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.

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Apple whole genome sequences : recent advances and new prospects
Peace, Cameron P. ; Bianco, Luca ; Troggio, Michela ; Weg, Eric van de; Howard, Nicholas P. ; Cornille, Amandine ; Durel, Charles Eric ; Myles, Sean ; Migicovsky, Zoë ; Schaffer, Robert J. ; Costes, Evelyne ; Fazio, Gennaro ; Yamane, Hisayo ; Nocker, Steve van; Gottschalk, Chris ; Costa, Fabrizio ; Chagné, David ; Zhang, Xinzhong ; Patocchi, Andrea ; Gardiner, Susan E. ; Hardner, Craig ; Kumar, Satish ; Laurens, Francois ; Bucher, Etienne ; Main, Dorrie ; Jung, Sook ; Vanderzande, Stijn - \ 2019
Horticulture Research 6 (2019)1. - ISSN 2052-7276

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for “what’s next” focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

A research roadmap for quantifying non-state and subnational climate mitigation action
Hsu, Angel ; Höhne, Niklas ; Kuramochi, Takeshi ; Roelfsema, Mark ; Weinfurter, Amy ; Xie, Yihao ; Lütkehermöller, Katharina ; Chan, Sander ; Corfee-Morlot, Jan ; Drost, Philip ; Faria, Pedro ; Gardiner, Ann ; Gordon, David J. ; Hale, Thomas ; Hultman, Nathan E. ; Moorhead, John ; Reuvers, Shirin ; Setzer, Joana ; Singh, Neelam ; Weber, Christopher ; Widerberg, Oscar - \ 2019
Nature Climate Change 9 (2019)1. - ISSN 1758-678X - p. 11 - 17.

Non-state and subnational climate actors have become central to global climate change governance. Quantitatively assessing climate mitigation undertaken by these entities is critical to understand the credibility of this trend. In this Perspective, we make recommendations regarding five main areas of research and methodological development related to evaluating non-state and subnational climate actions: defining clear boundaries and terminology; use of common methodologies to aggregate and assess non-state and subnational contributions; systematically dealing with issues of overlap; estimating the likelihood of implementation; and addressing data gaps.

Finite element analysis of trees in the wind based on terrestrial laser scanning data
Jackson, T. ; Shenkin, A. ; Wellpott, A. ; Calders, K. ; Origo, N. ; Disney, M. ; Burt, A. ; Raumonen, P. ; Gardiner, B. ; Herold, M. ; Fourcaud, T. ; Malhi, Y. - \ 2019
Agricultural and Forest Meteorology 265 (2019). - ISSN 0168-1923 - p. 137 - 144.
Critical wind speed - Finite element analysis - Resonant frequency - Terrestrial laser scanning - TLS - Wind damage

Wind damage is an important driver of forest structure and dynamics, but it is poorly understood in natural broadleaf forests. This paper presents a new approach in the study of wind damage: combining terrestrial laser scanning (TLS) data and finite element analysis. Recent advances in tree reconstruction from TLS data allowed us to accurately represent the 3D geometry of a tree in a mechanical simulation, without the need for arduous manual mapping or simplifying assumptions about tree shape. We used this simulation to predict the mechanical strains produced on the trunks of 21 trees in Wytham Woods, UK, and validated it using strain data measured on these same trees. For a subset of five trees near the anemometer, the model predicted a five-minute time-series of strain with a mean cross-correlation coefficient of 0.71, when forced by the locally measured wind speed data. Additionally, the maximum strain associated with a 5 ms−1 or 15 ms-1 wind speed was well predicted by the model (N = 17, R2 = 0.81 and R2 = 0.79, respectively). We also predicted the critical wind speed at which the trees will break from both the field data and models and find a good overall agreement (N = 17, R2 = 0.40). Finally, the model predicted the correct trend in the fundamental frequencies of the trees (N = 20, R2 = 0.38) although there was a systematic underprediction, possibly due to the simplified treatment of material properties in the model. The current approach relies on local wind data, so must be combined with wind flow modelling to be applicable at the landscape-scale or over complex terrain. This approach is applicable at the plot level and could also be applied to open-grown trees, such as in cities or parks.

