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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    Global wheat production with 1.5 and 2.0°C above pre‐industrial warming
    Liu, B. ; Martre, P. ; Ewert, F. ; Porter, J.R. ; Challinor, A.J. ; Muller, G. ; Ruane, A.C. ; Waha, K. ; Thorburn, Peter J. ; Aggarwal, P.K. ; Ahmed, M. ; Balkovic, Juraj ; Basso, B. ; Biernath, C. ; Bindi, M. ; Cammarano, D. ; Sanctis, Giacomo De; Dumont, B. ; Espadafor, M. ; Eyshi Rezaei, Ehsan ; Ferrise, Roberto ; Garcia-Vila, M. ; Gayler, S. ; Gao, Y. ; Horan, H. ; Hoogenboom, G. ; Izaurralde, Roberto C. ; Jones, C.D. ; Kassie, Belay T. ; Kersebaum, K.C. ; Klein, C. ; Koehler, A.K. ; Maiorano, Andrea ; Minoli, Sara ; Montesino San Martin, M. ; Kumar, S.N. ; Nendel, C. ; O'Leary, G.J. ; Palosuo, T. ; Priesack, E. ; Ripoche, D. ; Rötter, R.P. ; Semenov, M.A. ; Stockle, Claudio ; Streck, T. ; Supit, I. ; Tao, F. ; Velde, M. van der; Wallach, D. ; Wang, E. ; Webber, H. ; Wolf, J. ; Xiao, L. ; Zhang, Z. ; Zhao, Z. ; Zhu, Y. ; Asseng, S. - \ 2019
    Global Change Biology 25 (2019)4. - ISSN 1354-1013 - p. 1428 - 1444.
    Efforts to limit global warming to below 2°C in relation to the pre-industrial level are under way, in accordance with the 2015 Paris Agreement. However, most impact research on agriculture to date has focused on impacts of warming >2°C on mean crop yields, and many previous studies did not focus sufficiently on extreme events and yield interannual variability. Here, with the latest climate scenarios from the Half a degree Additional warming, Prognosis and Projected Impacts (HAPPI) project, we evaluated the impacts of the 2015 Paris Agreement range of global warming (1.5°C and 2.0°C warming above the pre-industrial period) on global wheat production and local yield variability. A multi-crop and multi-climate model ensemble over a global network of sites developed by the Agricultural Model Intercomparison and Improvement Project (AgMIP) for Wheat was used to represent major rainfed and irrigated wheat cropping systems. Results show that projected global wheat production will change by -2.3% to 7.0% under the 1.5 °C scenario and -2.4% to 10.5% under the 2.0 °C scenario, compared to a baseline of 1980-2010, when considering changes in local temperature, rainfall and global atmospheric CO2 concentration, but no changes in management or wheat cultivars. The projected impact on wheat production varies spatially; a larger increase is projected for temperate high rainfall regions than for moderate hot low rainfall and irrigated regions. Grain yields in warmer regions are more likely to be reduced than in cooler regions. Despite mostly positive impacts on global average grain yields, the frequency of extremely low yields (bottom 5 percentile of baseline distribution) and yield inter-annual variability will increase under both warming scenarios for some of the hot growing locations, including locations from the second largest global wheat producer -India, which supplies more than 14% of global wheat. The projected global impact of warming <2°C on wheat production are therefore not evenly distributed and will affect regional food security across the globe as well as food prices and trade.
    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.

    Simulation of soil organic carbon effects on long-term winter wheat (Triticum aestivum) production under varying fertilizer inputs
    Ghaley, Bhim B. ; Wösten, Henk ; Olesen, Jørgen E. ; Schelde, Kirsten ; Baby, Sanmohan ; Karki, Yubaraj K. ; Børgesen, Christen D. ; Smith, Pete ; Yeluripati, Jagadeesh ; Ferrise, Roberto ; Bindi, Marco ; Kuikman, Peter ; Lesschen, Jan Peter ; Porter, John R. - \ 2018
    Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
    Crop productivity - DAISY model - Grain yield - Long-term experiment - Nitrogen - Pedotransfer functions - Plant available water

    Soil organic carbon (SOC) has a vital role to enhance agricultural productivity and for mitigation of climate change. To quantify SOC effects on productivity, process models serve as a robust tool to keep track of multiple plant and soil factors and their interactions affecting SOC dynamics. We used soil-plant-atmospheric model viz. DAISY, to assess effects of SOC on nitrogen (N) supply and plant available water (PAW) under varying N fertilizer rates in winter wheat (Triticum aestivum) in Denmark. The study objective was assessment of SOC effects on winter wheat grain and aboveground biomass accumulation at three SOC levels (low: 0.7% SOC; reference: 1.3% SOC; and high: 2% SOC) with five nitrogen rates (0–200 kg N ha−1) and PAW at low, reference, and high SOC levels. The three SOC levels had significant effects on grain yields and aboveground biomass accumulation at only 0–100 kg N ha−1 and the SOC effects decreased with increasing N rates until no effects at 150–200 kg N ha−1. PAW had significant positive correlation with SOC content, with high SOC retaining higher PAW compared to low and reference SOC. The mean PAW and SOC correlation was given by PAW% = 1.0073 × SOC% + 15.641. For the 0.7–2% SOC range, the PAW increase was small with no significant effects on grain yields and aboveground biomass accumulation. The higher winter wheat grain and aboveground biomass was attributed to higher N supply in N deficient wheat production system. Our study suggested that building SOC enhances agronomic productivity at only 0–100 kg N ha−1. Maintenance of SOC stock will require regular replenishment of SOC, to compensate for the mineralization process degrading SOC over time. Hence, management can maximize realization of SOC benefits by building up SOC and maintaining N rates in the range 0–100 kg N ha−1, to reduce the off-farm N losses depending on the environmental zones, land use and the production system.

