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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    Seed dormancy back on track; its definition and regulation by DOG1
    Soppe, Wim J.J. ; Bentsink, Leónie - \ 2020
    New Phytologist (2020). - ISSN 0028-646X
    DELAY OF GERMINATION 1 - DSDS50 - germination rate - seed dormancy - T50
    REDUCED DORMANCY5 Encodes a Protein Phosphatase 2C That Is Required for Seed Dormancy in Arabidopsis
    Xiang, Y. ; Nakabayashi, K. ; Ding, J. ; He, F. ; Bentsink, L. ; Soppe, W.J.J. - \ 2014
    The Plant Cell 26 (2014)11. - ISSN 1040-4651 - p. 4362 - 4375.
    rna-binding proteins - abscisic-acid - messenger-rna - pp2c phosphatases - germination - thaliana - aba - reveals - gene - mutants
    Seed dormancy determines germination timing and contributes to crop production and the adaptation of natural populations to their environment. Our knowledge about its regulation is limited. In a mutagenesis screen of a highly dormant Arabidopsis thaliana line, the reduced dormancy5 (rdo5) mutant was isolated based on its strongly reduced seed dormancy. Cloning of RDO5 showed that it encodes a PP2C phosphatase. Several PP2C phosphatases belonging to clade A are involved in abscisic acid signaling and control seed dormancy. However, RDO5 does not cluster with clade A phosphatases, and abscisic acid levels and sensitivity are unaltered in the rdo5 mutant. RDO5 transcript could only be detected in seeds and was most abundant in dry seeds. RDO5 was found in cells throughout the embryo and is located in the nucleus. A transcriptome analysis revealed that several genes belonging to the conserved PUF family of RNA binding proteins, in particular Arabidopsis PUMILIO9 (APUM9) and APUM11, showed strongly enhanced transcript levels in rdo5 during seed imbibition. Further transgenic analyses indicated that APUM9 reduces seed dormancy. Interestingly, reduction of APUM transcripts by RNA interference complemented the reduced dormancy phenotype of rdo5, indicating that RDO5 functions by suppressing APUM transcript levels.
    Seed maturation in Arabidopsis is characterised by nuclear size reduction and increased chromatin condensation
    Zanten, M. van; Koini, M.A. ; Geyer, R. ; Liu, Y. ; Brambilla, V. ; Bartels, D. ; Koornneef, M. ; Fransz, P. ; Soppe, W.J.J. - \ 2011
    Proceedings of the National Academy of Sciences of the United States of America 108 (2011)50. - ISSN 0027-8424 - p. 20219 - 20224.
    plant craterostigma-plantagineum - desiccation tolerance - gene-regulation - dormancy - germination - heterochromatin - mutants - establishment - transcription - organization
    Most plant species rely on seeds for their dispersal and survival under unfavorable environmental conditions. Seeds are characterized by their low moisture content and significantly reduced metabolic activities. During the maturation phase, seeds accumulate storage reserves and become desiccation-tolerant and dormant. Growth is resumed after release of dormancy and the occurrence of favorable environmental conditions. Here we show that embryonic cotyledon nuclei of Arabidopsis thaliana seeds have a significantly reduced nuclear size, which is established at the beginning of seed maturation. In addition, the chromatin of embryonic cotyledon nuclei from mature seeds is highly condensed. Nuclei regain their size and chromatin condensation level during germination. The reduction in nuclear size is controlled by the seed maturation regulator ABSCISIC ACID-INSENSITIVE 3, and the increase during germination requires two predicted nuclear matrix proteins, LITTLE NUCLEI 1 and LITTLE NUCLEI 2. Our results suggest that the specific properties of nuclei in ripe seeds are an adaptation to desiccation, independent of dormancy. We conclude that the changes in nuclear size and chromatin condensation in seeds are independent, developmentally controlled processes
    DOG1 expression is predicted by the seed-maturation envornment and contributes to geographical variation in germination in Arabidopsis thaliana
    Chiang, G.C.K. ; Bartsch, M. ; Barua, D. ; Nakabayashi, K. ; Debieu, M. ; Kronholm, I. ; Koornneef, M. ; Soppe, W.J.J. ; Donohue, K. ; Meaux, J. De - \ 2011
    Molecular Ecology 20 (2011)16. - ISSN 0962-1083 - p. 3336 - 3349.
