Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    '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.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Veertig jaar onderzoek aan de bladvlekkenziekte van tomaat
Wit, P.J.G.M. de - \ 2019
Gewasbescherming 50 (2019)5. - ISSN 0166-6495 - p. 173 - 182.
Joint Assimilation of Leaf Area Index and Soil Moisture from Sentinel-1 and Sentinel-2 Data into the WOFOST Model for Winter Wheat Yield Estimation
Pan, Haizhu ; Chen, Zhongxin ; Wit, Allard de; Ren, Jianqiang - \ 2019
Sensors 19 (2019)14. - ISSN 1424-8220
data assimilation - EnKF - LAI - Sentinel-1 and Sentinel-2 - SM - winter wheat yield - WOFOST

It is well known that timely crop growth monitoring and accurate crop yield estimation at a fine scale is of vital importance for agricultural monitoring and crop management. Crop growth models have been widely used for crop growth process description and yield prediction. In particular, the accurate simulation of important state variables, such as leaf area index (LAI) and root zone soil moisture (SM), is of great importance for yield estimation. Data assimilation is a useful tool that combines a crop model and external observations (often derived from remote sensing data) to improve the simulated crop state variables and consequently model outputs like crop total biomass, water use and grain yield. In spite of its effectiveness, applying data assimilation for monitoring crop growth at the regional scale in China remains challenging, due to the lack of high spatiotemporal resolution satellite data that can match the small field sizes which are typical for agriculture in China. With the accessibility of freely available images acquired by Sentinel satellites, it becomes possible to acquire data at high spatiotemporal resolution (10-30 m, 5-6 days), which offers attractive opportunities to characterize crop growth. In this study, we assimilated remotely sensed LAI and SM into the Word Food Studies (WOFOST) model to estimate winter wheat yield using an ensemble Kalman filter (EnKF) algorithm. The LAI was calculated from Sentinel-2 using a lookup table method, and the SM was calculated from Sentinel-1 and Sentinel-2 based on a change detection approach. Through validation with field data, the inverse error was 10% and 35% for LAI and SM, respectively. The open-loop wheat yield estimation, independent assimilations of LAI and SM, and a joint assimilation of LAI + SM were tested and validated using field measurement observation in the city of Hengshui, China, during the 2016-2017 winter wheat growing season. The results indicated that the accuracy of wheat yield simulated by WOFOST was significantly improved after joint assimilation at the field scale. Compared to the open-loop estimation, the yield root mean square error (RMSE) with field observations was decreased by 69 kg/ha for the LAI assimilation, 39 kg/ha for the SM assimilation and 167 kg/ha for the joint LAI + SM assimilation. Yield coefficients of determination (R2) of 0.41, 0.65, 0.50, and 0.76 and mean relative errors (MRE) of 4.87%, 4.32%, 4.45% and 3.17% were obtained for open-loop, LAI assimilation alone, SM assimilation alone and joint LAI + SM assimilation, respectively. The results suggest that LAI was the first-choice variable for crop data assimilation over SM, and when both LAI and SM satellite data are available, the joint data assimilation has a better performance because LAI and SM have interacting effects. Hence, joint assimilation of LAI and SM from Sentinel-1 and Sentinel-2 at a 20 m resolution into the WOFOST provides a robust method to improve crop yield estimations. However, there is still bias between the key soil moisture in the root zone and the Sentinel-1 C band retrieved SM, especially when the vegetation cover is high. By active and passive microwave data fusion, it may be possible to offer a higher accuracy SM for crop yield prediction.

Novel carbapenemases FLC-1 and IMI-2 encoded by an enterobacter cloacae complex isolated from food products
Brouwer, Michael S.M. ; Tehrani, Kamaleddin H.M.E. ; Rapallini, Michel ; Geurts, Yvon ; Kant, Arie ; Harders, Frank ; Mashayekhi, Vida ; Martin, Nathaniel I. ; Bossers, Alex ; Mevius, Dik J. ; Wit, Ben ; Veldman, Kees T. - \ 2019
Antimicrobial Agents and Chemotherapy 63 (2019)6. - ISSN 0066-4804
Antimicrobial resistance - Carbapenemase - Enterobacter - Plasmid

Food for human consumption is screened widely for the presence of antibiotic-resistant bacteria to assess the potential for transfer of resistant bacteria to the general population. Here, we describe an Enterobacter cloacae complex isolated from imported seafood that encodes two carbapenemases on two distinct plasmids. Both enzymes belong to Ambler class A -lactamases, the previously described IMI-2 and a novel family designated FLC-1. The hydrolytic activity of the novel enzyme against aminopenicillins, cephalosporins, and carbapenems was determined.

