And ALS-Inhibitors in Alopecurus Myosuroides Huds. and Their Causes
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Analysis of the spatial and temporal dynamics of herbicide resistance to ACCase- and ALS-Inhibitors in Alopecurus myosuroides Huds. and their causes Von der Fakultat¨ Architektur, Bauingenieurwesen und Umweltwissenschaften der Technischen Universitat¨ Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte Dissertation von Johannes Karlfried Manfred Bruno Herrmann geboren am 22.06.1987 aus Bautzen Eingereicht am: 10. Mai 2016 Disputation am: 11. Oktober 2016 Berichterstatter: Prof. Dr. Otto Richter Prof. Dr. Peter Zwerger 2016 Acknowledgements First, I would like to thank Dr. Martin Hess and Dr. Roland Beffa from Bayer Crop- Science. Both of them provided me with good support and feedback about my work, giving valuable comments and helping me fully understand the topic of herbicide re- sistance in all its respects. Dr. Martin Hess supported me additionally with the field sampling, carrying out of experiments and with interviewing farmers. As one of the founders of the project he had already collected data prior to the start of my PhD work, enabling me to work with a great amount of data right from the start. I also like to thank Dr. Harry Strek for his valuable comments about this project. I would also like to thank my supervisors Professor Dr. Otto Richter and Professor Dr. Peter Zwerger for their useful comments and ideas relating to the work. I would like to express my appreciation for Bayer CropScience for funding of this work and for letting me use their facilities. Special thanks go to the team at Bayer CropScience in Frankfurt, namely Ragnhild Paul, Falco Peter, Julia Unger, Thomas Schubel, Veronika Brabetz, Rebecka D¨ucker, Dr. Susana Gonzalez and Andrea Figge for their help in car- rying out greenhouse experiments and laboratory work. Their input and mental support throughout the work was invaluable to me. I would also like to thank the team at the JKI in Braunschweig, namely Dr. Lena Ulber, Dr. Henning Nordmeyer and Dagmar Rissel, for their useful comments. Special thanks to Dr. Janin Rummland for her help in the development of the simulation model. Finally special thanks to all the farmers that let us sample their fields and provided me with management data of their fields. Contents 1 Introduction and Aim of the Study 1 1.1 Introduction . .2 1.2 Literature Review . .3 1.2.1 Alopecurus myosuroides . .3 1.2.2 ALS- and ACCase-Inhibitors . .8 1.2.3 Herbicide Resistance . .9 1.2.4 Development of herbicide resistance . 11 1.3 Goals of the Study . 13 1.4 Thesis Layout . 14 2 Temporal and Spatial Evolution of Herbicide Resistance to ACCase- and ALS-Inhibitors at the Field Level in Alopecurus myosuroides Huds. 15 2.1 Introduction . 16 2.2 Material & Methods . 20 2.2.1 Site Selection . 20 2.2.2 Seed Sampling . 21 2.2.3 Greenhouse Bioassay . 22 2.2.4 Laboratory Analysis . 24 2.2.5 Statistical Analysis . 24 2.3 Results . 27 2.3.1 Infestation . 27 2.3.2 Greenhouse Results . 29 2.3.3 Laboratory Results . 35 2.3.4 Population Analysis . 42 2.4 Discussion . 47 3 Analysis of Field History and Soil Information to Determine the Driving Factors behind Herbicide Resistance to ALS-Inhibitors in Alopecurus myosuroides Huds. 59 3.1 Introduction . 60 3.2 Material & Methods . 63 3.2.1 Soil Map Analysis-Derivation of Variables . 63 3.2.2 Field History Analysis . 67 3.3 Results . 72 3.3.1 Soil Data . 72 3.3.2 Field History Data . 76 3.4 Discussion . 86 3.4.1 Soil characteristics . 87 3.4.2 Crop Management . 88 4 Predicting Herbicide Resistance: A Comparison of Different Methods to Forecast an Event of Resistance to ALS-Inhibitors in Alopecurus myosuroides Huds. 95 4.1 Introduction . 96 4.2 Material & Methods . 100 4.2.1 Supervised Learning . 100 4.2.2 Resistance Simulation Model . 100 4.3 Results . 114 4.3.1 Supervised Learning . 114 4.3.2 Simulation Model . 117 4.3.3 Prediction Outcomes . 122 4.4 Discussion . 141 4.4.1 Supervised Learning . 141 4.4.2 Simulation Model . 142 4.4.3 Comparing the overall prediction accuracy . 145 4.4.4 Limitations of the prediction and outlook . 145 5 Conclusions and Perspectives 149 5.1 Conclusions . 150 5.2 Future Work . 156 6 Summary 159 7 Appendix 163 7.1 Soil Map Legend . 164 7.2 Maps of ACCase- and ALS-inhibitor distribution among years . 