    Concurrentie, concentratie en rentabiliteit in de glastuinbouw in Nederland
    Veerman, Kees - \ 2018
    Wageningen University. Promotor(en): O. van Kooten. - Wageningen : Wageningen University - ISBN 9789463438865 - 331


    The expansion of the market area of the European Union has caused a strong increase of supply and demand of fresh horticulture products of the Dutch glasshouse sector on the European market. Consequently there is increased competition with companies from new European member states, producing against lower prices, as well as changes in production and sales structure. In the Dutch food horticulture sector this led to a large horizontal and vertical merger between most of the auctions and a number of large exporters. From 1996 to 1998 VTN/The Greenery changed from a co-operative auction into a co-operative trade organisation. In the floriculture sector only horizontal mergers took place between co-operative auctions. The wholesalers/exporters remained independent. At present there are two Flower Auctions, FloraHolland te Naaldwijk (market share 98%) and Plantion in Ede (2%).

    Central research question

    This thesis explores the development of market structure, market strategy and market results in the horticulture glasshouse sector over the last thirty-five years. The central research question is whether the difference in market structure and market strategy in the Dutch sectors of glasshouse vegetables and glasshouse cut flowers and pot plants is a significant cause to explain the difference in market results for the growers and their co-operative organisations.

    The conceptual model

    A number of theories and models have been studied derived from the Industrial Organisation Theory. This theory focuses on the analysis of branches of industries, industry chains and markets involved. It examines the relation between market structure (S), market conduct (C) and market performance (P) through the SCP-model (in Dutch: SGR-model). A description and explanation is given of the static SCP-model of Bain, the dynamic SGR-model of De Jong and the branch-analysing models of Porter and Daems. The conceptual model of competition, concentration and performance (figure 1.1) has been constructed from these models to analyse the Dutch horticulture glasshouse sectors.

    Research of producers, sector research and research of auctions/sales organisations

    From 2006-2008 three research projects on producers were conducted amongst 40 growers of vegetables, 40 growers of cut flowers and 40 growers of pot plants, all under glass. Data and opinions of growers about their company, market strategy and performance were gathered. In the same period sector research of the development of total production, imports and exports took place in the three sectors of the glasshouse industry on sector level, on the level of sales organisations and the wholesalers/ exporters. The gathered data have been analysed and tested on selected variables. In three different chapters temporary conclusions have been drawn. The most important business and market characteristics and research outcomes are discussed in three separate tables at the end of these three chapters and the associated appendices. The research of producers was expanded in 2015/2016 on the basis of the data of the research 2006-2008 with econometric research and multiple analysis of a number of the most important variables of market structure and market conduct to explain the market results (Lerner Index).

    Results of sector research

    The three horticulture sectors under glass show a positive development in yearly production and export value over a period of thirty-five years, besides a small decrease in 2009 and 2011, as a result of the banking and EHEC crisis. In the Dutch floriculture sector the average growing figures are a bit higher than in the food horticulture sector because of a stronger yearly increase in the production of pot plants. In all three sectors the production and export values are increased almost every year until the banking crisis in 2009. After 2010/2011 the sectors have been recovering.

    Development of variables in Dutch horticulture glasshouse sector 1980-2016

    The sector cut flowers under glass show a decrease of area and production (m2 glass) in The Netherlands. However, there is an increase of import and direct supply of cut flowers from foreign growers and Dutch companies from the southern part of Africa (roses, chrysanthemums etc.). All sectors profit from the growing import/re-export function of vegetables and fruit, cut flowers and pot plants from The Netherlands to neighbouring countries and trade partners in Europe. The high share of the sector variables domestic share and export share in all three sectors stimulate the development of production value, export value and prices.

    Results of research into auctions/sales organisations

    In the food horticulture and floriculture sectors there has been quite a difference in market strategy and market structure since 1998. In the sector vegetables under glass the degree of concentration of the four largest sales organisations (C4) has decreased to the level of before the merger (60%). In 1997 this figure was 96%. Also the share of growers of VTN/The Greenery in the area of Dutch vegetables under glass has decreased. VTN/The Greenery did not reach her target of 1996 with their strategy of horizontal and vertical concentration: organizing a larger bundling of the turnover of the Dutch auctions and wholesalers/exporters.

    The search for a good working integration of horticultural production and trade in one company with an efficient and effective structure has not been completed yet and started in 2016 with a new sales organisation. The financial position of VTN/The Greenery on the European market is not strong. Since 1996 the annual turnover has strongly fluctuated between 0.9 and 1.5 billion euros, with a variation range of 25 to 30 %. The supply of their own members halved, just like the income out of commission. The position on the Dutch market is stable, on the most important European markets difficult. The return on investment is low. In 2015 and 2016 a careful recovery started after the difficult years of crisis 2009, 2011 and 2013.