Letter to the Editor: Recovery test results as a prerequisite for publication of gaseous exchange measurements
Gerrits, W.J.J. ; Labussiere, Etienne ; Reynolds, Chris ; Metges, Cornelia ; Kuhla, Björn ; Lund, Peter ; Weisbjerg, Martin Riis ; Dijkstra, J. - \ 2018
Journal of Dairy Science 101 (2018)6. - ISSN 0022-0302 - p. 4703 - 4704.
In the last decade, various applications of gaseous exchange measurements have been developed to quantify the production or consumption of particular gases by animals. Notably, booming research into methane emissions has led to an expansion of the number of facilities in which such measurements are made. Results of a ring test calibration of respiration chambers in the UK by Gardiner et al. (2015) confirmed our concern that not all research groups comply with the same standards of chamber operation.
Introduction: Exclusion and Struggles for Co-Decision : from Part III - Exclusion and Struggles for Co-Decision
Vos, J.M.C. ; Perreault, Tom ; Boelens, R.A. - \ 2018
In: Water Justice / Boelens, R., Perreault, T., Vos, J., Cambridge : Cambridge University Press - ISBN 9781107179080 - p. 188 - 192.
Water justice is often sought in “good water governance.” Yet, what “good governance” means is not something that can be straightforwardly decided or linearly implemented: different stakeholders hold different power positions, have conflicting interests and deploy different valuation languages regarding water, land and livelihoods. Deliberative policy-making processes, including local communities’ participation in decision-making, are often presented as the tool to help craft inclusive, democratic water governance arrangements. However, here, a fundamental but commonly neglected or actively suppressed question is, “who participates in whose project”? Although water governance is about institutional configurations, regulations and policy-making and implementation, it is also about capabilities, powers and social struggle over access to resources, setting the agenda and discursively framing problems. Water justice, then, is not something that can easily be crafted through tinkering with governance arrangements, but requires struggles and continuous renegotiation as part of larger battles for justice and democracy. Water injustices often imply exclusion of vulnerable groups from access to clean water and affordable services, but also from representation in water-control decision-making. This exclusion can be based on gender, race, caste, class, ethnicity, religion, or political affiliation. Maria Rusca, Cecilia Alda-Vidal, and Michelle Kooy (Chapter 11) provide clear examples of this in their chapter on drinking water in Kampala. Joyeeta Gupta (Chapter 14) contends that privatizing irrigation water services may often exclude smallholders. Climate Justice Climate change also causes major distributive injustices. Droughts and floods tend to affect the poor more severely than the relatively rich (Adger, 2001; Ikeme, 2003; IPCC 2014; Ribot, 2010; Schneider and Lane, 2006). Skewed vulnerabilities in relation to effects of climate change lead to asymmetrical impacts (Gardiner and Hartzell-Nichols, 2012). This is even more unfair and imbalanced considering that the poor’s share in emission of greenhouse gases is much less than the gigantic emissions by the rich. A report commissioned by the World Bank (2008) estimates the impacted populations killed or left homeless per region by seven common chronic and sudden disasters that are increasingly related to climate change: droughts, extreme temperatures, floods, landslides, tidal surges and wind storms. Already millions of people are affected by floods in Southern and Eastern Asia and droughts in South America, South Asia and East Africa. Likewise, health effects of climate change affect the poor disproportionally (Costello et al., 2009)
Are forest disturbances amplifying or canceling out climate change-induced productivity changes in European forests?
Reyer, Christopher Paul Oliver ; Bathgate, Stephan ; Blennow, K. ; Borges, J.G. ; Bugmann, Harald ; Delzon, Sylvain ; Faias, Sonia P. ; Garcia-Gonzalo, Jordi ; Gardiner, Barry ; Gonzalez-Olabarria, J.R. ; Gracia, Carlos ; Guerra Hernandez, Jordi ; Kellomaki, Seppo ; Kramer, K. ; Lexer, M.J. ; Lindner, Marcus ; Maaten, Ernest van der; Maroschek, M. ; Muys, Bart ; Nicoll, B. ; Palahi, M. ; Palma, J.H.N. ; Paulo, Joana A. ; Peltola, H. ; Pukkala, T. ; Rammer, W. ; Ray, D. ; Sabaté, S. ; Schelhaas, M. ; Seidl, R. ; Temperli, Christian ; Tomé, Margarida ; Yousefpour, R. ; Zimmerman, N.E. ; Hanewinkel, Marc - \ 2017
Environmental Research Letters 12 (2017)3. - ISSN 1748-9326
Recent studies projecting future climate change impacts on forests mainly consider either the effects of climate change on productivity or on disturbances. However, productivity and disturbances are intrinsically linked because 1) disturbances directly affect forest productivity (e.g. via a reduction in leaf area, growing stock or resource-use efficiency), and 2) disturbance susceptibility is often coupled to a certain development phase of the forest with productivity determining the time a forest is in this specific phase of susceptibility. The objective of this paper is to provide an overview of forest productivity changes in different forest regions in Europe under climate change, and partition these changes into effects induced by climate change alone and by climate change and disturbances. We present projections of climate change impacts on forest productivity from state-of-the-art forest models that dynamically simulate forest productivity and the effects of the main European disturbance agents (fire, storm, insects), driven by the same climate scenario in seven forest case studies along a large climatic gradient throughout Europe. Our study shows that, in most cases, including disturbances in the simulations exaggerate ongoing productivity declines or cancel out productivity gains in response to climate change. In fewer cases, disturbances also increase productivity or buffer climate-change induced productivity losses, e.g. because low severity fires can alleviate resource competition and increase fertilization. Even though our results cannot simply be extrapolated to other types of forests and disturbances, we argue that it is necessary to interpret climate change-induced productivity and disturbance changes jointly to capture the full range of climate change impacts on forests and to plan adaptation measures.
Comment on "critical wind speed at which trees break"
Albrecht, Axel ; Badel, Eric ; Bonnesoeur, Vivien ; Brunet, Yves ; Constant, Thiéry ; Défossez, Pauline ; Langre, Emmanuel De; Dupont, Sylvain ; Fournier, Meriem ; Gardiner, Barry ; Schelhaas, Mart Jan - \ 2016
Physical Review. E, Statistical nonlinear, and soft matter physics 94 (2016)6. - ISSN 2470-0045

