoren mit dem Hex-Motiv zeigten, im Vergleich zu Promotoren ohne dieses Motiv, eine Interaktion mit einer Vielzahl von unterschiedlichen Transkriptionsfaktoren, die zu den bZIP-Transkriptionsfaktoren gezählt werden.
Mit Hilfe zweier Proteine, Z174L und Z765R, deren Promotoren das Hex-Motiv besitzen, konnten mehrere mögliche Interaktionspartner mit Hilfe von „proximity based labeling“, darunter Proteine wie z.B. Actin, Thioredoxin und ein Histon-Acetlytransferase-Protein, identifiziert werden. Diese Proteine können mit der Transkription in Verbindung gebracht werden, was die vermutete Funktion von Z765R als Transkriptionsfaktor stützt. Z174L ist vermutlich ein Transkriptionsfaktor bzw. eine Endonuklease. Auch hierfür konnten Proteine, die diese Hypothese unterstützen, mit Hilfe der Massenspektrometrie identifiziert werden.
In dem dritten Teil der Arbeit konnte mit Hilfe von Yeast-1-Hybrid-Analysen und dem Promotor von Z063L ein neues Protein, Activating protein 63 (Ap63), in Chlamydomonas reinhardtii identifiziert werden. Dieses Protein besitzt Motive, die mit DNA-Bindung in Verbindung gebracht werden. Kombiniert mit Analysen der Sequenz, handelt es sich bei dem hier entdeckten Protein vermutlich um einen Transkriptionsfaktor.
Das Gesamtbild dieser Studie zeigt auf, wie abhängig das Virus von seinem Wirt für eine erfolgreiche Replikation ist und wie breit das Spektrum der Virus-Wirt-Interaktion ist. Die sehr frühe Genexpression (5 min p.i.) spielt eine essenzielle Rolle für die Replikation. Hierfür macht sich das Virus Proteine (vor allem Transkriptionsfaktoren) des Wirts zunutze, um die gesamte Genexpression der Wirtszelle auf die Virusreplikation umzuprogrammieren.
The paradox of the bryozoans
unravelling the relation between structure and stability in benthic competition networks
(2025) Koch, Franziska; Allhoff, Korinna T.
Classical ecological models struggle to explain the persistence of diverse communities, where many species compete for the same resources. For example, traditional stability theory based on large, random matrices predicts that diverse communities should generally be unstable. Furthermore, according to the principle of competitive exclusion, two species competing for one resource should not be able to coexist. Parametrising network models with empirical data has revealed that real networks tend to contain specific non-random patterns of weak and strong links, which enable their stability. However, such patterns have been studied in food webs as well as mutualistic networks, while potential stabilising patterns of interaction strengths in competitive systems remain largely unexplored. Instead, simplified competition networks are often used, in which interactions are binary, so that potential stabilising effects due to specific patterns in weak and strong links cannot be considered. In such studies, intransitive competition, where competitive links are arranged as in a rock-papers-scissors game, is considered the only mechanism that can avoid competitive exclusion.
In this thesis, I studied the role of interaction strengths in the stability of competition networks. To achieve this, I used data on encrusting bryozoan assemblages in order to parametrise weighted interaction networks. Bryozoans are small aquatic animals that grow in colonies on the sea bed. Individual colonies compete for space by overgrowing each other. My approach allowed me to obtain Jacobian matrices from species abundances and recorded overgrowths. I could thus connect this abstract mathematical modelling approach with empirical data. Based on the Jacobian matrices, I assessed network stability, as well as the strengths of amplifying and dampening feedback loops in the systems, which allowed me to draw connections between structure and stability.