    Flower auctions FloraHolland and VBA showed a clear strategy and good results around the merger of 2007. The merger was a good example of a carefully implemented strategy of horizontal concentration, bringing together the interests of the flower auctions and their members. For FloraHolland the period of the crisis 2009-2011 was a test with success.

    There was an expansion of horizontal concentration across the borders: a new joint venture auction Rhein-Maas, founded together with the German organisation Landgard and there was an integration with the import auction TFA in Aalsmeer. Both organisations are important for the market position of FloraHolland. In the Dutch floriculture sector under glass there are hardly any examples of vertical concentration of producers or sales organisations with wholesalers/exporters. There are examples, though, of vertical co-operation between these organisations and international retail, especially with the larger growers of pot plants.

    The auction clock, physical and digital, is the most important sales method the flower auctions use daily. For most products there is a public pricing system. It provides a transparent process of supply and demand against sharp tariffs of the auction. For cut flowers as well as for pot and garden plants a large part of the product groups are sold by way of the auction clock, which mostly ensures a reliable reference price for mediation and personal selling and provides a good match of supply and demand and a ‘clean’ market. Attention to strengthen the position of the auction clock, especially with the selling of pot and garden plants, is important. The turnover of FloraHolland decreased in 2009 (bank crisis) and increased in 2010 and 2011 just above the level of 2008. Incomes out of services dropped. As costs decreased more than incomes, profits and solvency improved in this period.

    In 2012 FloraHolland realised a turnover increase of 3% compared to 2011. However, the incomes out of services decreased. In 2013 the sector performed reasonably. The turnover of FloraHolland increased slightly but costs were higher than incomes and FloraHolland had an exploitation loss. 2014 was a year of slight recovery, 2015 and 2016 ended with an increasing turnover of 3 and 4%. Profit after tax in these years are 12 and 3 million euros. For most of the growers and customers the results in 2015 and 2016 were positive. The decision of the wholesale/export (VGB) to contribute again in the promotion costs of Bloemenbureau Holland was welcomed very positively. Along with the new strategy of 2020 FloraHolland is working on the strengthening and expansion of the physical and digital market places.

    Research results of producers

    On producers level there is also quite a difference in market strategy, structure and results between growers in the sectors of glasshouse vegetables and glasshouse cut flowers and pot plants. At present there is a fierce struggle to survive in each sector. It seems that the small grower of cut flowers and pot plants stands a better chance than the small grower in vegetables. The most striking single relations between structure, conduct and result will be mentioned.

    Most striking single relations glasshouse vegetables

    - The small company has relatively higher costs than the larger types. If the sales organisation uses the principle of ‘the user pays the total costs made’ this burden is rather heavy for the smallest companies.

    - Auction growers mainly deliver round or grape tomatoes, the majority of independent growers choose for the special varieties. This influences the pricing process.

    - Small and large auction growers differ significantly in business size from independent growers, but realise comparable margins. Large-scale production does not always lead to lower average costs and a better margin, but it does entail a greater risk of too much supply and low prices. Growers with a larger business size are faced with larger financial problems in difficult years than smaller ones.

    - Horizontal concentration of the four largest growers of vegetables lies at a low level and their sales power is low. The concentration of the four largest sales organisations is about 60%.

    - Vertically integrated auction growers are smaller in business size and invest less than non- integrated independent growers. They realise comparable margins.

    - The importance of the sales organisation to realise good prices and margins for the members’ products seems rather small. Sharp purchase prices are of equal importance for the trade organisation and influence the margin of the members.

    - Higher investments don’t produce higher results (directly). More innovative investments are needed to improve prices and margins.

    Most striking single relations glasshouse cut flowers

    - The small auction grower realises an expected smaller turnover and pays higher commission than the larger auction grower, member of a growers organisation. Although there is no significant relation between grower type and realised margin, higher commission can lead to higher prices and margins. Besides the higher price level, smaller growers realise a higher solvency than larger growers.

    - Growers of roses under glass realise a higher margin than growers of chrysanthemums because of a wide and deep assortment.

    - Small growers of cut flowers show comparable or better results than the larger ones.

    - Horizontal concentration of the four largest growers of cut flowers lies, just like the sectors of vegetables and pot plants under glass, at a low level. The small auction grower has little market power and needs the sales organisation for reasonable prices and successful sales.

    - There are no significant relations between the organisation of sales and growers’ turnover, realised margin and the height of commission. It looks as if every grower uses his own mix of marketing and sales activities in a way that no significant differences in results arise.

    - Selling of cut flowers by means of the auction clock gives good results.

    Most striking single relations glasshouse pot plants

    - The smaller auction grower, with or without personal selling, realises an expected smaller turnover but a higher margin than the larger auction grower, member of a growers organisation.

    - Smaller growers (in m2 glass) get higher results or results comparable to those of the larger ones. Old and new companies get comparable margins.

    - Growers of green plants get a significant lower yearly turnover than growers of blooming pot plants. Green plants are often more unique than blooming plants. That is why growers of green plants get higher prices and margins.

    - Horizontal concentration of the growers of pot plants lies, just like in the other sectors, at a low level. The small auction grower has little market power and needs the sales organisation for realising reasonable prices and successful sales.