Virot et al. [E. Virot, Phys. Rev. E 93, 023001 (2016)10.1103/PhysRevE.93.023001] assert that the critical wind speed at which ≥50% of all trees in a population break is ≈42 m/s, regardless of tree characteristics. We show that empirical data do not support this assertion, and that the assumptions underlying the theory used by Virot et al. are inconsistent with the biomechanics of trees.

Scab resistance in ‘Geneva’ apple is conditioned by a resistance gene cluster with complex genetic control
Bastiaanse, H. ; Bassett, H.C.M. ; Kirk, C. ; Gardiner, S.E. ; Deng, C. ; Groenwold, R. ; Chagné, D. ; Bus, V.G.M. - \ 2016
Molecular Plant Pathology 17 (2016)2. - ISSN 1464-6722 - p. 159 - 172.
Apple scab, caused by the fungal pathogen Venturia inaequalis, is one of the most severe diseases of apple worldwide. It is the most studied plant-pathogen interaction involving a woody species using modern genetic, genomic, proteomic and bioinformatic approaches in both species. Although ‘Geneva’ apple was recognised long ago as a potential source of resistance to scab, this resistance has not been previously characterised. Differential interactions between various monoconidial isolates of V. inaequalis and six segregating F1 and F2 populations indicate the presence of at least five loci governing the resistance in ‘Geneva’. The 17 chromosomes of apple were screened using genotyping-by-sequencing, as well as single marker mapping to position loci controlling the V. inaequalis resistance on linkage group 4. Next, we fine-mapped a 5 cM region containing five loci conferring both dominant and recessive scab resistance to the distal end of the linkage group. This region corresponds to 2.2 Mbp (from 20.3 to 22.5 Mbp) on the physical map of ‘Golden Delicious’ containing nine candidate NBS-LRR resistance genes. This study increases our understanding of the complex genetic basis of apple scab resistance conferred by ‘Geneva’ as well as the gene-for-gene (GfG) relationships between the effector genes in the pathogen and resistance genes in the host.
Risks For Ecosystem Services Provisioning From Natural Disturbance: A European Perspective
Schelhaas, M. ; Seidl, R. ; Rammer, W. ; Gardiner, B. ; Verkerk, H. - \ 2014
In: Proceedings of the XXIV IUFRO World Congress: Sustaining forests, sustaining people: the role of research. - - p. 10 - 10.
The amount of wood affected by natural disturbances in Europe has been increasing steadily over the last century. Climate change and changes in the state of the forest due to management have contributed equally to the observed increase in disturbance levels. Projected trends in climate change and forest development indicate that damage levels are likely to increase further in future. Furthermore, disturbance types are expected to expand their range as a consequence of changes in the climate. An increase in disturbance level, and changes in expected disturbance types, can have a large impact on forest service provisioning. Currently, natural disturbances are usually not incorporated into forest management planning and simulation models. Future projections should therefore be evaluated not only for their impact on various forest services, but also on their risks for natural disturbances. Carbon sequestration in forest biomass is the most obvious service under risk of disturbance, but also other services can be severely affected. Evaluating future disturbance risks across Europe calls for more generally applicable, mechanistic models than current (often deterministic and region-speci¿ c) models. A few examples of possible approaches will be demonstrated.
Future of European forestry
Prins, C. ; Schelhaas, M.J. - \ 2013
In: Living with Storm Damage to Forests: What Science Can Tell Us 3 / Gardiner, B., Schuck, A., Schelhaas, M.J., Orazio, C., Blennow, K., Nicoll, B., Joensuu, Finland : European Forest Institute (What Science can Tell US 3) - ISBN 9789525980080 - p. 116 - 122.
Storm damage in Europe – an overview
Schuck, A. ; Schelhaas, M.J. - \ 2013
