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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Op naar precisielandbouw 2.0 : eindrapport PPS PL2.0 2015-2019 topsectorproject AF-14275
Kempenaar, Corné ; Dijk, Chris van; Hermans, Geert ; Steele-Dun, Susan ; Sande, Corné van de; Verschoore, Jeroen ; Wal, Tamme van der; Roerink, Gerbert ; Visser, Juriaan ; Kamp, Jan ; Blok, Pieter ; Polder, Gerrit ; Wolf, Jan van de; Jalink, Henk ; Bulle, Annette ; Meurs, Bert ; Michielsen, Jean-Marie ; Zande, Jan van de; Hoving, Idse ; Riel, Johan van; Holshof, Gertjan ; Boheemen, Koen van; Evert, Frits van; Riemens, Marleen ; Keizer, Paul ; Schnabel, Sabine ; Egmond, Fenny van; Walvoort, Dennis ; Janssen, Henk ; Riviėre, Inge La; Kocks, Corné ; Pot, Alfred - \ 2019
Lelystad : Stichting Wageningen Research, Wageningen University & Research (Rapport WPR 921) - 138
De publiek private samenwerking (PPS) ‘Op naar precisielandbouw 2.0’ (PL2.0) is een R&D project van de topsector AgriFood. Het project is gestart in 2015 met doorlooptijd van 4 jaar. Voor u ligt het eindrapport. In deze PPS werkten ruim 20 private bedrijven en organisaties, publieke kennisinstellingen en overheden samen aan strategische onderwerpen binnen precisielandbouw. Het project omvatte 13 deelprojecten verdeeld over vijf specifieke R&D thema’s, te weten slim satellietbeeldengebruik, sensorontwikkeling (ziektedetectie), slimme integratie van technologieën in toepassingen, perceelkarakteristieken voor schatten van opbrengstpotentie en ondersteunende ICT, en een generiek thema communicatie en kennisverspreiding.Met betrekking tot het thema satellietbeeldengebruik is uitgezocht hoe optische satellietbeelden in combinatie met radarbeelden of beelden verkregen via drone-camera’s beter gebruikt kunnen worden om de variatie en status van de bovengrondse hoeveelheid biomassa van gewassen in kaart te brengen en opbrengsten te voorspellen. Op het gebied van ziektedetectie is door middel van sensor fusion en artificial intelligence de detectie van virus- en bacterieziekten in aardappelplanten verbeterd. En werd een prototype sensorsysteem voor veldonderzoek ontwikkeld. Door slimme integratie van data, adviesmodellen en mechanisatie zijn er enkele variabel-doseertoepassingen ontwikkeld en gevalideerd. Het gaat hier om variabel doseren van Stikstof en herbiciden binnen teelten d.m.v. taakkaarten. In het verlengde hiervan is ook een ontwerp geleverd en als prototype gevalideerd voor een innovatieve beddenspuit in bloembollenteelt. Op grond van perceelkarakteristieken en ondersteunende ICT zijn inzichten en tools voor het inschatten van opbrengst(potentie) geleverd en wordt een doorkijk gegeven naar software voor verbeterde rijpadenplanning en perceelinformatie. De inzet op communicatie en kennisdeling heeft ca. 100 publicaties en presentaties in 4 jaar tijd opgeleverd. Voor meer details over resultaten wordt naar de rapportage met samenvatting per deelproject verwezen in de hoofdstukken 2 tot en met 7.Het grote succes van PL2.0 ligt vooral bij ruime aandacht voor integratie van componenten van precisielandbouwtoepassingen en de doorstroming daarvan naar de praktijk en onderwijs.Geconcludeerd mag worden dat PL2.0 een bijdrage leverde aan gewasmonitoringtoepassingen en diverse variabel-doseertoepassingen (variable rate applications, VRA). Die VRA-toepassingen zien we nu op de agenda in het in 2018 gestarte precisielandbouw-adoptie project ‘Nationale Proeftuin Precisielandbouw’ (NPPL). Meerdere bedrijven passen taakkaarten variabel doseren op een resolutie van 30-50 m2 op praktijkschaal toe en besparen zo’n 20 -30% op gewasbeschermingsmiddelen met behoud van goede werking. De basis hiervoor is een bodem- of gewaskaart die de relevante variatie binnen de bodem of gewas in kaart brengt. Ook zijn er via PL2.0 mooie resultaten met optimalisatie van plantdichtheid en vermindering van meststoffengebruik via deze kaarten. Doorstroming van kennis naar het groene onderwijs werd gerealiseerd via PL2.0 en een versterkend WURKS-traject. Negen lesmodules over gebruik software en inzet taakkaarten in precisielandbouw werden opgeleverd. Precisielandbouw is geen doel op zich, maar een manier om de duurzaamheid van landbouw te vergroten. Met PL2.0 toepassingen kan meer met minder en beter geproduceerd worden. De trend van precisielandbouw c.q. data-gedreven landbouw of smart farming, zal zich alleen maar doorzetten. Er zal gewerkt gaan worden met meer en hoog-resolutie data, complexere adviesmodellen en meer robotisering. Daarmee zullen de doelen van kringlooplandbouw beter en sneller gerealiseerd kunnen worden.
Post-fire soil erosion mitigation at the scale of swales using forest logging residues at a reduced application rate
Prats, Sergio A. ; González-Pelayo, Óscar ; Silva, Flavio C. ; Bokhorst, Koen J. ; Baartman, Jantiene E.M. ; Keizer, Jan J. - \ 2019
Earth Surface Processes and Landforms (2019). - ISSN 0197-9337
effectiveness - erosion - mulch - organic matter - wildfire