    - Like in the other sectors the small grower invests less in his business than the larger ones. Higher investments do not directly produce higher results. More innovative investments are needed to improve prices and margins.

    - There is a significant relation between the organisation of sales and the yearly realised turnover: larger growers use more personal selling besides the sales services of the auction, as their own business activity or as an activity of the growers organisation.

    Boarding out all sales activities to FloraHolland is effective especially for the small grower and enlarges the chance of realising a higher margin. Although he pays a higher commission, he realises a higher margin because of the positive relation between commission and margin.

    Producers results through econometric research

    Most striking multiple relations glasshouse vegetables

    The results of the econometric analysis show that in the sector glasshouse vegetables membership of a growers association produces better results on average than membership of a traditional marketing corporation. Especially young producers with new ideas about the organisation of the company and vertical co-operation with on average large and modern companies are booking the best results.

    Most striking multiple relations glasshouse cut flowers

    Auction growers using the auction clock exclusively to sell their products realise a higher margin on average than growers using other selling methods. The membership of a growers association produces higher results on average than no membership and smaller companies get higher margins than large ones. Senior growers get higher results than junior growers. The auction clock is the best guarantee for realising higher margins. It seems that in the sector cut flowers a larger scale has less effect on the margin than producing ‘niche’ product types. For the latter the selling method via the auction clock plays an important role. Companies with ‘niche’ products have higher fixed costs although a higher margin gives fewer problems when it comes to finance the production.

    Final conclusion

    The answer to the central question confirms the following: the difference in market structure and market strategy in the Dutch sectors of glasshouse vegetables and glasshouse cut flowers is a significant cause to explain the difference in market results. If we follow the position and the results of the small grower in the sector glasshouse vegetables, we are looking at a producer in a tight spot with lower average results for the grower and his co-operation in comparison with the independent grower and his grower association. In the sector glasshouse cut flowers the position and results of the small auction clock grower is better in comparison with the grower who sells on his own or via a growers association.

    The results of this research indicate that in the sector glasshouse vegetables the highest margins are obtained by the independent growers associations, working either cooperativly with the classical co-operations or independent there from but in any case with their own marketing strategy. In the sector glasshouse cut flowers it is the grower selling through the auction clock who gets the highest margins. In the sector glasshouse pot plants, where the type of the product clearly differs from the perishable vegetables and cut flowers, there are too few data to draw conclusions.

    Adaptation response surfaces for managing wheat under perturbed climate and CO2 in a Mediterranean environment
    Ruiz-Ramos, M. ; Ferrise, R. ; Rodríguez, A. ; Lorite, I.J. ; Bindi, M. ; Carter, T.R. ; Fronzek, S. ; Palosuo, T. ; Pirttioja, N. ; 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. - \ 2018
    Agricultural Systems 159 (2018). - ISSN 0308-521X - p. 260 - 274.
    Adaptation of crops to climate change has to be addressed locally due to the variability of soil, climate and the specific socio-economic settings influencing farm management decisions. Adaptation of rainfed cropping systems in the Mediterranean is especially challenging due to the projected decline in precipitation in the coming decades, which will increase the risk of droughts. Methods that can help explore uncertainties in climate projections and crop modelling, such as impact response surfaces (IRSs) and ensemble modelling, can then be valuable for identifying effective adaptations. Here, an ensemble of 17 crop models was used to simulate a total of 54 adaptation options for rainfed winter wheat (Triticum aestivum) at Lleida (NE Spain). To support the ensemble building, an ex post quality check of model simulations based on several criteria was performed. Those criteria were based on the “According to Our Current Knowledge” (AOCK) concept, which has been formalized here. Adaptations were based on changes in cultivars and management regarding phenology, vernalization, sowing date and irrigation. The effects of adaptation options under changed precipitation (P), temperature (T), [CO2] and soil type were analysed by constructing response surfaces, which we termed, in accordance with their specific purpose, adaptation response surfaces (ARSs). These were created to assess the effect of adaptations through a range of plausible P, T and [CO2] perturbations. The results indicated that impacts of altered climate were predominantly negative. No single adaptation was capable of overcoming the detrimental effect of the complex interactions imposed by the P, T and [CO2] perturbations except for supplementary irrigation (sI), which reduced the potential impacts under most of the perturbations. Yet, a combination of adaptations for dealing with climate change demonstrated that effective adaptation is possible at Lleida. Combinations based on a cultivar without vernalization requirements showed good and wide adaptation potential. Few combined adaptation options performed well under rainfed conditions. However, a single sI was sufficient to develop a high adaptation potential, including options mainly based on spring wheat, current cycle duration and early sowing date. Depending on local environment (e.g. soil type), many of these adaptations can maintain current yield levels under moderate changes in T and P, and some also under strong changes. We conclude that ARSs can offer a useful tool for supporting planning of field level adaptation under conditions of high uncertainty.
    Toward a new generation of agricultural system data, models, and knowledge products: State of agricultural systems science
    Jones, James W. ; Antle, John M. ; Basso, Bruno ; Boote, Kenneth J. ; Conant, Richard T. ; Foster, Ian ; Godfray, H.C.J. ; Herrero, Mario ; Howitt, Richard E. ; Janssen, Sander ; Keating, Brian A. ; Munoz-Carpena, Rafael ; Porter, Cheryl H. ; Rosenzweig, Cynthia ; Wheeler, Tim R. - \ 2017
    Agricultural Systems 155 (2017). - ISSN 0308-521X - p. 269 - 288.
    Agricultural data - Crop models - Economic models - Integrated agricultural systems models - Livestock models - Use cases