In: Living with Storm Damage to Forests: What Science Can Tell Us 3 / Gardiner, B., Schuck, A., Schelhaas, M.J., Orazlo, C., Blennow, K., Nicoll, B., Joensuu, Finland : European Forest Institute - ISBN 9789525980080 - p. 15 - 23.
Living with storm damage to forests
Gardiner, B. ; Schuck, A. ; Schelhaas, M.J. ; Orazio, C. ; Blennow, K. ; Nicoll, B. - \ 2013
Joensuu, Finland : European Forest Institute (What science can tell us 3) - 132
bossen - windschade - risicoschatting - klimaatverandering - inventarisaties - europa - forests - wind damage - risk assessment - climatic change - inventories - europe
Windstorms are a major disturbance factor for European forests. In the past six decades wind storms have damaged standing forest volume, which on a yearly average equals about the size of Poland's annual fellings. The evedence also indicates that the actual severity of storms in the wake of climatic changes may increase during next decades.Windstorms damages have many environmental, economic and social implications.
Mapping the risk to European forests with a changing climate
Gardiner, B. ; Schelhaas, M.J. ; Nicoll, B. - \ 2013
In: Adapting to climate change in European forests – Results of the MOTIVE project / Fitzgerald, J., Lindner, M., Sofia : Pensoft Publishers - ISBN 9789546426901 - p. 28 - 33.
Mapping the risk to European forests
Gardiner, B. ; Schelhaas, M.J. ; Nicoll, B. - \ 2013
EFI News 21 (2013)1. - ISSN 1236-7850 - p. 6 - 6.
A multi-criteria risk analysis to evaluate impacts of forest management alternatives on forest health in Europe
Jactel, H. ; Branco, M. ; Duncker, P. ; Gardiner, B. ; Grodzki, W. ; Langström, B. ; Moreira, F. ; Netherer, S. ; Nicoll, B. ; Orazio, C. ; Piou, D. ; Schelhaas, M.J. ; Tojic, K. - \ 2012
Ecology and Society 17 (2012)4. - ISSN 1708-3087
decision-making - stand management - promethee method - climate-change - strong winds - model - damage - drought - insect - populations
Due to climate change, forests are likely to face new hazards, which may require adaptation of our existing silvicultural practices. However, it is difficult to imagine a forest management approach that can simultaneously minimize all risks of damage. Multicriteria decision analysis (MCDA) has been developed to help decision makers choose between actions that require reaching a compromise among criteria of different weights. We adapted this method and produced a multicriteria risk analysis (MCRA) to compare the risk of damage associated with various forest management systems with a range of management intensity. The objective was to evaluate the effect of four forest management alternatives (FMAs) (i.e., close to nature, extensive management with combined objectives, intensive even-aged plantations, and short-rotation forestry for biomass production) on biotic and abiotic risks of damage in eight regional case studies combining three forest biomes (Boreal, Continental, Atlantic) and five tree species (Eucalyptus globulus, Pinus pinaster, Pinus sylvestris, Picea sitchensis, and Picea abies) relevant to wood production in Europe. Specific forest susceptibility to a series of abiotic (wind, fire, and snow) and biotic (insect pests, pathogenic fungi, and mammal herbivores) hazards were defined by expert panels and subsequently weighted by corresponding likelihood. The PROMETHEE ranking method was applied to rank the FMAs from the most to the least at risk. Overall, risk was lower in short-rotation forests designed to produce wood biomass, because of the reduced stand susceptibility to the most damaging hazards. At the opposite end of the management intensity gradient, close-to-nature systems also had low overall risk, due to lower stand value exposed to damage. Intensive even-aged forestry appeared to be subject to the greatest risk, irrespective of tree species and bioclimatic zone. These results seem to be robust as no significant differences in relative ranking of the four FMAs were detected between the combinations of forest biomes and tree species.
Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple
Chagné, D. ; Crowhurst, R.N. ; Troggio, M. ; Davey, M.W. ; Gilmore, B. ; Lawley, C. ; Vanderzande, S. ; Hellens, R.P. ; Kumar, S. ; Cestaro, A. ; Velasco, R. ; Main, D. ; Rees, J.D. ; Iezzoni, A.F. ; Mockler, T. ; Wilhelm, L. ; Weg, W.E. van de; Gardiner, S.E. ; Bassil, N. ; Peace, C. - \ 2012
PLoS ONE 7 (2012)2. - ISSN 1932-6203
x-domestica borkh. - single-nucleotide polymorphisms - transcription factor - malus-domestica - genus vitis - shelf-life - fruit - markers - diversity - discovery
As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple
Destructive storms in European Forests: Past and Forthcoming Impacts. Final report to European Commission - DG Environment,
Gardiner, B. ; Blennow, K. ; Carnus, J.M. ; Fleischner, P. ; Ingemarson, F. ; Landmann, G. ; Lindner, M. ; Marzano, M. ; Nicoll, B. ; Orazio, C. ; Peyron, J.L. ; Reviron, M.P. ; Schelhaas, M. ; Schuck, A. ; Spielmann, M. ; Usbeck, T. - \ 2010
Joensuu, Finland : European Forest Institute - 138
bossen - bosschade - stormen - windschade - sociale economie - bosbeleid - herstel - europa - forests - forest damage - storms - wind damage - socioeconomics - forest policy - rehabilitation - europe
Functional molecular biology research in Fragaria
Schwab, W. ; Schaart, J.G. ; Rosati, C. - \ 2009
In: Genetics and Genomics of Rosaceae / Folta, K.M., Gardiner, S.E., Springer (Plant Genetics and Genomics: Crops and Models Volume 6) - ISBN 9780387774909 - p. 457 - 486.
Multiple repeats of a promoter segment causes transcription factor autoregulation in red apples
Espley, R.V. ; Brendolise, C. ; Chagné, D. ; Kutty-Amma, S. ; Green, S. ; Volz, R. ; Putterill, J. ; Schouten, H.J. ; Gardiner, S.E. ; Hellens, R.P. ; Allan, A.C. - \ 2009
The Plant Cell 21 (2009). - ISSN 1040-4651 - p. 168 - 183.
common morning glory - genetic-linkage map - loop-helix domain - arabidopsis-thaliana - regulatory genes - functional-analysis - protein-binding - bhlh factors - human dna - myb
Mutations in the genes encoding for either the biosynthetic or transcriptional regulation of the anthocyanin pathway have been linked to color phenotypes. Generally, this is a loss of function resulting in a reduction or a change in the distribution of anthocyanin. Here, we describe a rearrangement in the upstream regulatory region of the gene encoding an apple (Malus x domestica) anthocyanin-regulating transcription factor, MYB10. We show that this modification is responsible for increasing the level of anthocyanin throughout the plant to produce a striking phenotype that includes red foliage and red fruit flesh. This rearrangement is a series of multiple repeats, forming a minisatellite-like structure that comprises five direct tandem repeats of a 23-bp sequence. This MYB10 rearrangement is present in all the red foliage apple varieties and species tested but in none of the white fleshed varieties. Transient assays demonstrated that the 23-bp sequence motif is a target of the MYB10 protein itself, and the number of repeat units correlates with an increase in transactivation by MYB10 protein. We show that the repeat motif is capable of binding MYB10 protein in electrophoretic mobility shift assays. Taken together, these results indicate that an allelic rearrangement in the promoter of MYB10 has generated an autoregulatory locus, and this autoregulation is sufficient to account for the increase in MYB10 transcript levels and subsequent ectopic accumulation of anthocyanins throughout the plant
Analysing, forecasting and valuating the effects of landscape change on the ecosystem service of biological pest control
Werf, W. van der; Landis, D.A. ; Gardiner, M.M. ; Costamagna, A.C. ; Baveco, J.M. ; Bianchi, F.J.J.A. ; Schellhorn, N.C. ; Zhang, W. - \ 2009
In: Integrated Assessment of Agriculture and Sustainable Development: Setting the Agenda for Science and Policy (AgSAP 2009). - Wageningen : Wageningen University and Research Centre - ISBN 9789085854012 - p. 118 - 119.
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