Diversity of plasmids and genes encoding resistance to extended spectrum cephalosporins in commensal Escherichia coli From Dutch livestock in 2007-2017
Ceccarelli, Daniela ; Kant, Arie ; Essen-Zandbergen, Alieda Van; Dierikx, Cindy ; Hordijk, Joost ; Wit, Ben ; Mevius, Dik J. ; Veldman, Kees T. - \ 2019
Frontiers in Microbiology 10 (2019)FEB. - ISSN 1664-302X
ESBL - Escherichia coli - Livestock - PAmpC - Plasmid

Extended-spectrum β-lactamase (ESBL) and plasmid-mediated AmpC β-lactamase (pAmpC) genes confer resistance to extended spectrum cephalosporin's. The spread of these genes is mostly facilitated by plasmid-mediated horizontal transfer. National surveillance activities to detect ESBL/pAmpC-producers in commensal bacteria from livestock are in place in the Netherlands since several years. This study aimed at reporting gene and plasmid diversity of commensal ESBL/pAmpC-producing Escherichia coli isolated from healthy animals during surveillance activities between 2007 and 2017. A collection of 2304 extended-spectrum cephalosporin-resistant (ESC-R) E. coli isolated from feces of broilers, dairy cattle, slaughter pigs, turkeys, ducks, and veal calves was investigated and ESBL/pAmpC genes were determined. Gene location of a selection of 473 E. coli isolates was determined and typing of plasmids linked to the ESBL/pAmpC genes was performed. Twenty-two different ESBL/pAmpC genes were identified with bla CTX-M-1 being the most prevalent gene in livestock (43.7%), followed by bla CMY -2 and bla SHV -12 , independent of the animal source. Prevalence of typically human associated bla CTX-M-15 was highest in cattle. Less than 10% E. coli isolates owed their ESC-R phenotype to promoter mutations of the chromosomal ampC gene. Majority (92%) of ESBL/pAmpC genes analyzed were plasmid located, with IncI1α being the most represented plasmid family in isolates from all animals, followed by IncF (veal calves, dairy cattle and slaughter pigs), IncK (broilers and laying hens), IncX1 in broilers, and emerging IncX3 in broilers and dairy cattle. Prevalence and molecular diversity of ESC-R E. coli isolated from livestock over an 11-year period revealed a composite scenario of gene-plasmid combinations.

The Global Gridded Crop Model Intercomparison phase 1 simulation dataset
Müller, Christoph ; Elliott, Joshua ; Kelly, David ; Arneth, Almut ; Balkovic, Juraj ; Ciais, Philippe ; Deryng, Delphine ; Folberth, Christian ; Hoek, Steven ; Izaurralde, Roberto C. ; Jones, Curtis D. ; Khabarov, Nikolay ; Lawrence, Peter ; Liu, Wenfeng ; Olin, Stefan ; Pugh, Thomas A.M. ; Reddy, Ashwan ; Rosenzweig, Cynthia ; Ruane, Alex C. ; Sakurai, Gen ; Schmid, Erwin ; Skalsky, Rastislav ; Wang, Xuhui ; Wit, Allard de; Yang, Hong - \ 2019
Scientific Data 6 (2019). - ISSN 2052-4463 - 22 p.

