Staff Publications

Staff Publications

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    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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    Apports des typologies d'exploitations aux démarches de conception en agriculture de conservation: Une étude de cas dans le nord du Vietnam
    Hauswirth, Damien ; Pham, Thi-Sen ; Wery, Jacques ; Tittonell, Pablo ; Jourdain, Damien ; Affholder, François - \ 2015
    Cahiers Agricultures 24 (2015)2. - ISSN 1166-7699 - p. 102 - 112.
    Cropping systems - Direct seeding - Farming systems - Mountain farming - Mulch - Sustainability

    Conservation agriculture (CA) is considered a possible option for reducing the environmental impact of tilled maize on sloping land in two mountainous districts of northern Vietnam. Within this context, our study aimed at building a regional farm typology that can support the design of CA cropping systems, suiting different farm types. 411 maize-producing farms were surveyed. Using multivariate analysis, we identified 5 farm types with contrasting resources and sustainability performances. We discuss the range of possible CA systems to be designed for each type, according to its specific constraints and opportunities. We especially consider diverse intensification levels and kinds of cover plants. We propose the development of farm models to further explore the economic attractiveness of the options selected for each type.

    Quantifying beef production gaps of two farming systems in the Charolais basin, France
    Linden, A. van der; Ven, G.W.J. van de; Oosting, S.J. ; Ittersum, M.K. van; Boer, I.J.M. de - \ 2015
    In: Proceedings of the 5th International Symposium for Farming Systems Design. - - p. 9 - 10.
    1 Introduction Sustainable intensification of livestock production systems is a way to realise the increasing global demand for meat. Current empirical studies reveal meat production levels obtained by best practices, but do not clarify the theoretically achievable (i.e. potential) and feed limited production. Potential production is defined by animal genotype and climate only (Fig. 1). Feed limited production is determined by genotype, climate, availability of drinking water, and the quality and quantity of feed. Actual production is the production that farmers achieve in practice. This production level is, next to genotype, climate, water, and feed, determined by diseases and stress in livestock (Van de Ven et al., 2003). Fig. 1. Potential, limited, and actual production of crops (left) and livestock (right).In crop production, the production ecological concepts of potential, limited, and actual production (Fig. 1) (Van Ittersum & Rabbinge, 1997) are generally used to give insight in the scope to increase production from their actual levels (Van Ittersum et al., 2013). These concepts are also applicable to livestock production (Van de Ven et al., 2003 ; Van der Linden et al.), but so far the effects of genotype, climate, feed quality, and feed quantity have not been quantified systematically using production ecological concepts in livestock production. This research, therefore, aims to quantify potential, feed quality limited, and actual beef production in two French beef production systems at herd level. Feed quantity limitation is not included. 2 Materials and Methods A mechanistic, dynamic model was developed to simulate beef cattle growth based on genotype, climate, housing, feed quantity, and feed quality. This model is analogous to crop growth models that are based on the production ecological concepts. The beef cattle model combines feed digestion, thermoregulation, and feed utilisation sub-models in a novel way to simulate processes at animal level. Results from animal level are scaled up to herd level. Energy, heat, and protein flows are described in the model, which is programmed in R 3.0.2. Input data for the model are parameters for a specific genotype or breed, daily climate data, and information on housing, feed quality and feed quantity intake. The model was applied to two beef production systems with different feeding strategies of Charolais cattle in the Charolais Basin, France. System A corresponds to farm type 11111 and system B to farm type 31041 as described by Réseaux d’Elevage Charolais (2012). System A produced heavier animals and has a longer grazing period than system B. The fraction concentrates in the diet is larger in system B than in system A.Potential production was expressed as a feed efficiency (FE, g beef kg-1 DM feed). Potential production in both systems was simulated with an ad libitum fed diet containing 65.8 % barley and 34.2% hay. This diet prevented feed quality and quantity limitation. Under potential production, FE was maximized at herd level, and all female