    We review the current state of agricultural systems science, focusing in particular on the capabilities and limitations of agricultural systems models. We discuss the state of models relative to five different Use Cases spanning field, farm, landscape, regional, and global spatial scales and engaging questions in past, current, and future time periods. Contributions from multiple disciplines have made major advances relevant to a wide range of agricultural system model applications at various spatial and temporal scales. Although current agricultural systems models have features that are needed for the Use Cases, we found that all of them have limitations and need to be improved. We identified common limitations across all Use Cases, namely 1) a scarcity of data for developing, evaluating, and applying agricultural system models and 2) inadequate knowledge systems that effectively communicate model results to society. We argue that these limitations are greater obstacles to progress than gaps in conceptual theory or available methods for using system models. New initiatives on open data show promise for addressing the data problem, but there also needs to be a cultural change among agricultural researchers to ensure that data for addressing the range of Use Cases are available for future model improvements and applications. We conclude that multiple platforms and multiple models are needed for model applications for different purposes. The Use Cases provide a useful framework for considering capabilities and limitations of existing models and data.

    The habitat use and behavior of Indo-Pacific finless porpoise (Neophocaena phocaenoides) in Hong Kong SAR waters
    Double, Serena le; Scheidat, M. ; Porter, L. ; Lai, C. - \ 2017
    Diurnal pattern in habitat use of Hong Kong finless porpoises (Neophocona phocaenoides)
    Double, Serena le; Scheidat, M. ; Porter, L. ; Lai, C. - \ 2017
    Towards a new generation of agricultural system data, models and knowledge products : Information and communication technology
    Janssen, Sander J.C. ; Porter, Cheryl H. ; Moore, Andrew D. ; Athanasiadis, Ioannis N. ; Foster, Ian ; Jones, James W. ; Antle, John M. - \ 2017
    Agricultural Systems 155 (2017). - ISSN 0308-521X - p. 200 - 212.
    Agricultural models - Big data - ICT - Linked data - Open science - Sensing - Visualization

    Agricultural modeling has long suffered from fragmentation in model implementation. Many models are developed, there is much redundancy, models are often poorly coupled, model component re-use is rare, and it is frequently difficult to apply models to generate real solutions for the agricultural sector. To improve this situation, we argue that an open, self-sustained, and committed community is required to co-develop agricultural models and associated data and tools as a common resource. Such a community can benefit from recent developments in information and communications technology (ICT). We examine how such developments can be leveraged to design and implement the next generation of data, models, and decision support tools for agricultural production systems. Our objective is to assess relevant technologies for their maturity, expected development, and potential to benefit the agricultural modeling community. The technologies considered encompass methods for collaborative development and for involving stakeholders and users in development in a transdisciplinary manner.Our qualitative evaluation suggests that as an overall research challenge, the interoperability of data sources, modular granular open models, reference data sets for applications and specific user requirements analysis methodologies need to be addressed to allow agricultural modeling to enter in the big data era. This will enable much higher analytical capacities and the integrated use of new data sources + . Overall agricultural systems modeling needs to rapidly adopt and absorb state-of-the-art data and ICT technologies with a focus on the needs of beneficiaries and on facilitating those who develop applications of their models. This adoption requires the widespread uptake of a set of best practices as standard operating procedures.

    Competitiveness of agri-food chains in EU’s Eastern Neighbours. Quantifying Porter’s diamond
    Berkum, S. van; Wijnands, J.H.M. ; Verhoog, A.D. - \ 2016
    - 14 p.
    Identification and functional characterization of novel xylose transporters from the cell factories Aspergillus Niger and Trichoderma reesei
    Sloothaak, Jasper ; Tamayo-Ramos, Juan Antonio ; Odoni, Dorett I. ; Laothanachareon, Thanaporn ; Derntl, Christian ; Mach-Aigner, Astrid R. ; Martins Dos Santos, Vitor A.P. ; Schaap, Peter J. - \ 2016
    Biotechnology for Biofuels 9 (2016)1. - ISSN 1754-6834
    Aspergillus Niger - Hidden Markov model - Str1 - Str2 - Str3 - Sugar porter - Transport kinetics - Trichoderma reesei - XltA - XltB - XltC - Xylose