The Global Gridded Crop Model Intercomparison (GGCMI) phase 1 dataset of the Agricultural Model Intercomparison and Improvement Project (AgMIP) provides an unprecedentedly large dataset of crop model simulations covering the global ice-free land surface. The dataset consists of annual data fields at a spatial resolution of 0.5 arc-degree longitude and latitude. Fourteen crop modeling groups provided output for up to 11 historical input datasets spanning 1901 to 2012, and for up to three different management harmonization levels. Each group submitted data for up to 15 different crops and for up to 14 output variables. All simulations were conducted for purely rainfed and near-perfectly irrigated conditions on all land areas irrespective of whether the crop or irrigation system is currently used there. With the publication of the GGCMI phase 1 dataset we aim to promote further analyses and understanding of crop model performance, potential relationships between productivity and environmental impacts, and insights on how to further improve global gridded crop model frameworks. We describe dataset characteristics and individual model setup narratives.

De novo construction of polyploid linkage maps using discrete graphical models
Behrouzi, Pariya ; Wit, Ernst C. - \ 2019
Bioinformatics 35 (2019)7. - ISSN 1367-4803 - p. 1083 - 1093.

Motivation Linkage maps are used to identify the location of genes responsible for traits and diseases. New sequencing techniques have created opportunities to substantially increase the density of genetic markers. Such revolutionary advances in technology have given rise to new challenges, such as creating high-density linkage maps. Current multiple testing approaches based on pairwise recombination fractions are underpowered in the high-dimensional setting and do not extend easily to polyploid species. To remedy these issues, we propose to construct linkage maps using graphical models either via a sparse Gaussian copula or a non-paranormal skeptic approach. Results We determine linkage groups, typically chromosomes, and the order of markers in each linkage group by inferring the conditional independence relationships among large numbers of markers in the genome. Through simulations, we illustrate the utility of our map construction method and compare its performance with other available methods, both when the data are clean and contain no missing observations and when data contain genotyping errors. Our comprehensive map construction method makes full use of the dosage SNP data to reconstruct linkage map for any bi-parental diploid and polyploid species. We apply the proposed method to three genotype datasets: Barley, peanut and potato from diploid and polyploid populations.