Mulching with forest residues has proved to be highly effective in reducing post-fire soil losses at the plot scale. However, its effectiveness has not been quantified at the application rates that are typically used in operational post-fire land management (2–3 Mg ha-1 using straw), as well as at scales larger than 100 m2. The present study compared post-fire erosion rates for six convergent hillslopes or swales of 500 to 800 m2, three of which were left untreated while the other three were mulched immediately after the fire with shredded eucalypt bark at a rate of 2.4 Mg ha-1. Erosion rates were monitored at irregular intervals during the first three post-fire years, whilst ground cover was assessed yearly. Selected topsoil properties (0–2 cm) such as organic matter content and aggregate stability were determined at a single occasion – two years after the wildfire, for three micro-environments separately: bare soil, and under mulch/litter and vegetation. Soil losses on the untreated swales decreased with post-fire year from 2.2 to 0.4 and 0.11 Mg ha-1 yr-1 (respectively for the first, second and third post-fire years), while the mulched swales produced 84%, 77% and 38% less soil losses than the untreated swales. Soil losses also depended on slope aspect, with the north-facing swales producing less erosion than the west-facing ones. This could be linked to their significant differences in bare soil, vegetation and stone cover, or a combination thereof. The type of micro-environment also played a significant role in topsoil properties (stone content, bulk density, resistance to penetration/shear stress, porosity and organic matter content). The present results add to the increasing evidence that forest residues should be duly considered for operational post-fire land management. Forest residues were highly effective in reducing erosion from swales at application rates as low as the typical 2 Mg ha-1 of post-fire straw mulch.

Quantifying the effectiveness of stakeholder-selected measures against individual and combined soil threats
Keizer, J.J. ; Hessel, R. - \ 2019
Catena 182 (2019). - ISSN 0341-8162
Live cell imaging of meiosis in Arabidopsis thaliana
Prusicki, Maria A. ; Keizer, Emma M. ; Rosmalen, Rik P. van; Komaki, Shinichiro ; Seifert, Felix ; Müller, Katja ; Wijnker, Erik ; Fleck, Christian ; Schnittger, Arp - \ 2019
eLife 8 (2019). - ISSN 2050-084X
A. thaliana - cell biology - cyclin - development - meiosis - phragmoplast - plant biology - reproduction - spindle

To follow the dynamics of meiosis in the model plant Arabidopsis, we have established a live cell imaging setup to observe male meiocytes. Our method is based on the concomitant visualization of microtubules (MTs) and a meiotic cohesin subunit that allows following five cellular parameters: cell shape, MT array, nucleus position, nucleolus position, and chromatin condensation. We find that the states of these parameters are not randomly associated and identify 11 cellular states, referred to as landmarks, which occur much more frequently than closely related ones, indicating that they are convergence points during meiotic progression. As a first application of our system, we revisited a previously identified mutant in the meiotic A-type cyclin TARDY ASYNCHRONOUS MEIOSIS (TAM). Our imaging system enabled us to reveal both qualitatively and quantitatively altered landmarks in tam, foremost the formation of previously not recognized ectopic spindle- or phragmoplast-like structures that arise without attachment to chromosomes.