calves were kept for replacement. Culling was set at 50% per year after birth of the first calf. Feed quality limited production was simulated with a diet containing concentrates and hay when cattle were housed during winter, and grass during other periods of the year. Concentrate intake (barley) was 4.8% of the DM intake in system A and 18.3% of the DM intake in system B, which corresponded to the diet under actual production. Feed quality limited production was simulated with the same culling rates and slaughter weights as under potential production. Actual production was calculated from data provided by Réseaux d’Elevage Charolais (2012). Yield gaps were calculated as the difference between potential and actual production, and the difference between feed quality limited production and actual production. Relative yield gaps were calculated as the yield gap divided by potential or feed quality limited production. 3 Results and discussion FE at herd level was highest under potential production and feed quality limited production, when male calves were slaughtered at 1000 kg. Potential production in systems A and B (Fig. 2) was slightly different (64.0 vs 64.4 g beef kg-1 DM feed). FE in system A was lower due to a longer grazing period and hence a higher energy requirement for grazing. Feed quality limited production, with the same culling rates and slaughter weights as under potential production, was lower in system A than in system B (51.7 vs 54.1 g beef kg-1 DM feed), which is explained by a lower fraction of concentrates in the diet. Actual production was lower in system A than in system B (24.9 vs 31.2 g beef kg-1 DM feed). Fig. 2. Simulated feed efficiency in beef production systems A and B under potential, feed quality limited, and actual production. The relative yield gap between actual and potential production was 61% in system A and 52% in system B, and the relative yield gap between actual and feed quality limited production was 52% in system A and 42% in system B. The latter yield gaps can be explained by feed quality limitation, as well as stress and diseases. In crop production, yields tend to plateau at 75-85% of potential or water limited production (i.e. minimum yield gaps equal 15-25%), and further yield gap mitigation is not economically or practically feasible (Van Ittersum et al., 2013). In our study, simulated yield gaps are much larger than such minimum yield gaps. Grazing and suckler cow premiums might not urge farmers to mitigate current yield gaps, but also social factors (e.g. labour availability) may play a role. More model validation is required to further improve accuracy of the simulation results. Multiplying beef production (kg beef t-1 DM feed) and feed crop production (t DM ha-1 year-1) results in the beef production per unit of land (kg beef ha-1 year-1). Quantifying potential and limited production of crops and livestock according to production ecology allows us to assess land use per kg of animal product. 4 Conclusions The production ecological concepts were successfully applied to livestock production. We benchmarked actual beef production relative to potential and feed quality limited production of two French beef production systems at herd level. Results indicate that potential production is more than two times the actual production in both systems. Hence, there is considerable scope to increase beef production in the Charolais basin, from a bio-physical perspective. References Réseaux d’Elevage Charolais (2012). Bassin Charolais. Conjoncture économique des systèmes bovins Charolais, Campagne 2012. Document, Chambre d’Agriculture, Institut de l’Elevage, 50pp.Van de Ven, G.W.J., de Ridder, N., van Keulen, H. & van Ittersum M.K. (2003). Concepts in production ecology for analysis and design of animal and plant-animal production systems. Agricultural Systems, 76, 507-525.Van der Linden, A., Oosting, S.J., van de Ven, G.W.J, de Boer, I.J.M. & van Ittersum, M.K. A framework for quantitative analysis of livestock systems using the theoretical concepts of production ecology. Submitted to Agricultural Systems.Van Ittersum, M.K. & Rabbinge, R. (1997). Concepts in production ecology for analysis and quantification of agricultural input-output combinations. Field Crops Research, 52, 197-208.Van Ittersum, M.K., Cassman, K.G., Grassini, P., Wolf, J., Tittonell, P. & Hochman, Z. (2013). Yield gap analysis with local to global relevance-A review. Field Crops Research, 143, 4-17.
    Innovative participatory farming system design: combining on-farm crop/livestock trials with ex- ante trade-off analysis
    Falconnier, G.N. ; Descheemaeker, K.K.E. ; Mourik, T. van; Giller, K.E. - \ 2015
    In: Proceedings of the 5th International Symposium for farming Systems Design, Montpellier, 7-10 September 2015. - - p. 483 - 484.