Creating a window of opportunity for establishing ecosystem engineers by adding substratum: a case study on mussels
Capelle, Jacob J. ; Leuchter, Lennet ; Wit, Maurice ; Hartog, Eva ; Bouma, Tjeerd J. - \ 2019
Ecosphere 10 (2019)4. - ISSN 2150-8925 - p. e02688 - e02688.
aggregation - Density dependence - dislodgement - disturbance - flume - Mytilus edulis - positive feedback - stable state
Ecosystem engineers typically exert positive feedback on their environment, which enhances their performance. Such positive feedback is lacking in the establishment phase, when densities are too low and/or patches are too small. There is a strong need to unravel the mechanisms for overcoming the resulting
establishment thresholds, both for ecological restoration purposes and to be able to use their services. In the present study, we question whether providing a transient substratum can be used as tool to overcome establishment thresholds, by creating a window of opportunity for initial settlement, using mussels (Mytilus edulis) as a model system. Combining field and flume experiments, we study how biogenic substratum enrichment in the form of a shell layer on a soft mudflat affects the critical dislodgement thresholds and, thus, the chances of mussel establishment at different mussel densities and aggregation states. Flume results showed that the presence of a shell layer reduced dislodgement of mussel patches in low-energy environments but was conditional for establishment in high-energy environments. That is, in high-energy environments with shells, aggregation into clumps enhanced dislodgement, while dislodgement was reduced with increasing overall mussel biomass and overall mussel patch weight. Without shells, dislodgement was always 100%. These findings agreed with our field studies, which showed that coarse shell material reduced mussel losses (by a factor of 3), reduced aggregation (by a factor of 2.4), and increased attachment strength (by a factor of 2.4). Overall, our results show that the local presence of biogenic substratum increases the
chance of mussel establishment by enhancing the critical hydrodynamic dislodgement threshold. Thus, the local addition of a biogenic substratum may create a window of opportunity to initiate settlement in more
dynamic environments, to shift at a local scale from a bare mudflat state into an established biogenic reef state. Our findings have clear implications for how to approach restoration and management of ecosystem engineers dominated systems. For instance, when positive feedback of ecosystem engineers is lacking, (1) the transient offering of suitable settling substratum may be a necessary step to overcome establishment thresholds, and (2) this becomes increasingly important with increasing abiotic stress.
State-of-the-art global models underestimate impacts from climate extremes
Schewe, Jacob ; Gosling, Simon N. ; Reyer, Christopher ; Zhao, Fang ; Ciais, Philippe ; Elliott, Joshua ; Francois, Louis ; Huber, Veronika ; Lotze, Heike K. ; Seneviratne, Sonia I. ; Vliet, Michelle T.H. Van; Vautard, Robert ; Wada, Yoshihide ; Breuer, Lutz ; Büchner, Matthias ; Carozza, David A. ; Chang, Jinfeng ; Coll, Marta ; Deryng, Delphine ; Wit, Allard De; Eddy, Tyler D. ; Folberth, Christian ; Frieler, Katja ; Friend, Andrew D. ; Gerten, Dieter ; Gudmundsson, Lukas ; Hanasaki, Naota ; Ito, Akihiko ; Khabarov, Nikolay ; Kim, Hyungjun ; Lawrence, Peter ; Morfopoulos, Catherine ; Müller, Christoph ; Müller Schmied, Hannes ; Orth, René ; Ostberg, Sebastian ; Pokhrel, Yadu ; Pugh, Thomas A.M. ; Sakurai, Gen ; Satoh, Yusuke ; Schmid, Erwin ; Stacke, Tobias ; Steenbeek, Jeroen ; Steinkamp, Jörg ; Tang, Qiuhong ; Tian, Hanqin ; Tittensor, Derek P. ; Volkholz, Jan ; Wang, Xuhui ; Warszawski, Lila - \ 2019
Nature Communications 10 (2019). - ISSN 2041-1723
Global impact models represent process-level understanding of how natural and human systems may be affected by climate change. Their projections are used in integrated assessments of climate change. Here we test, for the first time, systematically across many important systems, how well such impact models capture the impacts of extreme climate conditions. Using the 2003 European heat wave and drought as a historical analogue for comparable events in the future, we find that a majority of models underestimate the extremeness of impacts in important sectors such as agriculture, terrestrial ecosystems, and heat-related human mortality, while impacts on water resources and hydropower are overestimated in some river basins; and the spread across models is often large. This has important implications for economic assessments of climate change impacts that rely on these models. It also means that societal risks from future extreme events may be greater than previously thought.
WUR en de provincie
Westerink, Judith ; Wit-de Vries, Esther de - \ 2019
Extrinsic wheat fibre consumption enhances faecal bulk and stool frequency; A randomized controlled trial
Wit, Nicole De; Esser, Diederik ; Siebelink, Els ; Fischer, Anne ; Sieg, Juergen ; Mes, Jurriaan - \ 2019
Food & Function 10 (2019)2. - ISSN 2042-6496 - p. 646 - 651.

The beneficial effect of wheat fibres on faecal bulk and stool pattern has mainly been observed with intact wheat fibres. This study investigates the effect of extrinsic wheat fibre (VITACEL® wheat fibre), which can be easily incorporated in many food products, on faecal bulk, stool pattern, gastrointestinal complaints, satiety and food liking. In a double-blind randomized crossover trial, healthy male volunteers received meal boxes for 10 days, containing various food products enriched with extrinsic wheat fibre (∼20 grams of additional fibre per day) or control food products containing conventional levels of fibre with similar taste, appearance and caloric values. Meal boxes were integrated in the normal dietary pattern. Stool frequency, stool consistency, gastrointestinal complaints, satiety and product liking were assessed daily, and the last 5 days of each intervention, participants collected all their faeces to analyse faecal bulk. We found that consumption of extrinsic wheat fibre-enriched products significantly enhanced faecal bulk; faecal wet and dry weight showed a 1.41 ± 0.1 and 1.55 ± 0.1 times increase compared to control, respectively (p < 0.01). Extrinsic wheat fibre intervention furthermore increased stool frequency (1.3 ± 0.1 defecations per day compared to 1.1 ± 0.1 defecations per day during control diet, p < 0.05), but did not affect stool consistency, satiety, gastrointestinal complaints or product liking. So, increased consumption of extrinsic wheat fibre enhances faecal bulk and stool frequency. As this extrinsic wheat fibre can be easily incorporated in many food products without affecting appearance or taste, it might facilitate the increase of overall fibre intake and subsequently improve (intestinal) health.