Extending the linear-noise approximation to biochemical systems influenced by intrinsic noise and slow lognormally distributed extrinsic noise
Keizer, Emma M. ; Bastian, Björn ; Smith, Robert W. ; Grima, Ramon ; Fleck, Christian - \ 2019
Physical Review. E, Statistical nonlinear, and soft matter physics 99 (2019)5. - ISSN 2470-0045

It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from the interaction of unknown molecular components with the network and from the cell's changing environment. While there are many methods to study the effect of intrinsic noise on the system dynamics, few exist to study the influence of both types of noise. Here we show how one can extend the conventional linear-noise approximation to allow for the rapid evaluation of the molecule numbers statistics of a biochemical network influenced by intrinsic noise and by slow lognormally distributed extrinsic noise. The theory is applied to simple models of gene regulatory networks and its validity confirmed by comparison with exact stochastic simulations. In particular, we consider three important biological examples. First, we investigate how extrinsic noise modifies the dependence of the variance of the molecule number fluctuations on the rate constants. Second, we show how the mutual information between input and output of a network motif is affected by extrinsic noise. And third, we study the robustness of the ubiquitously found feed-forward loop motifs when subjected to extrinsic noise.

Last Frontier of Agricultural Big Data in Rotation?
Keizer, L.C.P. ; Schnabel, S.K. ; Riemens, M.M. - \ 2018
- 1 p.
Last Frontier of Agricultural BigData in Rotation?
Keizer, Paul - \ 2018
Nutrient mineralization and organic matter reduction performance of RAS-based sludge in sequential UASB-EGSB reactors
Goddek, Simon ; Delaide, Boris P.L. ; Joyce, Alyssa ; Wuertz, Sven ; Jijakli, M.H. ; Gross, Amit ; Eding, Ep H. ; Bläser, Ingo ; Reuter, Michael ; Keizer, L.C.P. ; Morgenstern, Rolf ; Körner, Oliver ; Verreth, Johan ; Keesman, Karel J. - \ 2018
Aquacultural Engineering 83 (2018). - ISSN 0144-8609 - p. 10 - 19.
Anaerobic digestion - Aquaculture sludge - Aquaponics - Biofertilizer - Nutrient recycling - Organic reduction - Phosphorus recovery - UASB

There is a recognized need for mineralizing aquaculture-derived sludge in aquaponics systems in order to reduce waste production. Many recent studies of aquacultural waste treatment have focused only the production of biogas as opposed to the potential for mineralization of nutrient-rich sludge. Upflow anaerobic sludge blanket (UASB) reactors provide one possible solution for breaking down sludge into bioavailable nutrients that can subsequently be delivered to plants. As such, this study examines the mineralization performance of sequential UASB reactors that are designed with an expanded granular sludge bed (EGSB) and compared to standard aerobic and anaerobic batch reactors. Results of our experiments demonstrate that only chemical oxygen demand reduction is significantly different. An unexpected drop in pH of one of the three reactor systems revealed that a pH below 6 was able to significantly increase the mineralization and mobilization of nutrients. Approximately 25% of phosphorus, potassium, and calcium could also be recovered from the sludge under lower pH conditions, as compared to the mineralization performance of standard UASB reactors running at a higher pH. However, the opposite effect was observed with respect to organic sludge reduction, where diminished performance was observed in the low-pH reactor. The current study implies that anaerobic reactors operating at low pH can potentially contribute towards improved nutrient recovery in multi-loop aquaponics systems and reduction of additive agents for pH control of the hydroponic subsystem.

Classification of European and Mediterranean coastal dune vegetation
Marcenò, Corrado ; Guarino, Riccardo ; Loidi, Javier ; Herrera, Mercedes ; Isermann, Maike ; Knollová, Ilona ; Tichý, Lubomír ; Tzonev, Rossen T. ; Acosta, Alicia Teresa Rosario ; Fitzpatrick, Úna ; Iakushenko, Dmytro ; Janssen, John A.M. ; Jiménez-Alfaro, Borja ; Kacki, Zygmunt ; Keizer-Sedláková, Iva ; Kolomiychuk, Vitaliy ; Rodwell, John S. ; Schaminée, Joop H.J. ; Šilc, Urban ; Chytrý, Milan - \ 2018
Applied Vegetation Science 21 (2018)3. - ISSN 1402-2001 - p. 533 - 559.
Ammophiletea - Biogeography - Expert system - Honckenyo-Elymetea - Koelerio-Corynephoretea canescentis - Phytosociology - Sand dune - Vegetation classification