    Sustainable extensification—breathing new life into Africa's sleeping giant
    Ollenburger, M.H. ; Descheemaeker, K.K.E. ; Crane, T.A. ; Giller, K.E. - \ 2015
    In: Proceedings of the 5th International Symposium for Farming Systems Design. - - p. 233 - 234.
    Re-designing smallholder farming futures for reduced vulnerability to climate change in semi-arid southern Africa
    Homann-Kee Tui, S. ; Descheemaeker, K.K.E. ; Masikati, P. ; Gama, A.C. - \ 2015
    In: Proceedings of the 5th International Symposium for farming Systems Design, Montpellier, 7-10 September 2015. - - p. 155 - 156.
    Co-design of improved climbing bean technologies for smallholder farmers in Uganda
    Ronner, E. ; Descheemaeker, K.K.E. ; Almekinders, C.J.M. ; Ebanyat, P. ; Giller, K.E. - \ 2015
    In: Proceedings of the 5th International Symposium for farming Systems Design, Montpellier, 7-10 September 2015. - - p. 263 - 264.
    A systematic approach for re-assembly of crop models: An example to simulate pea growth from wheat growth
    Adam, M.Y.O. ; Wery, J. ; Leffelaar, P.A. ; Ewert, F. ; Corbeels, M. ; Keulen, H. van - \ 2013
    Ecological Modelling 250 (2013). - ISSN 0304-3800 - p. 258 - 268.
    nitrogen nutrition - expert knowledge - use efficiency - water-deficit - legume - apsim - integration - parameters - frameworks - selection
    The process of crop modelling to develop operational software requires different skills, from conceptualization of the biophysical system to computer programming, involving three main scientific disciplines: agronomy, mathematics, and software engineering. Model building implies transforming a conceptual model into sets of mathematical equations and then translating these equations into a computer program. Although recent crop modelling frameworks can technically support model building, the modelling process is not always well documented and difficult to repeat. The focus of this paper is therefore on developing and documenting an approach to re-assemble crop models, i.e. develop a new model from an existing one, using a crop modelling framework and crop physiological knowledge. Modifications to an initial crop model were classified according to three categories: (i) changes in parameter values, (ii) changes in equations, and (iii) changes in overall model structure. We illustrate the approach with a case study transforming a wheat crop model into a pea crop model. We discuss the role of each actor in the process to document diverse uncertainties related to the model (i.e. contextual situation, data, structure), and the general applicability of the approach for different crop modelling frameworks. We conclude that the use of our approach to re-assemble a crop model within a modelling framework facilitates integration of different disciplines around a modelling objective, and facilitates creating transparent and reproducible models
    Protocol to support model selection and evaluation in a modular crop modelling framework: An application for simulating crop response to nitrogen supply
    Adam, M.Y.O. ; Belhouchette, H. ; Corbeels, M. ; Ewert, F. ; Perrin, A. ; Casellas, E. ; Celette, F. ; Wery, J. - \ 2012
    Computers and Electronics in Agriculture 86 (2012). - ISSN 0168-1699 - p. 43 - 54.
    agricultural systems - growth simulation - use efficiency - radiation - wheat - software - soil - knowledge - dynamics - science
    Crop models require different structures for different applications. Modular and flexible crop modelling frameworks, such as the recently developed agricultural production and externalities simulator (APES), support the change of model structure. However, the assembly of different modules to create a model may not always result in the best model structure. We developed and tested a protocol for a systematic selection and evaluation of a crop growth model structure. The novelty of the presented protocol relies on a throughout analysis of the different modelling approaches (modules) and on how to assemble them to create new modelling solutions (i.e. model). We use a case study to demonstrate that we can explicitly express and test the different assumptions behind the choice of a specific modelling approach. Our case study refers to the simulation of crop growth in response to nitrogen management and the importance of an accurate simulation of the nitrogen uptake. Applying the proposed protocol, we identify the need to improve the initially selected nitrogen mineralisation module. We conclude that not only is the protocol suitable to provide guidance for systematic testing of different crop processes modelled, but also its use highlights the importance of the documentation of the modelling process and of the clarification of the uncertainty associated with the model structure.