Agrohydrological analysis of groundwater recharge and land use changes in the Pampas of Argentina
Kroes, Joop ; Dam, Jos van; Supit, Iwan ; Abelleyra, Diego de; Verón, Santiago ; Wit, Allard de; Boogaard, Hendrik ; Angelini, Marcos ; Damiano, Francisco ; Groenendijk, Piet ; Wesseling, Jan ; Veldhuizen, Ab - \ 2019
Agricultural Water Management 213 (2019). - ISSN 0378-3774 - p. 843 - 857.
Argentina - Capillary rise - Groundwater recharge - Land use - Pampas - Soybean - SWAP - WOFOST

This paper studies the changes of groundwater, climate and land use in the Pampas of Argentina. These changes offer opportunities and threats. Lowering groundwater without irrigation causes drought and successive crop and yield damage. Rising groundwater may alleviate drought as capillary rise supports root water uptake and crop growth, thus narrowing the difference between potential and actual yields. However, rising groundwater may also limit soil water storage, cause flooding in metropolitan areas and have a negative impact on crop yields. Changing land use from continuous soy bean into crop rotations or natural vegetation may decrease groundwater recharge and thus decrease groundwater levels. In case of crop rotation however, leaching of nutrients like nitrate may increase. We quantified these impacts using integrated dynamic crop growth and soil hydrology modelling. The models were tested at field scale using a local dataset from Argentina. We applied distributed modelling at regional scale to evaluate the impacts on groundwater recharge and crop yields using long term weather data. The experiments showed that threats arise from continuous monotone land use. Opportunities are created when a proper balance is found between supply and demand of soil water using a larger differentiation of land use. Increasing the areas of land use types with higher evapotranspiration, like permanent grassland and trees, will contribute to a more stable hydrologic system with more water storage capacities in the soil system and lower groundwater levels. Modelling tools clearly support the evaluation of the impact of land use and climate change on groundwater levels and crop yields.

25 years of the WOFOST cropping systems model
Wit, Allard de; Boogaard, Hendrik ; Fumagalli, Davide ; Janssen, Sander ; Knapen, Rob ; Kraalingen, Daniel van; Supit, Iwan ; Wijngaart, Raymond van der; Diepen, Kees van - \ 2019
Agricultural Systems 168 (2019). - ISSN 0308-521X - p. 154 - 167.
open source - Regional scale - Simulation Model - yield forecasting

The WOFOST cropping systems model has been applied operationally over the last 25 years as part of the MARS crop yield forecasting system. In this paper we provide an updated description of the model and reflect on the lessons learned over the last 25 years. The latter includes issues like system performance, model sensitivity, spatial model setup, parameterization and calibration approaches as well as software implementation and version management. Particularly for spatial model calibrations we provide experience and guidelines on how to execute calibrations and how to evaluate WOFOST model simulation results, particularly under conditions of limited field data availability. As an open source model WOFOST has been a success with at least 10 different implementations of the same concept. An overview is provided for those implementations which are managed by MARS or Wageningen groups. However, the proliferation of WOFOST implementations has also led to questions on the reproducibility of results from different implementations as is demonstrated with an example from MARS. In order to certify that the different WOFOST implementations and versions available can reproduce basic sets of inputs and outputs we make available a large set of test cases as appendix to this publication. Finally, new methodological extensions have been added to WOFOST in simulating the impact of nutrients limitations, extreme events and climate variability. Also, a difference is made in the operational and scientific versions of WOFOST with different licensing models and possible revenue generation. Capitalizing both on academic development as well as model testing in real-world situations will help to enable new applications of the WOFOST model in precision agriculture and smart farming.