Aims: Although many phytosociological studies have provided detailed local and regional descriptions of coastal dune vegetation, a unified classification of this vegetation in Europe and the Mediterranean Basin has been missing. Our aim is to produce a formalized classification of this vegetation and to identify the main factors driving its plant species composition at a continental scale. Location: Atlantic and Baltic coasts of Europe, Mediterranean Basin and the Black Sea region. Methods: We compiled a database of 30,759 plots of coastal vegetation, which were resampled to reduce unbalanced sampling effort, obtaining a data set of 11,769 plots. We classified these plots with TWINSPAN, interpreted the resulting clusters and used them for developing formal definitions of phytosociological alliances of coastal dune vegetation, which were included in an expert system for automatic vegetation classification. We related the alliances to climatic factors and described their biogeographic features and their position in the coastal vegetation zonation. We examined and visualized the floristic relationships among these alliances by means of DCA ordination. Results: We defined 18 alliances of coastal dune vegetation, including the newly described Centaureo cuneifoliae-Verbascion pinnatifidi from the Aegean region. The main factors underlying the differentiation of these alliances were biogeographic and macroclimatic contrasts between the Atlantic-Baltic, Mediterranean and Black Sea regions, along with ecological differences between shifting and stable dunes. The main difference in species composition was between the Atlantic-Baltic and Mediterranean-Black Sea regions. Within the former region, the main difference was driven by the different ecological conditions between shifting and stable dunes, whereas within the latter, the main difference was biogeographic between the Mediterranean and the Black Sea. Conclusions: The first formal classification of the European coastal dune vegetation was established, accompanied by an expert system containing the formal definitions of alliances, which can be applied to new data sets. The new classification system critically revised the previous concepts and integrated them into a consistent framework, which reflects the main gradients in species composition driven by biogeographic influences, macroclimate and the position of the sites in the coast-inland zonation of the dune systems. A revision of the class concept used in EuroVegChecklist is also proposed.

