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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Taxonomy of the order Mononegavirales : update 2016
Afonso, Claudio L. ; Amarasinghe, Gaya K. ; Bányai, Krisztián ; Bào, Yīmíng ; Basler, Christopher F. ; Bavari, Sina ; Bejerman, Nicolás ; Blasdell, Kim R. ; Briand, François Xavier ; Briese, Thomas ; Bukreyev, Alexander ; Calisher, Charles H. ; Chandran, Kartik ; Chéng, Jiāsēn ; Clawson, Anna N. ; Collins, Peter L. ; Dietzgen, Ralf G. ; Dolnik, Olga ; Domier, Leslie L. ; Dürrwald, Ralf ; Dye, John M. ; Easton, Andrew J. ; Ebihara, Hideki ; Farkas, Szilvia L. ; Freitas-Astúa, Juliana ; Formenty, Pierre ; Fouchier, Ron A.M. ; Fù, Yànpíng ; Ghedin, Elodie ; Goodin, Michael M. ; Hewson, Roger ; Horie, Masayuki ; Hyndman, Timothy H. ; Jiāng, Dàohóng ; Kitajima, Elliot W. ; Kobinger, Gary P. ; Kondo, Hideki ; Kurath, Gael ; Lamb, Robert A. ; Lenardon, Sergio ; Leroy, Eric M. ; Li, Ci Xiu ; Lin, Xian Dan ; Liú, Lìjiāng ; Longdon, Ben ; Marton, Szilvia ; Maisner, Andrea ; Mühlberger, Elke ; Netesov, Sergey V. ; Nowotny, Norbert ; Patterson, Jean L. ; Payne, Susan L. ; Paweska, Janusz T. ; Randall, Rick E. ; Rima, Bertus K. ; Rota, Paul ; Rubbenstroth, Dennis ; Schwemmle, Martin ; Shi, Mang ; Smither, Sophie J. ; Stenglein, Mark D. ; Stone, David M. ; Takada, Ayato ; Terregino, Calogero ; Tesh, Robert B. ; Tian, Jun Hua ; Tomonaga, Keizo ; Tordo, Noël ; Towner, Jonathan S. ; Vasilakis, Nikos ; Verbeek, Martin ; Volchkov, Viktor E. ; Wahl-Jensen, Victoria ; Walsh, John A. ; Walker, Peter J. ; Wang, David ; Wang, Lin Fa ; Wetzel, Thierry ; Whitfield, Anna E. ; Xiè, Jiǎtāo ; Yuen, Kwok Yung ; Zhang, Yong Zhen ; Kuhn, Jens H. - \ 2016
Archives of Virology 161 (2016)8. - ISSN 0304-8608 - p. 2351 - 2360.

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Phylogenetic analysis of newly described Neosartorya species
Varga, J. ; Vida, Z. ; Toth, B. ; Rigo, K. ; Debets, A.J.M. ; Horie, Y. - \ 2000
Antonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygiëne, microbiologie en serologie 77 (2000)3. - ISSN 0003-6072 - p. 235 - 239.
Isolates representing newly described Neosartorya species, and isolates with abnormal morphologies from Aspergillus section Fumigati were examined by phylogenetic analysis of sequences of part of their beta-tubulin gene. Phylogenetic analyses supported the earlier suggestions that heterothallism is a derived character, and that sexuality was lost several times during the evolution of Aspergillus section Fumigati. The heterothallic N. fennelliae and N. udagawae strains were found to be closely related to the homothallic Neosartorya sp. NRRL 4179 and N. aureola, respectively. Aspergillus sp. FRR 1266, which was earlier described as a variant of A. fumigatus, was found to be closely related to A. viridinutans. Another abnormal asexual isolate was found to be closely related to A. fumigatus and N. fischeri. Phylogenetic relationships among newly described Neosartorya species and other taxa were successfully established based on phylogenetic analysis of beta-tubulin sequences.
A model for photothermal responses of flowering in rice. I. Model description and parameterization.
Yin, X. ; Kropff, M.J. ; Horie, T. ; Nakagawa, H. ; Centeno, H.G.S. ; Zhu, D. ; Goudriaan, J. - \ 1997
Field Crops Research 51 (1997)3. - ISSN 0378-4290 - p. 189 - 200.
Most models that predict crop development based on temperature and photoperiod ignore critical changes in photothermal responses during crop ontogeny. A new, detailed model was developed to predict development to flowering in rice (Oryza sativa L.), based on the Beta function which is commonly used for skewed probability density functions in statistics. As the model accounts for different photothermal responses of three successive phases during preflowering ontogeny, it was referred to as the three-stage Beta model. The model was parameterized for 17 rice cultivars using data of two controlled-environment experiments. Model parameters which do not vary strongly among cultivars and parameters which can be estimated from values of other parameters were identified. This analysis reduced the number of parameters to be estimated to five. The parameters from the controlled-environment experiments were used to predict rice development as observed from an independent three-location field experiment with 12 cultivars. The model accurately predicted varietal and locational variation in rice flowering date.