Quantitative land evaluation implemented in Dutch water management
Hack-ten Broeke, M.J.D. ; Mulder, H.M. ; Bartholomeus, R.P. ; Dam, J.C. van; Holshof, G. ; Hoving, I.E. ; Walvoort, D.J.J. ; Heinen, M. ; Kroes, J.G. ; Bakel, P.J.T. van; Supit, I. ; Wit, A.J.W. de; Ruijtenberg, R. - \ 2019
Geoderma 338 (2019). - ISSN 0016-7061 - p. 536 - 545.
Agro-hydrology - Crop yield assessment - Land use - Meta-model - Simulation modelling - Soil management

Both in land evaluation and in water management quantitative methods, GIS and simulation modelling are well-known techniques for quantifying the effects of changes, such as land use or climate change. For hydrological management decisions information is often required on the effect of those decisions on agricultural production. To serve the needs of different types of users, like water authorities, provinces, drinking water companies and the National Department of Infrastructure and Water Management we developed a toolbox named WaterVision Agriculture as an instrument that can determine effects on crop yield and the farm economy as a result of drought, too wet or too saline conditions for both current and future climatic conditions. WaterVision Agriculture is based on the hydrological simulation model SWAP, the crop growth model WOFOST and farm management and economic assessments such as DairyWise for dairy farming. The WaterVision Agriculture (WVA) project resulted in two products, namely i) an easily applicable tool (also called the WVA-table) and ii) the operational models for hydrology and crop growth SWAP and WOFOST for calculating effects on field scale combined with calculating farm economic results and indirect effects. SWAP simulates water transport in the unsaturated zone using meteorological data, boundary conditions (like groundwater level or drainage) and soil parameters. WOFOST simulates crop growth as a function of meteorological conditions and crop parameters. Using the combination of these process-based models and methods for describing crop management and economic value we derived a meta-model, i.e. a set of easily applicable simplified relations for assessing crop growth as a function of soil type and groundwater level. These relations are based on multiple model runs for at least 72 soil units and the possible groundwater regimes in the Netherlands. The easily applicable tool (WVA-table) uses this meta-model. Applying the meta-model of WaterVision Agriculture should allow for better decisions on land use or soil and water management because the instrument can help to quantify the effects of changes in climate, land use, hydrological conditions or combinations of these effects on agricultural production.

Implications of crop model ensemble size and composition for estimates of adaptation effects and agreement of recommendations
Rodríguez, A. ; Ruiz-Ramos, M. ; Palosuo, T. ; Carter, T.R. ; Fronzek, S. ; Lorite, I.J. ; Ferrise, R. ; Pirttioja, N. ; Bindi, M. ; Baranowski, P. ; Buis, S. ; Cammarano, D. ; Chen, Y. ; Dumont, B. ; Ewert, F. ; Gaiser, T. ; Hlavinka, P. ; Hoffmann, H. ; Höhn, J.G. ; Jurecka, F. ; Kersebaum, K.C. ; Krzyszczak, J. ; Lana, M. ; Mechiche-Alami, A. ; Minet, J. ; Montesino, M. ; Nendel, C. ; Porter, J.R. ; Ruget, F. ; Semenov, M.A. ; Steinmetz, Z. ; Stratonovitch, P. ; Supit, I. ; Tao, F. ; Trnka, M. ; Wit, A. de; Rötter, R.P. - \ 2019
Agricultural and Forest Meteorology 264 (2019). - ISSN 0168-1923 - p. 351 - 362.
Climate change - Decision support - Outcome confidence - Response surface - Uncertainty - Wheat adaptation

Climate change is expected to severely affect cropping systems and food production in many parts of the world unless local adaptation can ameliorate these impacts. Ensembles of crop simulation models can be useful tools for assessing if proposed adaptation options are capable of achieving target yields, whilst also quantifying the share of uncertainty in the simulated crop impact resulting from the crop models themselves. Although some studies have analysed the influence of ensemble size on model outcomes, the effect of ensemble composition has not yet been properly appraised. Moreover, results and derived recommendations typically rely on averaged ensemble simulation results without accounting sufficiently for the spread of model outcomes. Therefore, we developed an Ensemble Outcome Agreement (EOA) index, which analyses the effect of changes in composition and size of a multi-model ensemble (MME) to evaluate the level of agreement between MME outcomes with respect to a given hypothesis (e.g. that adaptation measures result in positive crop responses). We analysed the recommendations of a previous study performed with an ensemble of 17 crop models and testing 54 adaptation options for rainfed winter wheat (Triticum aestivum L.) at Lleida (NE Spain) under perturbed conditions of temperature, precipitation and atmospheric CO2 concentration. Our results confirmed that most adaptations recommended in the previous study have a positive effect. However, we also showed that some options did not remain recommendable in specific conditions if different ensembles were considered. Using EOA, we were able to identify the adaptation options for which there is high confidence in their effectiveness at enhancing yields, even under severe climate perturbations. These include substituting spring wheat for winter wheat combined with earlier sowing dates and standard or longer duration cultivars, or introducing supplementary irrigation, the latter increasing EOA values in all cases. There is low confidence in recovering yields to baseline levels, although this target could be attained for some adaptation options under moderate climate perturbations. Recommendations derived from such robust results may provide crucial information for stakeholders seeking to implement adaptation measures.