Effect of fire occurrence and frequency on topsoil properties and soil (fertility) losses by runoff
Hosseini, Mohammadreza - \ 2018
Wageningen University. Promotor(en): V. Geissen; C.J. Ritsema, co-promotor(en): J.J. Keizer. - Wageningen : Wageningen University - ISBN 9789463437455 - 130
Developing generalized parameters for post-fire erosion risk assessment using the revised Morgan-Morgan-Finney model : A test for north-central Portuguese pine stands
Hosseini, Mohammadreza ; Nunes, João Pedro ; Pelayo, Oscar González ; Keizer, Jan Jacob ; Ritsema, Coen ; Geissen, Violette - \ 2018
Catena 165 (2018). - ISSN 0341-8162 - p. 358 - 368.
Management - Morgan-Morgan-Finney model - Post-fire erosion - Repeated wildfires - Surface runoff
Models can be useful for predicting the hydrological impacts of natural phenomenon such as wildfires and to help implement effective post-fire land management options. In this research, the revised Morgan–Morgan–Finney (MMF) model was used to simulate runoff and soil erosion in recently burned maritime pine plantations with contrasting fire regimes, in a wet Mediterranean region of north-central Portugal. The MMF model was adapted for burnt areas by implementing seasonal changes in model parameters in order to accommodate seasonal patterns in runoff and soil erosion, attributed to changes in soil water repellency and vegetation recovery. The model was then evaluated by applying it for a total of 18 experimental micro-plots (0.25 m2) at 9 once burned and 9 four times burned slopes, using both previously published and newly calibrated parameters, with observed data used to evaluate the robustness and wider applicability of each parameterization. The prediction of erosion was more accurate than that of runoff, with an overall Nash-Sutcliffe efficiency of 0.54. Slope angle and the soils' effective hydrological depth (which depends on vegetation and/or crop cover) were found to be the main parameters improving model outcomes, and different parameters were needed to differentiate between the two contrasting fire regimes. This case study showed that most existing benchmark parameters can be used to apply MMF in burned pine forest areas with moderate severity fires to support post-fire management, but indicated that further efforts should focus on mapping soil depth and vegetation cover to improve these assessments.
Afforestation, Subsequent Forest Fires and Provision of Hydrological Services : A Model-Based Analysis for a Mediterranean Mountainous Catchment
Nunes, João Pedro ; Naranjo Quintanilla, Paula ; Santos, Juliana Marisa ; Serpa, Dalila ; Carvalho-Santos, Cláudia ; Rocha, João ; Keizer, Jan Jacob ; Keesstra, Saskia Deborah - \ 2018
Land Degradation and Development 29 (2018)3. - ISSN 1085-3278 - p. 776 - 788.
Forest fires - Hydrological services - Mediterranean region - Soil erosion - Water resources
Mediterranean landscapes have experienced extensive abandonment and reforestation in recent decades, which should have improved the provision of hydrological services such as flood mitigation, soil erosion protection and water quality regulation. However, these forests are fire-prone, and the postfire increase in runoff, erosion and sediment exports could negatively affect service provision. This issue was assessed by using the Soil and Water Assessment Tool model for the Macieira de Alcôba mountain catchment in northwestern Portugal, covered by agriculture and forest plantations, monitored in 2010-2014 and partially burnt in 2011. The model was validated for streamflow, sediment yield and erosion in agricultural fields and burnt hillslopes, showing that it can be adapted for postfire simulation. Model results for a decadal assessment (2004-2014) show that the fire increased erosion in the burnt slopes from 0.1 to 46.5 Mg ha-1 y-1 and catchment sediment yield from 0.14 to 2.1 Mg ha-1 y-1. Erosion in the burnt forest during this decade was 1 order of magnitude above that in agricultural fields. Model results for different fire and land-use scenarios indicate that postfire erosion and sediment yield were lower without postfire soil management for reforestation and when the fire occurred in pine forests (land use before the 1990s) or in shrublands (land-use before afforestation in the 1930s). These impacts were robust to changes in postfire weather and to a longer (20 years) unburnt period. The results suggest that, in the long term, Mediterranean fire-prone forests might not provide the anticipated soil protection and water quality regulation services.
Stochastic gene expression in Arabidopsis thaliana
Araújo, Ilka Schultheiß ; Pietsch, Jessica Magdalena ; Keizer, Emma Mathilde ; Greese, Bettina ; Balkunde, Rachappa ; Fleck, Christian ; Hülskamp, Martin - \ 2017
Nature Communications 8 (2017)1. - ISSN 2041-1723
Although plant development is highly reproducible, some stochasticity exists. This developmental stochasticity may be caused by noisy gene expression. Here we analyze the fluctuation of protein expression in Arabidopsis thaliana. Using the photoconvertible KikGR marker, we show that the protein expressions of individual cells fluctuate over time. A dual reporter system was used to study extrinsic and intrinsic noise of marker gene expression. We report that extrinsic noise is higher than intrinsic noise and that extrinsic noise in stomata is clearly lower in comparison to several other tissues/cell types. Finally, we show that cells are coupled with respect to stochastic protein expression in young leaves, hypocotyls and roots but not in mature leaves. Our data indicate that stochasticity of gene expression can vary between tissues/cell types and that it can be coupled in a non-cell-autonomous manner.
Notitie 'Natuurambitie in de praktijk' : stand van natuurdoelen in het Markermeer en gevolgen van de ontwikkeling van de Marker Wadden
Riel, Mariëlle C. van; Leopold, Mardik F. ; Keizer-Vlek, Hanneke E. - \ 2017
Wageningen : Wageningen Environmental Research - 49
Voor het ministerie van Economische Zaken (EZ) is het van belang te weten in welke mate de aanleg van de Marker Wadden aansluit op de Natura 2000-doelen in aanvulling op het onderzoek in het kader van de Nb-wetvergunning, de aanleg van de Marker Wadden en de MWTL-monitoring. Deze studie richt zich daarom op de vraag: ‘Hoe de aanleg van een eilandensysteem met een dynamische ontwikkeling (als paaiplaats voor vissen en voedselplek voor vogels) bijdraagt aan de realisatie van de Natura 2000-doelen’.
The short-term effectiveness of surfactant seed coating and mulching treatment in reducing post-fire runoff and erosion
Hosseini, Mohammadreza ; Pelayo, Oscar Gonzalez ; Vasques, Ana ; Ritsema, Coen ; Geissen, Violette ; Keizer, Jan Jacob - \ 2017
Geoderma 307 (2017). - ISSN 0016-7061 - p. 231 - 237.
Logistics network design for perishable products with heterogeneous quality decay
Keizer, Marlies de; Akkerman, Renzo ; Grunow, Martin ; Bloemhof-Ruwaard, Jacqueline ; Haijema, Rene ; Vorst, Jack G.A.J. van der - \ 2017
European Journal of Operational Research 262 (2017)2. - ISSN 0377-2217 - p. 535 - 549.
Customer order decoupling point - Distribution - Location - OR in agriculture - Postponement