    Ad hoc modeling in agronomy: What have we learned in the last 15 years?
    Affholder, F. ; Tittonell, P.A. ; Corbeels, M. ; Roux, S. ; Motisi, N. ; Tixier, P. ; Wery, J. - \ 2012
    Agronomy Journal 104 (2012)3. - ISSN 0002-1962 - p. 735 - 748.
    systems simulation-model - crop growth simulation - soil-water deficit - agricultural systems - environmental-models - maize production - decision-making - carbon-dioxide - use efficiency - climatic risk
    The “Use and Abuse of Crop Simulation Models” special issue of Agronomy Journal published in 1996 ended with the myth of the universal crop model. Sinclair and Seligman consequently recommended tailoring models to specific problems. This paper reviews the fate of the idea of such ad hoc approaches to crop simulation modeling during the past 15 yr. Most crop modelers have since adhered to the principles formulated by Sinclair and Seligman, but yet their practice faces two major issues: (i) how to define the structure of the model as depending on the question to be addressed (model conceptualization) and (ii) how to minimize efforts in software development (model computerization). Progress in model conceptualization as reported in the literature concerns (i) inferring a conceptual model from what is known of the problem to address, (ii) deriving summary models from comprehensive ones, and (iii) using multivariate methods to analyze the hierarchy of drivers of variability in the variable to be predicted. Considerable effort has been invested in the development of frameworks to facilitate model computerization, and the commercial modeling software is constantly improving. But there are limits in the flexibility permitted by these tools. Acquiring basic skills in coding a model using a scientific programming language is preferred by scientists wishing to keep the fullest understanding and control on their crop models. Connecting the model to commercial database software may facilitate this strategy. However, the computerization issue may still lead to tensions between modeling teams concerning the legitimacy to develop their own model.
    Building crop models within different crop modelling frameworks
    Adam, M.Y.O. ; Corbeels, M. ; Leffelaar, P.A. ; Keulen, H. van; Wery, J. ; Ewert, F. - \ 2012
    Agricultural Systems 113 (2012). - ISSN 0308-521X - p. 57 - 63.
    environmental-models - systems simulation - uncertainty - responses - protocol - apsim
    Modular frameworks for crop modelling have evolved through simultaneous progress in crop science and software development but differences among these frameworks exist which are not well understood, resulting in potential misuse for crop modelling. In this paper we review differences and similarities among different developed frameworks and identify some implications for crop modelling. We consider three modelling frameworks currently used for crop modelling: CROSPAL (CROp Simulator: Picking and Assembling Libraries), APES (Agricultural Production and Externalities Simulator) and APSIM (Agricultural Production Systems sIMulator). The frameworks are implemented differently and they provide more or less flexibility and guidance, to facilitate assembly of crop model from model components. We underline the importance of systematic approaches to facilitate the selection of appropriate model structure and derive suggestions to facilitate it. We particularly stress the need for better documentation of the underlying assumptions of the modules on simulated processes and on the criteria applied in the selection of these modules for a particular simulation objective. Such documentation should help to point out the sources of uncertainties associated with the development of crop models and to reinforce the role of the crop modeller as an intermediary between the software engineer, coding the modules, and the end users, agronomists or crop physiologists using the model for a specific objective. Finally, the key contributions of modelling frameworks in the crop modelling domain are discussed and we draw conclusions for the prospects of such frameworks in the crop modelling field which should continue to reside on the principles of systems analysis but combined with up-to-date advances in software engineering techniques
    Generation of a catR deficient mutant of P. putida KT2440 that produces cis, cis-muconate from benzoate at high rate and yield
    Duuren, J.B.J.H. van; Wijte, D. ; Leprince, A. ; Karge, B. ; Puchalka, J. ; Wery, J. ; Martins Dos Santos, V.A.P. ; Eggink, G. ; Mars, A.E. - \ 2011
    Journal of Biotechnology 156 (2011)3. - ISSN 0168-1656 - p. 163 - 172.