Improving WOFOST model to simulate winter wheat phenology in Europe : Evaluation and effects on yield
Ceglar, A. ; Wijngaart, R. van der; Wit, A. de; Lecerf, R. ; Boogaard, H. ; Seguini, L. ; Berg, M. van den; Toreti, A. ; Zampieri, M. ; Fumagalli, D. ; Baruth, B. - \ 2019
Agricultural Systems 168 (2019). - ISSN 0308-521X - p. 168 - 180.
Calibration - Crop yield forecasting - Europe - Phenology - Triticum aestivum - WOFOST

This study describes and evaluates improvements to the MARS crop yield forecasting system (MCYFS) for winter soft wheat (Triticum aestivum) in Europe, based on the WOFOST crop simulation model, by introducing autumn sowing dates, realistic soil moisture initialization, adding vernalization requirements and photoperiodicity, and phenology calibration. Dataset of phenological observations complemented with regional cropping calendars across Europe is used. The calibration of thermal requirements for anthesis and maturity is done by pooling all available observations within European agro-environmental zones and minimizing an objective function that combines the differences between observed and simulated anthesis, maturity and harvest dates. Calibrated phenology results in substantial improvement in simulated dates of anthesis with respect to the original MCYFS simulations. The combined improvements to the system result in a physically more plausible spatial distribution of crop model indicators across Europe. Crop yield indicators point to better agreement with recorded national winter wheat yields with respect to the original MCYFS simulations, most pronounced in central, eastern and southern Europe. However, model skill remains low in large parts of western Europe, which may possibly be attributed to the impacts of wet conditions.

Detecting epistatic selection with partially observed genotype data by using copula graphical models
Behrouzi, Pariya ; Wit, Ernst C. - \ 2019
Journal of the Royal Statistical Society. Series C: Applied Statistics 68 (2019)1. - ISSN 0035-9254 - p. 141 - 160.
Epistasis - Epistatic selection - Gaussian copula - Graphical models - Linkage disequilibrium - Penalized inference

In cross-breeding experiments it can be of interest to see whether there are any synergistic effects of certain genes. This could be by being particularly useful or detrimental to the individual. This type of effect involving multiple genes is called epistasis. Epistatic interactions can affect growth, fertility traits or even cause complete lethality. However, detecting epistasis in genomewide studies is challenging as multiple-testing approaches are underpowered. We develop a method for reconstructing an underlying network of genomic signatures of high dimensional epistatic selection from multilocus genotype data. The network captures the conditionally dependent short- and long-range linkage disequilibrium structure and thus reveals 'aberrant' marker-marker associations that are due to epistatic selection rather than gametic linkage. The network estimation relies on penalized Gaussian copula graphical models, which can account for a large number of markers p and a small number of individuals n. We demonstrate the efficiency of the proposed method on simulated data sets as well as on genotyping data in Arabidopsis thaliana and maize.