    Background: Global climate change and fossil fuels limitations have boosted the demand for robust and efficient microbial factories for the manufacturing of bio-based products from renewable feedstocks. In this regard, efforts have been done to enhance the enzyme-secreting ability of lignocellulose-degrading fungi, aiming to improve protein yields while taking advantage of their ability to use lignocellulosic feedstocks. Access to sugars in complex polysaccharides depends not only on their release by specific hydrolytic enzymes, but also on the presence of transporters capable of effectively transporting the constituent sugars into the cell. This study aims to identify and characterize xylose transporters from Aspergillus Niger and Trichoderma reesei, two fungi that have been industrially exploited for decades for the production of lignocellulose-degrading hydrolytic enzymes. Results: A hidden Markov model for the identification of xylose transporters was developed and used to analyze the A. Niger and T. reesei in silico proteomes, yielding a list of candidate xylose transporters. From this list, three A. Niger (XltA, XltB and XltC) and three T. reesei (Str1, Str2 and Str3) transporters were selected, functionally validated and biochemically characterized through their expression in a Saccharomyces cerevisiae hexose transport null mutant, engineered to be able to metabolize xylose but unable to transport this sugar. All six transporters were able to support growth of the engineered yeast on xylose but varied in affinities and efficiencies in the uptake of the pentose. Amino acid sequence analysis of the selected transporters showed the presence of specific residues and motifs recently associated to xylose transporters. Transcriptional analysis of A. Niger and T. reesei showed that XltA and Str1 were specifically induced by xylose and dependent on the XlnR/Xyr1 regulators, signifying a biological role for these transporters in xylose utilization. Conclusions: This study revealed the existence of a variety of xylose transporters in the cell factories A. Niger and T. reesei. The particular substrate specificity and biochemical properties displayed by A. Niger XltA and XltB suggested a possible biological role for these transporters in xylose uptake. New insights were also gained into the molecular mechanisms regulating the pentose utilization, at inducer uptake level, in these fungi. Analysis of the A. Niger and T. reesei predicted transportome with the newly developed hidden Markov model showed to be an efficient approach for the identification of new xylose transporting proteins.