    flowering time gene - natural-selection - dormancy - brassicaceae - evolution - field - diversification - adaptation - characters - plasticity
    Seasonal germination timing of Arabidopsis thaliana strongly influences overall life history expression and is the target of intense natural selection. This seasonal germination timing depends strongly on the interaction between genetics and seasonal environments both before and after seed dispersal. DELAY OF GERMINATION 1 (DOG1) is the first gene that has been identified to be associated with natural variation in primary dormancy in A. thaliana. Here, we report interaccession variation in DOG1 expression and document that DOG1 expression is associated with seed-maturation temperature effects on germination; DOG1 expression increased when seeds were matured at low temperature, and this increased expression was associated with increased dormancy of those seeds. Variation in DOG1 expression suggests a geographical structure such that southern accessions, which are more dormant, tend to initiate DOG1 expression earlier during seed maturation and achieved higher expression levels at the end of silique development than did northern accessions. Although elimination of the synthesis of phytohormone abscisic acid (ABA) results in the elimination of maternal temperature effects on dormancy, DOG1 expression predicted dormancy better than expression of genes involved in ABA metabolism
    The conserved splicing factor SUA controls alternative splicing of the developmental regulator ABI3 in Arabidopsis.
    Sugliani, M. ; Brambilla, V. ; Clerkx, E.J.M. ; Koornneef, M. ; Soppe, W.J.J. - \ 2010
    The Plant Cell 22 (2010). - ISSN 1040-4651 - p. 1936 - 1946.
    rna-binding proteins - messenger-rna - higher-plants - seed development - gene-regulation - factor u2af - thaliana - complex - domain - aba
    ABSCISIC ACID INSENSITIVE3 (ABI3) is a major regulator of seed maturation in Arabidopsis thaliana. We detected two ABI3 transcripts, ABI3- and ABI3-ß, which encode full-length and truncated proteins, respectively. Alternative splicing of ABI3 is developmentally regulated, and the ABI3-ß transcript accumulates at the end of seed maturation. The two ABI3 transcripts differ by the presence of a cryptic intron in ABI3-, which is spliced out in ABI3-ß. The suppressor of abi3-5 (sua) mutant consistently restores wild-type seed features in the frameshift mutant abi3-5 but does not suppress other abi3 mutant alleles. SUA is a conserved splicing factor, homologous to the human protein RBM5, and reduces splicing of the cryptic ABI3 intron, leading to a decrease in ABI3-ß transcript. In the abi3-5 mutant, ABI3-ß codes for a functional ABI3 protein due to frameshift restoration
    Remote Sensing and Economic Indicators for Supporting Water Resources Management Decisions
    Hellegers, P.J.G.J. ; Soppe, R. ; Perry, C.J. - \ 2010
    Water Resources Management 24 (2010)11. - ISSN 0920-4741 - p. 2419 - 2436.
    indus basin - productivity - land - evapotranspiration - precipitation - irrigation - pakistan - scales
    This paper demonstrates that combining spatial land surface data with socio-economic analysis provides a number of indicators to strengthen decision making in integrated water and environmental management. It provides a basis to: track current water consumption in the Inkomati Basin in South-Africa; adjust irrigation water management; select crop types; facilitate planning; estimate crop yields before harvesting, and consequently to forecast market price development. Remote sensing data and economic analysis can also be used to study the spatial distribution of water consumption as an indicator of equity in access to water resources. It even enables identification of farms that consume more irrigation water than formally allocated. Finally, it provides a basis to assess the cost-effectiveness of various ways to reduce agricultural water consumption. So, this approach is potentially useful for determining water consumption, refining water allocation policies, and determining the potential for water transfers through mechanisms such as water trading
    Natural modifiers of seed longevity in the Arabidopsis mutants abscisic acid insensitive3-5 (abi3-5) and leafy cotyledon1-3 (lec1-3)
    Sugliani, M.R.L. ; Rajjou, L. ; Clerkx, E.J.M. ; Koornneef, M. ; Soppe, W.J.J. - \ 2009
    New Phytologist 184 (2009)4. - ISSN 0028-646X - p. 898 - 908.