Analyse van provinciale natuurbeleidsstrategieën : Realiseren van het natuurnetwerk en vergroten van maatschappelijke betrokkenheid bij natuur
Wit, Esther de; Doren, Didi van; Bouwma, Irene ; Broekhoven, Saskia van; Kamphorst, Dana ; Kuindersma, Wiebren - \ 2018
Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-paper 49) - 20
Comparing cities of the world according to their food security risks and opportunities
Hennen, Wil ; Diogo, Vasco ; Polman, Nico ; Dijkshoorn-Dekker, Marijke - \ 2018
In: Sustainable Development and Planning X. - WIT Press (WIT Transactions on Ecology and the Environment ) - ISBN 9781784662912 - p. 953 - 962.
Due to the combined effect of climate change, expected population growth and increased concentration of population in cities and towns, food insecurity in urban areas is becoming of increasing concern and is regarded as one of the most prominent development challenges for the 21st century. Cities differ with respect to their specific food security risks and opportunities of local food supply to meet the increasing demand for food. The tool “Global Metropolitan Detector” has been developed to compare cities of the world based on different dimensions of food security, particularly availability, accessibility, and affordability of food, risk of floods and climate change, and healthy diets. Worldwide publicly available datasets, e.g. from FAOSTAT, EarthStat and WorldClim, are used. These are separately converted (aggregated/disaggregated) to a homogenous 5 arc-minute grid and combined in the tool to calculate (by weighted average) and compare the demand and local supply of food, including the required area of land to meet the city-specific consumption needs (measured in “Food Metres”). The purpose is to benchmark 850 cities based on several aspects related to food security. The resulting benchmark of cities and their indicator values can be visualised in maps showing their position with respect to food security in general, or investigate particular aspects in more detail, e.g. cities having low/high flood risks or cities that are better able to meet the demand of (fresh) vegetables and fruit from local producers. The maps can support policymakers to identify causes and locations of food insecurity, and the indicative results – based on limited available worldwide data – can serve as an inducement for further investigation with more detailed data from cities.
Van meerdere kanten bekeken : een meervoudig analyse- & evaluatiekader voor beleid gericht op maatschappelijkebetrokkenheid bij natuur : op maat te maken met behulp van kaarten
Westerink, J. ; Kamphorst, D.A. ; Wit, E. de; Heide, C.M. van der; Boer, T.A. de; Gerritsen, A.L. - \ 2018
Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (Rapporten Wettelijke Onderzoekstaken Natuur &amp; Milieu. WOt-rapport 130) - 147
Encouraging societal engagement with nature has become a goal of Dutch nature policy in its ownright. As such, there is a growing need to evaluate policies for societal engagement. However, lessexperience has been gained on evaluating this type of policy than, for example, policies for protectingand promoting biodiversity. The Netherlands Environmental Assessment Agency (PBL) asked StatutoryResearch Tasks Unit for Nature & the Environment of Wageningen University & Research to develop ananalysis & evaluation framework for policies that seek to foster societal engagement with nature. The framework can be used for the reflexive evaluation of the Nature Pact (Natuurpact) and of theAssessments of the Dutch Human Environment. This report contains a multiple analysis & evaluation framework that can be used to compile specific analysis & evaluation frameworks for policies that seek to foster societal engagement with nature. The framework is presented in the form of a set of cards in the Appendix. The main body of the reportcontains the conceptual underpinnings and explanatory manual.
Noodzaak voor genetisch beheer van de Nederlandse trekpaardenpopulatie
Schurink, Anouk ; Hiemstra, Sipke Joost ; Oldenbroek, Kor ; Wit, Agnes de; Ducro, Bart ; Windig, Jack - \ 2018
Wageningen : Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research (CGN rapport 41) - 37
The Dutch Draught horse is a rare Dutch horse breed. To conserve rare breeds, it is of great importance to monitor population size and increase in inbreeding and kinship in a population. When screening the Dutch Draught horse population, it turned out that inbreeding (and potential consequences) should be controlled by the studbook (KVTH) with participation of breeders. During the most recent generation (2010-2017) fewer foals were born annually compared to the generation before. Also, the percentage of foals that is used in breeding at a later age decreased steadily. At the same time there is a considerable increase in the kinship between horses that are used in breeding. The increase in inbreeding passes the FAO threshold of 0.5% per generation. In light of the increase in kinship, we expect that the increase in inbreeding will even be higher in the future. Screening the population clearly showed that genetic management is needed to be able to better control inbreeding (and potential accompanying consequences). It is possible to drastically reduce the inbreeding increase through genetic management.
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