165 List of Figures 2.1 Excerpt of the Hohenlohe area with the three locations H, M and Z in circles 20 2.2 Maps of relative infestation levels across all samples for fields in the core area of location H, M and Z. Q10= <10% quantile, Q25= <25% quan- tile, Q50 = 25% <x >75% quantile, Q75= >75% quantile, Q90= >90% quantile. The number of observations considered is indicated for every field. 30 2.3 Observed control to ALS-inhibitors and three ACCase-inhibitors tested in the greenhouse. Differences are shown across different crops and infestation levels. Red, yellow and green background color indicate the three rating groups, "Low", "Reduced", "High", that were used previously. 36 2.4 Closely related clusters (>90% AU) in color for the three sample locations. Grey color indicates fields that did not show high similarity to any other field and are therefore independent at the accuracy level assessed. 44 3.1 Distribution of soil groups (clusters) among the three components analyzed byPCA .................................... 75 3.2 Maps of the eight soil clusters extracted using Kmeans clustering and their distribution in the core fields of location H, M and Z . 77 3.3 Boxplot of individual PCA scores of the 6 management clusters on the 5 Principal Component (PC) from table 3.15 . 83 4.1 Model Scheme with corresponding equation (Eq.) and tables (Tab.) used at each point . 102 4.2 Representation of Soil Clusters for Z038 among the cells of the Cellular Automaton (CA) . 104 4.3 Variance importance plot ranking the variables by mean accuracy decrease (left) and mean decrease gini (Gini Index, right) . 114 4.4 Frequency of prediction of resistance for 36 fields using a trained random forest model. The test dataset consists out of of 16, 7 and 13 fields that were classified as Resistant (R), developing resistance (I) and Sensitive (S) respectively. 116 4.5 Simulation Output for field "Z038" with total number of plants and the respective portion of homozygous(AA), heterozygous (Aa) and wildtype (aa) plants . 119 4.6 Annual Number and Distribution of homozygous(AA), heterozygous (Aa) and wildtype (aa) plants within the field simulated by CA . 121 4.7 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field H012. Field Management by the farmer indicates information about the crop, tillage and herbicide regime.123 4.8 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field H289. Field Management by the farmer indicates information about the crop, tillage and herbicide regime.124 4.9 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field H362. Field Management by the farmer indicates information about the crop, tillage and herbicide regime.125 4.10 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field M001. Field Management by the farmer indicates information about the crop, tillage and herbicide regime. 126 4.11 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field M007. Field Management by the farmer indicates information about the crop, tillage and herbicide regime. 127 4.12 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field M017. Field Management by the farmer indicates information about the crop, tillage and herbicide regime. 128 4.13 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field M018. Field Management by the farmer indicates information about the crop, tillage and herbicide regime. 129 4.14 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field M027. Field Management by the farmer indicates information about the crop, tillage and herbicide regime. 130 4.15 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field Z002. Field Management by the farmer indicates information about the crop, tillage and herbicide regime.131 4.16 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field Z009. Field Management by the farmer indicates information about the crop, tillage and herbicide regime.132 4.17 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field Z023. Field Management by the farmer indicates information about the crop, tillage and herbicide regime.133 4.18 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field Z029. Field Management by the farmer indicates information about the crop, tillage and herbicide regime.134 4.19 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field Z116. Field Management by the farmer indicates information about the crop, tillage and herbicide regime.135 4.20 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field Z279. Field Management by the farmer indicates information about the crop, tillage and herbicide regime.136 4.21 Comparison of the predicted resistance status by random forest and sim- ulation model to observational data for field Z284.