    heat-shock proteins - desiccation tolerance - genetic-variation - allelic variation - leafy cotyledon1 - germination - maturation - thaliana - expression - networks
    • Seed longevity is an important trait in many crops and is essential for the success of most land plant species. Current knowledge of its molecular regulation is limited. The Arabidopsis mutants abscisic acid insensitive3-5 (abi3-5) and leafy cotyledon1-3 (lec1-3) have impaired seed maturation and quickly lose seed viability. abi3-5 and lec1-3 were used as sensitized genetic backgrounds for the study of seed longevity. • We exploited the natural variation of Arabidopsis to create introgression lines from the Seis am Schlern and Shahdara accessions in, respectively, the abi3-5 and lec1-3 backgrounds. These lines carry natural modifiers of the abi3 and lec1 phenotypes. Longevity tests and a proteomic analysis were conducted to describe the seed physiology of each line. • The modifier lines showed improved seed longevity. The Shahdara modifiers can partially re-establish the seed developmental programs controlled by LEC1 and restore the accumulation of seed storage proteins that are reduced in abi3-5 and lec1-3. • The isolation and characterization of natural modifiers of the seed maturation mutants abi3-5 and lec1-3, and the analysis of their seed proteomes, advance our current understanding of seed longevity
    Combining remote sensing and economic analysis to support decisions that affect water productivity
    Hellegers, P.J.G.J. ; Soppe, R.W.O. ; Perry, C.J. ; Bastiaanssen, W.G.M. - \ 2009
    Irrigation Science 27 (2009)3. - ISSN 0342-7188 - p. 243 - 251.
    irrigated wheat - management
    In this paper, an innovative method - that combines a technical and socio-economic analysis - is presented to assess the implications of policy decisions on water productivity. In the technical part, the variability in crop water productivity (CWP) is analyzed on the basis of actual water consumption and associated biomass production using the Surface Energy Balance Algorithm for Land (SEBAL). This generates input for the socio-economic analysis, which aims to quantify the foregone economic water productivity (EWP) of policy decisions to allocate water in a social optimal way. The basis for arguments to transfer water between categories of users will be strengthened and be more objective when the productivity in existing and alternative uses is known. The usefulness of such an approach is shown in the South African part of the Inkomati Basin, where according to the Water Act, water has to be reserved for basic human needs and to protect aquatic ecosystems. The opportunity costs, in terms of foregone EWP, of decisions to divert water away from agriculture are assessed. The results show that diverting water away from crops with a low CWP is not always the most cost-effective way in terms of foregone EWP. This paper is written in the framework of "A demonstration project in the Inkomati Basin" (Soppe et al. 2006) funded by the "Partners for Water II"program of the Dutch government
    El uso de la teledetección para fortalecer el trabajo de los COTAS
    Hoogesteger van Dijk, J.D. ; Soppe, R.W.O. ; Wester, P. ; Vos, H. de - \ 2008
    Aqua Forum 48 (2008). - p. 26 - 28.
    The absence of histone H2B monoubiquitination in the Arabidopsis hub 1 (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy
    Liu, Y. ; Koornneef, M. ; Soppe, W.J.J. - \ 2007
    The Plant Cell 19 (2007)2. - ISSN 1040-4651 - p. 433 - 444.
    abscisic-acid - functional-analysis - gene-expression - h3 methylation - germination - thaliana - protein - aba - ubiquitination - yeast
    Seed dormancy is defined as the failure of a viable seed to germinate under favorable conditions. Besides playing an adaptive role in nature by optimizing germination to the most suitable time, a tight control of dormancy is important in crop plants. Extensive genetic and physiological studies have identified the involvement of several factors, but the molecular mechanisms underlying this process are still largely unknown. Wecloned the HISTONE MONOUBIQUITINATION1 (HUB1) gene, of which the mutant ( previously identified as reduced dormancy4) has reduced seed dormancy and several pleiotropic phenotypes. HUB1 encodes a C3HC4 RING finger protein. The Arabidopsis thaliana genome contains one HUB1 homolog, which we named HUB2. The hub2 mutant also has reduced seed dormancy and is not redundant with hub1. Homologs of HUB1 and HUB2 in other species are required for histone H2B monoubiquitination. In agreement with this, the ubiquitinated form of histone H2B could not be detected in the hub1 and hub2 mutants. In yeast and human cells, histone H2B monoubiquitination is associated with actively transcribed genes. The hub1 mutant showed altered expression levels for several dormancy-related genes. We propose a role for chromatin remodeling in seed dormancy by H2B monoubiquitination through HUB1 and HUB2.