    Data Interoperability Tools for Regional Integrated Assessments
    Porter, C.H. ; Villabolos, C. ; Holzworth, D. ; Nelson, R. ; White, J.W. ; Athanasiadis, I.N. ; Zhang, M. ; Janssen, S.J.C. ; Knapen, M.J.R. ; Jones, J.W. ; Boote, K.J. ; Hargreaves, J. - \ 2015
    In: Handbook of Climate Change and Agroecosystems / Hillel, Daniel, Rosenzweig, Cynthia, Imperial College Press (ICP Series on Climate Change Impacts, Adaptation and Mitigation ) - ISBN 9781783265633 - p. 147 - 171.
    This chapter describes the AgMIP approach to achieving data interoperability across multiple crop models, which consists of establishing an efficient standardized data-exchange mechanism with specifications defined in accordance with international standards; implementing a flexibly structured data schema to store experimental datasets; and providing consistent procedures for supplementing model-required inputs. Some of the challenges encountered with design of data interoperability protocols involve (1) the use of heterogeneous data from disparate sources, (2) uniformly supplying the required model assumptions where data are insufficient to parameterize the crop models, (3) supplying observed and supplemental data equivalently to multiple models each with different input formats, and (4) harmonizing model outputs for use in further analyses.
    Sharing values or maximizing profits?: ethical discourses and sustainable food initiatives
    Bakker, E. de; Dagevos, H. - \ 2015
    In: Know your food: food ethics and innovation / Dumitras, D.E., Jitea, I.M., Aerts, S., Wageningen : Wageningen Academic Publishers - ISBN 9789086862641 - p. 81 - 88.
    In this paper we pose that in a social context dominated by neoliberal politics utilitarian and contractarian ethics tend to hinder and can even smother critical alternatives of our food system that have more holistic narratives on the consequences of our food choices. First of all, we will argue that the dominant (neo) liberal view on society and economy, featured by the principles of value pluralism and freedom of choice, has a strong affinity with utilitarian and contractarian ethics. We will then take a closer look at 11 sustainable food initiatives in the Netherlands, ranging from larger agricultural projects with an international orientation to small-scale initiatives of crowdbutching. Particularly initiatives operating at the fringes of the agri-food system showed affiliation with an ethical virtue approach questioning the ends of our agricultural and food system. Instead of focusing on the maximization of profits these initiatives were thinking in terms of shared values. To some extent this approach shows a resemblance with the strategy of creating shared values that has been announced by Porter and Kramer as an innovative route that could reinvent capitalism. However, when we probe a bit deeper it turns out that more profound issues are at stake here. Resuming the fundamental tension between ‘oikonomia’ and ‘chremastike’, as originally brought to the fore by Aristotle, we finally formulate the following hypothesis regarding the ethical discourses on our food system: in a situation where economy and society are dominated by neoliberal politics, more virtue ethics are needed as a counterweight in the ethical and political debate on our current system of food production and consumption.
    Crop modelling for integrated assessment of risk to food production from climate change
    Ewert, F. ; Rötter, R.P. ; Bindi, M. ; Webber, Heidi ; Trnka, M. ; Kersebaum, K.C. ; Olesen, J.E. ; Ittersum, M.K. van; Janssen, S.J.C. ; Rivington, M. ; Semenov, M.A. ; Wallach, D. ; Porter, J.R. ; Stewart, D. ; Verhagen, J. ; Gaiser, T. ; Palosuo, T. ; Tao, F. ; Nendel, C. ; Roggero, P.P. ; Bartosová, L. ; Asseng, S. - \ 2015
    Environmental Modelling & Software 72 (2015). - ISSN 1364-8152 - p. 287 - 303.
    The complexity of risks posed by climate change and possible adaptations for crop production has called for integrated assessment and modelling (IAM) approaches linking biophysical and economic models. This paper attempts to provide an overview of the present state of crop modelling to assess climate change risks to food production and to which extent crop models comply with IAM demands. Considerable progress has been made in modelling effects of climate variables, where crop models best satisfy IAM demands. Demands are partly satisfied for simulating commonly required assessment variables. However, progress on the number of simulated crops, uncertainty propagation related to model parameters and structure, adaptations and scaling are less advanced and lagging behind IAM demands. The limitations are considered substantial and apply to a different extent to all crop models. Overcoming these limitations will require joint efforts, and consideration of novel modelling approaches.
    Embryonic development, energy utilization, and heat production of broiler and layer embryos
    Nangsuay, A. ; Meijerhof, R. ; Anker, I. van den; Heetkamp, M.J.W. ; Kemp, B. ; Brand, H. van den - \ 2014
    In: Abstract of the Poultry Science Association 103rd Annual Meeting. - - p. 55 - nr 162.
    Different selection traits of broiler and layer strains result in physiological differences that might be present during incubation. This study aims to investigate an influence of strain on egg composition, development, nutrient metabolism, and heat production (HP) of the embryos. Hatching eggs with an egg weight range of 62.0 to 64.0 g of Lohmann Brown lite and Ross 308 at 41 or 42 wk were selected in 2 batches of 120 eggs per strain. For each batch, 30 eggs of each strain were used for egg composition determination and 90 eggs were separately incubated in 1 of 2 climate respiration chambers with an eggshell temperature (EST) of 37.8 °C. Oxygen and carbon dioxide concentrations were measured in both chambers and in fresh air and the data was used for respiratory quotient (RQ) and heat production (HP) calculation. Embryonic development was determined at D16 and at 6 h post hatch. Gross energy determination was performed for albumen, yolk, residual yolk (RSY), and yolk free body (YFBM). Results showed that broiler eggs had a higher ratio of yolk: albumen with 2.41 g more yolk and 1.48 g less albumen than layers. Yolk energy content of broiler eggs was 42.86 kJ higher than that of layer eggs, whereas albumen energy content did not differ. As a result, energy in albumen + yolk of broiler eggs was 45.26 kJ higher than that of layer eggs. YFBM at D16 and at hatch, chick weight and chick length of broiler was higher than that of layer. RQ of broiler embryos was higher than layer embryos during D8 to D10. A slightly higher RSY weight of broiler embryos than layer embryos at D16 (0.8 g) and at hatch (0.2 g) indicated more yolk used, which resulted in more energy utilization and energy deposited into YFBM. Embryonic HP of broiler embryos was higher than that of layer from D12 to D18, but efficiency of converting energy used by embryos to YFBM was similar. In conclusion, broiler and layer embryos have different growth trajectory, which affect energy utilization and embryonic HP during incubation.
    Harmonization and translation of crop modeling data to ensure interoperability
    Porter, C. ; Villalobos, C. ; Holzworth, D. ; Nelson, R. ; White, J.W. ; Athanasiadis, I.N. ; Janssen, S.J.C. ; Ripoche, D. ; Cufi, J. ; Raes, D. ; Zhang, M. ; Knapen, M.J.R. ; Sahajpal, R. ; Boote, K. ; Jones, J.W. - \ 2014
    Environmental Modelling & Software 62 (2014). - ISSN 1364-8152 - p. 495 - 508.
    simulate yield response - systems simulation - climate-change - integration - framework - protocols - seamless - nitrogen - openmi