In Chapter 1, I analysed a data set of 30 polar bryozoan assemblages. These assemblages were quite hierarchical, meaning that species could be sorted from strongest to weakest competitors. I showed that as a result of this hierarchy, the Jacobian matrices contained asymmetric patterns of interaction strengths and that these patterns had a stabilising effect. While all empirical networks were unstable, destroying asymmetry by randomising the matrix elements increased the level of instability. This is because the asymmetric patterns keep feedback loops of all lengths weak. This applies to short, positive 2-link loops which can destabilise the system by amplifying perturbations, as well as to longer, negative loops which can cause unstable oscillations. Positive 2-link loops that are formed between each pair of competing species played a key role, and I found that the strongest 2-link loop in a matrix could be used as a predictor of network instability. I could thus identify hierarchy to have a stabilising effect in weighted competition networks, which contrasts with the common idea that intransitive competition stabilised complex systems.
In Chapter 2, I additionally looked at the role of distributions of interaction strengths. I showed that the interaction strengths in my empirical data sets were very skewed, with few strong and many weak links. Similar patterns have also been found in the link strengths of both food webs and mutualistic networks, pointing towards a general pattern. I tested whether this skewed distribution of link strengths influenced the stabilising effect of asymmetry by building theoretical community matrices with asymmetric patterns and various distributions of link strengths. My results indicated that the full stabilising effect of asymmetry could only be reproduced when a skewed distribution of interaction strengths was used. This has important implications for many theoretical studies, where normal and uniform distributions of link strengths are often used, meaning that some stabilising patterns might be overlooked.
Finally, in Chapter 3, I contrasted networks from polar regions to additional data sets collected at temperate and tropical locations. By comparing several network indices, I identified latitudinal differences in the strength of asymmetric patterns, which were generally stronger in polar networks. Due to the stabilising effect of asymmetry, this also leads to differences in network stability, with tropical networks having stronger positive 2-link feedback loops and thus being more unstable. Across all data sets, I found that again, the strongest 2-link loop closely predicted stability, emphasising the generality of this stability predictor. However, the strength of asymmetry varied significantly within some regions, which could potentially be linked to assemblage age and disturbance history.
To summarise, my work extends our understanding of stabilising patterns in interaction strengths to competitive systems. A key result is that positive, amplifying 2-link feedback loops determine the stability of competition networks, and that asymmetric arrangement of link strengths reduce their amplifying effect. I identified the maximum 2-link loop weight as a predictor of network stability, which is in line with previous results on food webs, where the maximum 3-link loop determines stability. Finally, I was able to show that some insights derived from random matrix models and models of intransitive competition, which are both commonly used in theoretical ecology, might not be transferable to real systems. This highlights a further need to combine mathematical modelling approaches with empirical research.
Towards transdisciplinary identification of suitable woody perennials for resilient agro-silvopastoral systems in the Sudano-Sahelian zone of West Africa
(2025) Roessler, Regina; Cicek, Harun; Cournac, Laurent; Gnissien, Moussa; Männle, Julia; Koomson, Eric; Founoune-Mboup, Hassna; Coulibaly, Kalifa; Diouf, Abdoul Aziz; Sanon, Hadja Oumou; Cadisch, Georg; Graefe, Sophie; Roessler, Regina; Animal Husbandry in the Tropics and Subtropics, University of Kassel, Steinstr. 19, 37213, Witzenhausen, Germany; Cicek, Harun; Department of International Cooperation, Research Institute of Organic Agriculture, Ackerstrasse 113, 5070, Frick, Switzerland; Cournac, Laurent; Eco&Sols, CIRAD, INRAE, IRD, Institut Agro, Université de Montpellier, Montpellier, France; Gnissien, Moussa; Laboratoire d’étude Et de Recherche Sur La Fertilité Des Sols Et Les Systèmes de Production (LERF-SP), Institut du Développement Rural, Université Nazi BONI, Bobo-Dioulasso, Burkina Faso; Männle, Julia; Institute of Development Research, BOKU University, Peter-Jordan-Straße 76/I 1190, Vienna, Austria; Koomson, Eric; Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Garbenstr. 