Optimal preflowering phenology of irrigated rice for high yield potential in three Asian environments: a simulation study.
Yin, X. ; Kropff, M.J. ; Aggarwal, P.K. ; Peng, S. ; Horie, T. - \ 1997
Field Crops Research 51 (1997). - ISSN 0378-4290 - p. 19 - 27.
One of the critical traits of rice ideotypes with an increased yield potential is the length of the period from sowing to flowering. The objective of this study was to optimize preflowering phenology of irrigated rice (a L.) for hig L.) for high yield potential in different Asian environments. A well-evaluated ecophysiological model for irrigated rice production, ORYZA1, was used in this study. This model was coupled to the 3s-Beta model for preflowering phenology that accounts for critical changes in photothermal responses of rice during ontogeny. Using a random number generator programme, 808 combinations of parameter values of the 3s-Beta model, each equivalent to a hypothetical plant type, were created. The yield potential of these plant types was estimated by ORYZA1 for three locations, representing tropical, subtropical and temperate climatic environments, respectively. For each environment there was an optimal preflowering period (PFP) that produced the highest yield. That PFP was not suitable in the subtropical and tropical environments from a cropping system viewpoint, however. In the subtropical environment, rice yield potential was restricted by the available growing season. In the tropical location, a critical flowering time was found, beyond which yield did not increase much by extending PFP. This critical value can be determined as the practically optimum PFP for the location as it allows a minimum growth duration without sacrificing yield potential. Yield was not sensitive to changes in individual phenological characteristics at the same PFP. As current standard cultivars in the different environments have a PFP that is very close to the optimum, the possibility for further improvement of yield potential by manipulating preflowering phenology is limited.
A model for photothermal responses of flowering in rice. II. Model evaluation.
Yin, X. ; Kropff, M.J. ; Nakagawa, H. ; Horie, T. ; Goudriaan, J. - \ 1997
Field Crops Research 51 (1997)3. - ISSN 0378-4290 - p. 201 - 211.
A detailed nonlinear model, the 3s-Beta model, for photothermal responses of flowering in rice (Oryza sativa L.) was evaluated for predicting rice flowering date in field conditions. This model was compared with other three models: a three-plane linear model and two nonlinear models, viz, the modified rice clock model (m-RCM) and a logistic model. Two existing multilocational data sets for photoperiod sensitive and nearly insensitive genotypes were used to evaluate the models. For a photoperiod-sensitive cultivar, nonlinear models described the data more accurately than the linear one; the performance of the three nonlinear models was similar although the logistic model overpredicted days to flowering in a tropical environment. For nearly photoperiod-insensitive genotypes, the models were evaluated first using experiments started in 1984. The models performed best in the order of the 3s-Beta, m-RCM, logistic, and linear. When the coefficients derived from the 1984 experiments were used to predict flowering dates observed in experiments of 1983, relative performance of the models remained the same although the differences became smaller. The results related to model performance and methods for model parameterization under field conditions were discussed.
Simulating the impact of climate change on rice production in Asia and evaluating options for adaptation.
Matthews, R.B. ; Kropff, M.J. ; Horie, T. ; Bachelet, D. - \ 1997
Agricultural Systems 53 (1997). - ISSN 0308-521X - p. 3 - 425.
The likely effects of climate change caused by increasing atmospheric carbon dioxide levels on rice production in Asia were evaluated using two rice crop simulation models, ORYZA1 and SIMRIW, running under fixed-change' climate scenarios and scenarios predicted for a doubled-CO2 (2xCO2) atmosphere by the General Fluid Dynamics Laboratory (GFDL), the Goddard Institute of Space Studies (GISS) and the United Kingdom Meteorological Office (UKMO) General Circulation Models. In general, an increase in CO2 level was found to increase yields while increases in temperature reduced yields. Overall rice production in the region was predicted by the ORYZA1 model to change by 6.5, -4.4 and -5.6% under the GFDL, GISS and UKMO 2xCO2 scenarios, respectively, while the corresponding changes predicted by the SIMRIW model were 4.2, -10.4 and -12.8%. The average of these estimates would suggest that rice production in the Asian region may decline by -3.8% under the climate of the next century. Declines in yield were predicted under the GISS and UKMO scenarios for Thailand, Bangladesh, southern China and western India, while increases were predicted for Indonesia, Malaysia, and Taiwan and parts of India and China. Modification of sowing dates at high latitudes, where warmer temperatures allowed a longer growing season, permitted a possible transition from single-cropping to double-cropping at some locations, an adaption that could potentially have a large positive impact on national rice production in some countries. Planting date could also be adjusted to avoid high temperatures at the time of flowering which can cause severe spikelet sterility in some varieties, although a delay in planting in some cases may prevent a second crop from being obtained because of high temperatures later in the season. Selection for varieties with a higher tolerance of spikelet fertility to temperature was shown to be capable of restoring yield levels to those predicted for current climates. The use of longer-maturing varieties to take advantage of longer growing seasons at higher latitudes may instead result in lower yields, due to the grain formation and ripening periods being pushed to less favorable conditions later in the season. A better strategy might be to select for shorter-maturing varieties to allow a second crop to be grown in these regions.