    The Agricultural Model Intercomparison and Improvement Project (AgMIP) seeks to improve the capability of ecophysiological and economic models to describe the potential impacts of climate change on agricultural systems. AgMIP protocols emphasize the use of multiple models; consequently, data harmonization is essential. This interoperability was achieved by establishing a data exchange mechanism with variables defined in accordance with international standards; implementing a flexibly structured data schema to store experimental data; and designing a method to fill gaps in model-required input data. Researchers and modelers are able to use these tools to run an ensemble of models on a single, harmonized dataset. This allows them to compare models directly, leading ultimately to model improvements. An important outcome is the development of a platform that facilitates researcher collaboration from many organizations, across many countries. This would have been very difficult to achieve without the AgMIP data interoperability standards described in this paper.
    Fewer invited talks by women in evolutionary biology sympsosia
    Schroeder, J. ; Dugdale, H.L. ; Radersma, R. ; Hinsch, M. ; Buehler, D.M. ; Saul, J. ; Porter, L. ; Liker, A. ; Cauwer, I. de; Johnson, P.J. ; Santure, A.W. ; Griffin, A.S. ; Bolund, E. ; Ross, L. ; Webb, T.J. ; Feulner, P.G.D. ; Winney, I. ; Szulkin, M. ; Komdeur, J. ; Versteegh, M.A. ; Hemelrijk, C.K. ; Svensson, E.I. ; Edwards, H. ; Karlsson, M. ; West, S.A. ; Barrett, E.L.B. ; Richardson, D.S. ; Brink, V. van den; Wimpenny, J.H. ; Ellwood, S.A. ; Rees, M. van; Matson, K.D. - \ 2013
    Journal of Evolutionary Biology 26 (2013)9. - ISSN 1010-061X - p. 2063 - 2069.
    gender-differences - job applicants - science - recommendation - visibility - professors - female
    Lower visibility of female scientists, compared to male scientists, is a potential reason for the under-representation of women among senior academic ranks. Visibility in the scientific community stems partly from presenting research as an invited speaker at organized meetings. We analysed the sex ratio of presenters at the European Society for Evolutionary Biology (ESEB) Congress 2011, where all abstract submissions were accepted for presentation. Women were under-represented among invited speakers at symposia (15% women) compared to all presenters (46%), regular oral presenters (41%) and plenary speakers (25%). At the ESEB congresses in 2001–2011, 9–23% of invited speakers were women. This under-representation of women is partly attributable to a larger proportion of women, than men, declining invitations: in 2011, 50% of women declined an invitation to speak compared to 26% of men. We expect invited speakers to be scientists from top ranked institutions or authors of recent papers in high-impact journals. Considering all invited speakers (including declined invitations), 23% were women. This was lower than the baseline sex ratios of early-mid career stage scientists, but was similar to senior scientists and authors that have published in high-impact journals. High-quality science by women therefore has low exposure at international meetings, which will constrain Evolutionary Biology from reaching its full potential. We wish to highlight the wider implications of turning down invitations to speak, and encourage conference organizers to implement steps to increase acceptance rates of invited talks.
    Research delves into effects of shorter dry periods on health and fertility; Short and sweet?
    Porter, R. ; Knegsel, A.T.M. van; Drysdale, R. - \ 2013
    Cow Management 11 (2013)8. - p. 34 - 35.
    melkveehouderij - melkkoeien - gustperiode - diergezondheid - uiers - vrouwelijke vruchtbaarheid - dairy farming - dairy cows - dry period - animal health - udders - female fertility
    Shortening the dry period could have positive health, fertility and milk production benefits, but more research is needed to ensure that science and husbandry keep pace with the modern dairy cow. We spoke to a leading dairy research scientist and a vet to find out more.
    The Agricultural Model Intercomparison and Improvement Project (AgMIP): Protocols and pilot studies
    Rosenzweig, C. ; Jones, W. ; Hatfield, J.L. ; Ruane, A.C. ; Boote, K.J. ; Thorburn, P. ; Antle, J.M. ; Nelson, G.C. ; Porter, C. ; Janssen, S.J.C. ; Asseng, S. ; Basso, B. ; Ewert, F. ; Wallach, D. ; Baigorria, G. ; Winter, J.M. - \ 2013
    Agricultural and Forest Meteorology 170 (2013). - ISSN 0168-1923 - p. 166 - 182.
    stochastic weather generators - climate-change research - cropgro-soybean model - integrated assessment - us agriculture - system model - elevated co2 - yield - impacts - variability
    The Agricultural Model Intercomparison and Improvement Project (AgMIP) is a major international effort linking the climate, crop, and economic modeling communities with cutting-edge information technology to produce improved crop and economic models and the next generation of climate impact projections for the agricultural sector. The goals of AgMIP are to improve substantially the characterization of world food security due to climate change and to enhance adaptation capacity in both developing and developed countries. Analyses of the agricultural impacts of climate variability and change require a transdisciplinary effort to consistently link state-of-the-art climate scenarios to crop and economic models. Crop model outputs are aggregated as inputs to regional and global economic models to determine regional vulnerabilities, changes in comparative advantage, price effects, and potential adaptation strategies in the agricultural sector. Climate, Crop Modeling, Economics, and Information Technology Team Protocols are presented to guide coordinated climate, crop modeling, economics, and information technology research activities around the world, along with AgMIP Cross-Cutting Themes that address uncertainty, aggregation and scaling, and the development of Representative Agricultural Pathways (RAPs) to enable testing of climate change adaptations in the context of other regional and global trends. The organization of research activities by geographic region and specific crops is described, along with project milestones. Pilot results demonstrate AgMIP's role in assessing climate impacts with explicit representation of uncertainties in climate scenarios and simulations using crop and economic models. An intercomparison of wheat model simulations near Obregón, Mexico reveals inter-model differences in yield sensitivity to [CO2] with model uncertainty holding approximately steady as concentrations rise, while uncertainty related to choice of crop model increases with rising temperatures. Wheat model simulations with mid-century climate scenarios project a slight decline in absolute yields that is more sensitive to selection of crop model than to global climate model, emissions scenario, or climate scenario downscaling method. A comparison of regional and national-scale economic simulations finds a large sensitivity of projected yield changes to the simulations’ resolved scales. Finally, a global economic model intercomparison example demonstrates that improvements in the understanding of agriculture futures arise from integration of the range of uncertainty in crop, climate, and economic modeling results in multi-model assessments.
    . Challenges for Agro-Ecosystem Modelling in Climate Change Risk Assessment for major European Crops and Farming systems
    Rotter, R.P. ; Ewert, F. ; Palosuo, T. ; Bindi, M. ; Kersebaum, K.C. ; Olesen, J.E. ; Trnka, M. ; Ittersum, M.K. van; Janssen, S.J.C. ; Rivington, M. ; Semenov, M. ; Wallach, D. ; Porter, J.R. ; Stewart, D. ; Verhagen, J. ; Angulo, C. ; Gaiser, T. ; Nendel, C. ; Martre, P. ; Wit, A. de - \ 2013
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