    aromatic catabolic pathways - swiss-model repository - pseudomonas-putida - microarray experiments - cis,cis-muconic acid - degradation - cloning - genes - proteomics - proteins
    Pseudomonas putida KT2440-JD1 was derived from P. putida KT2440 after N-methyl-N'-nitro-N-nitrosoguanidine (NTG)-mutagenesis and exposure to 3-fluorobenzoate (3-FB). The mutant was no longer able to grow using benzoate as a sole carbon source, but co-metabolized benzoate to cis, cis-muconate during growth on glucose, which accumulated in the growth medium. The specific production rate (qpm) was 0.18 ± 0.03 g cis, cis-muconate/(gDCW h) in continuous cultures, and increased to 1.4 g cis, cis-muconate/(gDCW h) during wash-out cultivation. Transcriptome analysis showed that the cat operon was not induced in P. putida KT2440-JD1 in the presence of 5 mM benzoate, due to a point mutation in the highly conserved DNA binding domain of the transcriptional regulator (catR) of the cat operon. The ben operon was highly expressed in the presence of benzoate in the mutant and its parental strain. This operon contains PP_3166 (catA2), which was shown to be a second catechol 1,2-dioxygenase besides catA. P. putida KT2440-JD1 is the first cis, cis-muconate-accumulating mutant that was characterized at the genetic level. The specific production rate achieved is at least eight times higher than those reported for other cis, cis-muconate-producing strains
    Using a cropping system model at regional scale: Low-data approaches for crop management information and model calibration
    Therond, O. ; Hengsdijk, H. ; Casellas, E. ; Wallach, D. ; Adam, M.Y.O. ; Belhouchette, H. ; Oomen, R. ; Russell, G. ; Ewert, F. ; Bergez, J.E. ; Janssen, S.J.C. ; Wery, J. ; Ittersum, M.K. van - \ 2011
    Agriculture, Ecosystems and Environment 142 (2011)1-2. - ISSN 0167-8809 - p. 85 - 94.
    simulation-models - climate-change - wheat yields - environment - adaptation - impacts - europe - level - co2
    Cropping system models are powerful tools for regional impact assessment, but their input data requirements for large heterogeneous areas are difficult to fulfil. Hence, the objectives of this paper are to present low-data approaches for specifying detailed management data required by cropping system models, and for calibrating default crop parameters applied to 12 regions in the European Union (EU). Various downscaling and upscaling procedures for different data types are applied to address both objectives. The Agricultural Production and Externalities Simulator (APES) model is used for illustrative purposes. Combining easy-to-collect regional crop management information and expert knowledge enables to develop generic, expert-based rules for specifying crop management. Effects of these expert-based management rules on simulated yields and nitrogen leaching are illustrated using APES. Simulated yields of grain maize, soft wheat and durum wheat using default crop parameters for phenology are compared with crop yields observed in 12 EU regions. The accuracy of the simulated yields was variable, but generally poor. A regional calibration factor Kpheno is developed based on the temperature sum of the average sowing and harvest dates of the three crops in each region. Applying this calibration factor improved the simulated yields in all cases. Results suggest that it is possible to develop expert-based management rules and to capture yield variation across the EU by using the presented low-data approaches.
    Assessing the impact of the Nitrate Directive on farming systems using a bio-economic modelling chain
    Belhouchette, H. ; Louhichi, K. ; Therond, O. ; Mouratiadou, I. ; Wery, J. ; Ittersum, M.K. van; Flichman, G. - \ 2011
    Agricultural Systems 104 (2011)2. - ISSN 0308-521X - p. 135 - 145.