The rice simulation model SIMRIW and its testing
Horie, T. ; Nakagawa, H.N. ; Centeno, H.G.S. ; Kropff, M.J. - \ 1995
In: Modeling the impact of climate change on rice production in Asia / Matthews, R.B., Kropff, M.J., Bachelet, D., van Laar, H.H., - p. 95 - 139.
A regional evaluation of the effect of future climate change on rice production in Asia
Matthews, R.B. ; Horie, T. ; Kropff, M.J. ; Bachelet, D. ; Centeno, H.G. ; Shin, J.C. ; Mohandass, S. ; Singh, S. ; Zhu Defeng, ; Moon Hee Lee, - \ 1995
In: Modelling the impact of climate change on rice production in Asia / Matthews, R.B., Kropff, M.J., Bachelet, D., van Laar, H.H., - p. 95 - 139.
Predicting the yield potential of rice in different environments
Kropff, M.J. ; Williams, R.J. ; Horie, R. ; Angus, J.F. ; Singh, U. ; Centeno, H.G. ; Cassman, K.G. - \ 1995
In: Temperate rice-achievements and potential. Proceedings of the temperate rice conference, Yanco, Australia, February 1994 / Humphreys, E., Murray, E.A., Clampett, W.S., Lewinn, L.G., - p. 657 - 664.
Modeling the impact of climate change on rice production in Asia.
Matthews, R.B. ; Kropff, M.J. ; Bachelet, D. ; Horie, T. ; Lee, M.H. ; Centeno, H.G.S. ; Shin, J.C. ; Mohandass, S. ; Singh, S. ; Defeng, Z. - \ 1995
In: Climate change and rice, S. Peng et al. (eds.). Springer-Verlag, Berlin and International Rice Research Institute, Manila - p. 314 - 325.
Effect of anticipated change in global environment on rice yields in Japan.
Horie, T. ; Kropff, M.J. ; Centeno, H.G. ; Nakagawa, H. ; Nakano, J. ; Kim, H.Y. ; Ohnishi, M. - \ 1995
In: Climate change and rice, S. Peng et al. (eds.). Springer-Verlag, Berlin and International Rice Research Institute, Manila - p. 291 - 302.
The IUNS cross-cultural study of 'Food habits in later life' -an overview of key findings.
Wahlqvist, M.L. ; Davies, L. ; Hsu-Hage, B.H.H. ; Horie, Y. ; Hermanova, H. ; Kouris-Blazos, A. ; Prinsley, D.M. ; Roe, D. ; Scrimshaw, N.S. ; Solomons, N. ; Sleen, B. ; Sun, M.T. ; Trichoupoulos, A. ; Staveren, W.A. van; Zao, X.H. - \ 1995
Asia Pacific Journal of Clinical Nutrition 4 (1995). - ISSN 0964-7058 - p. 233 - 243.
Optimizing the phenology of pre-flowering development to increase yield potential of irrigated rice in Asia.
Yin, X. ; Kropff, M.J. ; Aggarwal, P.K. ; Horie, T. - \ 1995
In: Abstract 2nd Int. Symp. Systems Approaches for Agricultural Development (SAAD) and Workshop on Applications of Simulation and Systems Analysis for Rice Production (SARP), IRRI, Los Baños, Philippines - p. 91 - 91.
Evaluation of the model ORYZA1.
Kropff, M.J. ; Cassman, K.G. ; Laar, H.H. van; Torres, R.O. ; Liboon, S.P. ; Williams, R.L. ; Horie, T. - \ 1994
In: ORYZA1: An ecophysiological model for irrigated rice production / Kropff, M.J., - p. 57 - 60.
A formal template for the development of cucumber in its vegetative stage (I, II and III)
Horie, T. ; Wit, C.T. de; Goudriaan, J. ; Bensink, J. - \ 1979
Proceedings of the Koninklijke Nederlandse Akademie van Wetenschappen. Serie C: Biological and medical sciences 82 (1979)4. - ISSN 0023-3374 - p. 433 - 479.
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