    Genetics aspects of seed dormancy
    Bentsink, L. ; Soppe, W.J. ; Koornneef, M. - \ 2007
    In: Seed Development, Dormancy and Germination / Bradford, K.J., Nonogaki, H., Oxford, Ames, Carlton : Blackwell Publishing Ltd. - ISBN 9781405139830 - p. 113 - 132.
    Well hydraulics and aquifer tests
    Boonstra, J. ; Soppe, R.W.O. - \ 2007
    In: The handbook of groundwater engineering; 2nd ed. / Delleur, J.W., Boca Raton FL (USA) : CRC Press - ISBN 9780849343162 - p. 10.1 - 10.35.
    Well design and construction
    Boonstra, J. ; Soppe, R.W.O. - \ 2007
    In: The handbook of groundwater engineering; 2nd ed. / Delleur, J.W., Boca Raton FL (USA) : CRC Press - ISBN 9780849343162 - p. 11.1 - 11.30.
    Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats
    Kinoshita, Y. ; Saze, H. ; Kinoshita, T. ; Miura, A. ; Soppe, W.J. ; Koornneef, M. ; Kakutani, T. - \ 2007
    The Plant Journal 49 (2007)1. - ISSN 0960-7412 - p. 38 - 45.
    novo dna methylation - medea polycomb gene - epigenetic control - cytosine methylation - tandem repeats - small rnas - transposons - maintenance - mutants - locus
    A unique feature of late-flowering fwa epigenetic mutations is that the phenotype is caused by ectopic expression of the homeobox gene FWA. During normal development the FWA gene is expressed specifically in the endosperm in an imprinted manner. Ectopic FWA expression and disruption of imprinting can be induced in mutants of a CG methyltransferase MET1 (methyltransferase 1) or a chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), suggesting that the proper FWA expression depends on cytosine methylation. However, critical methylated residues controlling FWA silencing are not pinpointed. Nor is it understood how the FWA gene is initially methylated and silenced in wild-type plants. Here we mapped sequences critical for FWA silencing by application of RdDM (RNA-directed DNA methylation) to a ddm1-induced stable fwa epiallele. Transcription of double-stranded RNA corresponding to the tandem direct repeats around the FWA transcription start site induced de novo DNA methylation, transcriptional suppression and phenotypic reversion. The induced changes were heritable even without the transgene, which correlates with inheritance of CG methylation in the direct repeats. The newly silenced FWA allele was transcribed in an endosperm-specific and imprinted manner, as is the case for the wild-type FWA gene. The results indicate that methylation of the direct repeats, which presumably originated from a short interspersed nuclear element (SINE), is sufficient to induce proper epigenetic control of the FWA gene
    Combining remote sensing and economic analysis to assess water productivity; A demonstration project in the Inkomati Basin
    Soppe, R.W.O. ; Hellegers, P.J.G.J. ; Perry, C.J. ; Boon, D. ; Bastiaanssen, M. - \ 2006
    Den Haag : LEI Wageningen UR
    Effects of shallow groundwater management on the spatial and temporal variability of boron and salinity in an irrigated field
    Shouse, P.J. ; Goldberg, S. ; Skaggs, T.H. ; Soppe, R.W.O. ; Ayars, J.E. - \ 2006
    Vadose Zone Journal 5 (2006)1. - ISSN 1539-1663 - p. 377 - 390.
    san-joaquin valley - soil electrical-conductivity - selenium - crops - water - growth - cotton
    In some irrigated regions, the disposal of agricultural drainage waters poses significant environmental challenges. Efforts are underway to develop irrigation water management practices that reduce the volume of drainage generated. One such management strategy involves restricting flow in subsurface drains in an effort to raise the water table and induce the consumption of groundwater by crops. A potential complication with this management approach is that upward groundwater flow may salinize the soil and increase concentrations of phytotoxic elements such as B. In this study, salinity and B concentrations were monitored for 3 yr in a 60-ha agricultural field located in San Joaquin Valley, California. The irrigated field was managed according to a restricted drainage, shallow groundwater management technique. Salinity and B measurements were made biannually at approximately 75 sites within the field. Soil salinity and B concentrations were found to be highly correlated in the field. The observed spatial and temporal variability in B and salinity was largely a product of soil textural variations within the field and the associated variations in salt leaching. During the 3-yr study, the field changed very little from one year to the next, although within a given year there were fluctuations related to cropping and irrigation practices and to environmental conditions. However, any changes arising during the growing season were erased in the fallow season by winter rainfall and preplant irrigations that uniformly leached salts from approximately the top 1 m of the field. Overall, it appears that the shallow groundwater management program used in this study could be continued and sustained in this field without increasing soil salinity or B concentrations, and without decreases in yield.