13, 70593, Stuttgart, Germany; Founoune-Mboup, Hassna; Institut Sénégalais de Recherches Agricoles (ISRA), BP 15532, Fann Residence, Dakar, Senegal; Coulibaly, Kalifa; Laboratoire d’étude Et de Recherche Sur La Fertilité Des Sols Et Les Systèmes de Production (LERF-SP), Institut du Développement Rural, Université Nazi BONI, Bobo-Dioulasso, Burkina Faso; Diouf, Abdoul Aziz; Centre de Suivi Ecologique (CSE), Dakar, Senegal; Sanon, Hadja Oumou; Department of Animal Production, Institut de L’Environment Et de Recherches Agricoles (INERA), BP 8645, 1973 Boulevard Tansoba Wam-Godi, 04, Ouagadougou 04, Burkina Faso; Cadisch, Georg; Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Garbenstr. 13, 70593, Stuttgart, Germany; Graefe, Sophie; International Climate Initiative (IKI), Zukunft – Umwelt – Gesellschaft (ZUG) gGmbH, Stresemannstraße 69-71, Berlin, Germany
Parkland systems in the Sudano-Sahelian zone of West Africa are commonly perceived as a resilient agroforestry practice well adapted to the semi-arid climatic conditions of the region. However, there exist several knowledge gaps regarding the interplay between the different components of this agro-silvopastoral land use system. A literature review with subsequent meta-analysis was conducted to analyze the effects of woody perennials on soil, crops and livestock, for which our study found very context-specific responses. A scoring of tree and shrub species indicated a general trend of trade-off between positive impact on crops and livestock vs. impact on soil organic carbon content. The study further confirmed that Faidherbia albida (Del.) Chev. is one of the most promising parkland species, but also revealed that there are no multipurpose single species that should be promoted exclusively. The focus should rather shift to species mixtures that satisfy multiple human and environmental needs. The study also pointed out that information on the nutritional properties of the majority of browse species is particularly limited. Transdisciplinary modelling is suggested as a tool to assess the complex interactions between the different components that shape this agro-silvopastoral system at different scales.
On-farm use of recycled liquid ammonium sulphate in Southwest Germany using a participatory approach
(2023) Müller, Benedikt; Hartung, Jens; von Cossel, Moritz; Lewandowski, Iris; Müller, Torsten; Bauerle, Andrea; Müller, Benedikt; Biobased Resources in the Bioeconomy, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany; Hartung, Jens; Biostatistics, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany; von Cossel, Moritz; Biobased Resources in the Bioeconomy, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany; Lewandowski, Iris; Biobased Resources in the Bioeconomy, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany; Müller, Torsten; Fertilization and Soil Matter Dynamics, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany; Bauerle, Andrea; Biobased Resources in the Bioeconomy, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
For political and environmental reasons, there is an urgent need for alternatives to energy-intensive synthetic fertilizers. One solution is the targeted recycling of nutrients within agriculture. In this study, liquid ammonium sulphate (LAS) as a recycling product derived from digestate treatment was compared to calcium ammonium nitrate, manure and original digestates in an on-farm experiment using a participatory approach. Based on regular meetings with the farmers involved, a flexible experimental design was developed which integrated the fertilization legislation and the farmers’ operational structures already in place, such as crop rotation, available application techniques and manure management demands. The aim was to achieve both implementation practicability and acceptance of the study results by the farmers. Results from the year 2020 showed that LAS applied with three-jet nozzles in barley and wheat had significantly lower yields than the other fertilizers. Applied with a slurry tanker trailing shoe applicator in 2021, LAS had comparable yields to the other fertilizers in maize (51.2 t ha −1 ) and comparable yields to digestate in rapeseed (4.4 t ha −1 ). Application techniques that minimize environmental impacts and lower the LAS pH could potentially increase the effectiveness of the fertilizer. We recommend that farmers use this fertilizer not as a single solution but as a mineral compensatory fertilizer in addition to organic fertilizers following local fertilizer legislation. In this case, LAS could potentially substitute calcium ammonium nitrate (CAN).