    agricultural systems - maximum-entropy - management - framework - policy - farmers - simulation - cropsyst - future - scale
    Bio-economic models can be used to assess the impact of policy and environmental measures through economic and environmental indicators. Focusing on agricultural systems, farmers’ decisions in terms of cropping systems and the associated crop management at field scale are essential in such studies. The objective of this paper is to present a study using a bio-economic model to assess the impact of the Nitrate Directive in the Midi-Pyrenees region (France) by analyzing, at the farm scale, farm income and three environmental indicators: nitrate leaching, erosion and water consumption. Two scenarios, the 2003 CAP reform (baseline scenario) and the Nitrate Directive (policy scenario), with a 2013 time horizon, were developed and compared for three representative arable farm types in the Midi-Pyrenees region. Different types of data characterizing the biophysical context in the region (soil, climate), the current cropping systems (rotation, crop management) and farm resources (irrigated land, labor) were collected to calibrate and run the models. Results showed that the implementation of the Nitrate Directive may not affect farm income. However, significant modifications to cropping systems and crop allocation to soil types were simulated. Contrary to expectations, nitrogen leaching at the farm scale did not change. Overall water consumption increased and soil erosion decreased due mainly to a modification in cropping patterns and management by soil type. This study provides an example of unanticipated effects of policy and trade-offs between environmental issues.
    Integrated assessment of agricultural land use policies aiming at reducing nutrient pollution in Taihu Basin, China
    Reidsma, P. ; Feng, S. ; Lubbers, M.T.M.H. ; Loon, M. van; Kang, C. ; Kanellopoulos, A. ; Wolf, J. ; Ittersum, M.K. van; Keulen, H. van; Qu, F. - \ 2010
    In: Proceedings of Agro 2010 the XIth ESA Congress, Montpellier, France, September 29 to September 03, 2010. - Montpellier, France : ESA - p. 431 - 432.
    Mulch economic value in cereal-cotton rotation of Northern Cameroon: a plot scale evaluation of Direct-seeding Mulch-based cropping systems
    Balarabe, O. ; Naudin, K. ; Lifran, R. - \ 2010
    In: Proceedings of Agro 2010: the XIth ESA Congress, Montpellier, France, 28 August - 3 September 2010. - Montpellier, France : ESA European Society for Agronomy - ISBN 9782909613017 - p. 403 - 404.
    Development and evaluation of a crop modelling system for regional yield estimation
    Roetter, R.P. ; Virtanen, N.K. ; Salo, T. ; Palosuo, T. ; Grönroos, J. ; Fronzek, S. ; Wolf, J. ; Carter, T.R. - \ 2010
    In: Proceedings of Agro 2010 the XIth ESA Congress, Montpellier, France, 29 August - 03 September, 2010. - Montpellier, France : ESA - ISBN 9782909613017 - p. 325 - 326.
    Supporting change in farming systems research
    DeVoil, P. ; Rodriguez, D. ; Rossing, W.A.H. ; Power, B. - \ 2010
    In: Proceedings of ‘Agro2010 the XIth ESA Congress’, Montpellier, France, 29 August - 03 September, 2010. - Montpellier, France : - p. 903 - 904.
    Sustainable futures for vegetable family farmers in Uruguay: a model-based exploration
    Casagrande, M. ; Dogliotti, S. ; Groot, J.C.J. ; Aguerre, V. ; Abbas, A. ; Albín, A. ; Claassen, F. ; Chilibroste, P. ; Rossing, W.A.H. - \ 2010
    In: Proceedings of ‘Agro2010 the XIth ESA Congress’, Montpellier, France, 29 August - 03 September, 2010. - Montpellier, France : - p. 407 - 408.
    Designing agro-ecosystem provisioning by agro-landscapes
    Rossing, W.A.H. ; Groot, J.C.J. ; Kessel, G.J.T. ; Skelsey, P. ; Werf, W. van der - \ 2010
    In: Proceedings of ‘Agro2010 the XIth ESA Congress’, Montpellier, France. 29 August - 3 September, 2010. - Montpellier, France : - p. 871 - 872.
    Co-Innovation as a strategy to develop sustainable farming systems in South Uruguay
    Dogliotti, S. ; Pombo, C. ; Scarlato, M. ; Rossing, W.A.H. - \ 2010
    In: Proceedings of ‘Agro2010 the XIth ESA Congress’, Montpellier, France, 29 August - 3 September, 2010. - Montpellier, France : - p. 391 - 392.
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