    Capacity Building in IWRM: The IWRM MSc Curriculum at the Water and Environment Centre, Republic of Yemen
    Soppe, R.W.O. ; Babaqi, A.S. ; Huibers, F.P. - \ 2005
    - 9 p.
    Integrated Water Resources Management (IWRM) is an interdisciplinary approach to water resources management, as opposed to water resources development. In developing an MSc curriculum at the Water and Environment Centre (WEC) at Sana'a University in the republic of Yemen, three goals were defined. The first goal is to integrate the knowledge and skills developed at the different faculties at Sana'a University into an integrated teaching curriculum. The second goal is to meet the demands from the Yemeni water sector, such that graduates have the skills and knowledge required for their future jobs. The third goal is to make the IWRM curriculum institutionally and financially sustainable, such that it can continue to be part of the Sana'a University MSc Program. The development of the IWRM MSc curriculum is done in a participative way, using support of other international universities, to ensure that the complete 2-year program of the curriculum is a coherent package, and not a collection of individual classes. The first semester is designed to develop the same level of knowledge for the inflow students, who will likely have a variable background. The second semester is designed to teach integration of knowledge and skills on the topic of water management. The third and fourth semester are designed to improve research skills and finish the MSc with thesis work. The program will start at the end of 2005, but the process of development of the curriculum has already developed a common sense of integration in Water Resources Management with lecturers from multiple disciplines.
    Systeemverkenning Quarles van Ufford
    Soppe, R.W.O. ; Roelsma, J. ; Bergersen, E. ; Bolt, F.J.E. van der - \ 2005
    Wageningen : Alterra (Reeks monitoring stroomgebieden 2-IV) - 64
    watersystemen - waterkwaliteit - monitoring - mest - voedingsstoffen - uitspoelen - oppervlaktewater - waterbeheer - gelderland - land van maas en waal - water systems - water quality - monitoring - manures - nutrients - leaching - surface water - water management - land van maas en waal - gelderland
    In 2004 is een systeemverkenning van het bemalingsgebied Quarles van Ufford gemaakt op basis van vooral literatuurstudie. Het gebied is gelegen in het westelijk deel van het Land van Maas en Waal en is ca 12.000 ha groot. Voor dit kleigebied is de nutriëntenbelasting bekeken, in relatie tot kwel, grondgebruik, wateraanvoer en waterafvoer
    Drainage is an integral part of agricultural water management
    Ritzema, H.P. ; Soppe, R.W.O. - \ 2004
    In: Proceedings of the Symposium 'Water of a secure future. - - p. 9 - 9.
    Potential for up-scaling Nimr reed bed facilities, Oman : feasibility study
    Schrevel, A. ; Hellegers, P.J.G.J. ; Soppe, R.W.O. - \ 2004
    Wageningen : Alterra (Alterra-reeds beds ) - 73
    verontreinigd water - olieverontreinigingen - helofytenfilters - biologische behandeling - phragmites australis - zout water - bebossing - eucalyptus - haalbaarheidsstudies - oman - biologische waterzuiveringsinstallaties - polluted water - oil spills - artificial wetlands - biological treatment - phragmites australis - saline water - afforestation - eucalyptus - feasibility studies - oman - biological water treatment plants
    This report describes the findings of a feasibility study to treat oil contaminated water using reed beds, and consume the treated saline water using forestry. The feasibility study focused on the social, technical and economical feasibility of a project designed to process 45,000 m3 of water per day. Possible effects of a large scale operation on interactions between Petroleum Development Oman and local population are listed, and suggestions on the social processes involved are made. The economics of reed bed water treatment and water consumption through the use of forestry are determined and compared with the current practise of deep well disposal. The economics of the treatment-forestry system are more favorable than the economics of the deep well disposal. The technical analysis shows that the reed beds are able to treat water to remove hydrocarbons, and suggestions for management, design and development of the system are given.
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