The duration of logistics operations, as well as the environmental conditions during these operations, significantly impact the performance of a logistics network for fresh agricultural products. When durations or temperatures increase, product quality decreases and more effort is required to deliver products in time and with the right quality. Different network designs lead to different durations and conditions of transport, storage, processing, etc. Therefore, when making network design decisions, consequences for lead time and product quality should be taken into account. As decay of perishable products, for instance food, is often not uniform, heterogeneity in product quality decay also has to be considered. The aim of this paper is to show how product quality decay as well as its heterogeneity can be integrated in a network design model. A new mixed integer linear programming formulation is presented, which positions stocks and allocates processes to maximise profit under quality constraints. It is applied to several test instances from the horticultural sector. Results show that different levels of decay lead to different network structures. Changing decay rates due to processing particularly affect the level of postponement. Heterogeneity in product quality causes a split in product flows with high and low product quality. All in all, it is shown that heterogeneous product quality decay should be taken into account in network design as it significantly influences network designs and their profitability, especially when the supply chain includes processes that change the level of decay, and product quality differences can be exploited in serving different markets.

Effects of fire occurrence and recurrence on nitrogen and phosphorus losses by overland flow in maritime pine plantations in north-central Portugal
Hosseini, Mohammadreza ; Geissen, Violette ; González-Pelayo, Oscar ; Serpa, Dalila ; Machado, Ana Isabel ; Ritsema, Coen ; Keizer, Jan Jacob - \ 2017
Geoderma 289 (2017). - ISSN 0016-7061 - p. 97 - 106.
Wildfires have increased in Portugal in the recent decades, raising concerns about the long-term negative effects of fire recurrence on the environment. We studied the impacts of recurrent fires on the nitrogen (N) and phosphorus (P) content of mineral soil in the first year after a fire. Total nitrogen (TN) and phosphorus (TP) losses by runoff were also evaluated within the two years after a fire. Nine sites in a maritime pine forest were selected following a large wildfire in September 2012 that affected roughly 3000 ha of the Viseu municipality. Three sites had been burnt four times in the past 40 years (4 ×), three sites had been burnt once in September 2012 (1 ×), and three control sites had not been burnt (0 ×). Runoff was collected in 9 micro-plots (0.25 m2) at each site after rain events from September 2012 to September 2014. Soil N and P content were significantly higher in both burnt sites relatively to the control sites. Nitrogen as well as phosphorus losses via runoff were significantly higher at the 4 × burnt sites than at both the 1 × burnt and unburnt sites. Nutrient loss was particularly high after heavy rains. Vegetation and litter cover played an important role in reducing runoff and the associated N and P transport at the 4 × burnt sites, since a decrease in both variables was observed with the increase in vegetation cover after fire.
Vliv akumulace dusíku na vřesoviště a suché trávníky v Národním parku Podyjí
Zahora, Jaroslav ; Chytrý, Milan ; Holub, Petr ; Fiala, Karel ; Tuma, Ivan ; Vavrikova, Jana ; Fabsicova, Martina ; Keizer-Sedlakova, I. ; Filipova, Lenka - \ 2016
Životné prostredie (2016). - ISSN 0044-4863 - p. 97 - 107.
The increasing availability of soil mineral nitrogen is often considered as a cause of expansion of nitrogen-demanding tall grasses into oligotrophic species-rich heathlands and dry grasslands dominated by Festuca ovina. Consequently
these ecosystems tend to lose their biodiversity. This paper summarizes the main results of different studies focused on the soil nitrogen transformation and availability in the heathlands and dry grasslands in the Podyjí National Park (southern Czech Republic). Increasing soil mineral nitrogen availability ccelerates expansion of competitive tall grasses Calamagrostis epigejos and Arrhenatherum elatius there. Subsequently, due to higher plant and microbial
demands for soil mineral nitrogen, the soil nitrogen availability in the tall-grass sites decreases. At the same time, experimental addition of carbon in the form of cellulose into dry grassland decreased nitrogen availability, which indicates that such ecosystem needs more carbon to effectively use the current levels of available soil nitrogen.
Substantial differences between A. elatius a C. epigejos were found in their capability to (i) accumulate nitrogen in plant tissues, (ii) resorb nitrogen from above-ground biomass during senescence and (iii) release nitrogen from
plant litter during decomposition. These observations point out to different growth and nutrient use strategies of the studied grass species and associated microbial communities in the rhizosphere.
Soil threats in Europe: status, methods, drivers and effects on ecosystem services : deliverable 2.1 RECARE project
Stolte, Jannes ; Tesfai, Mehreteab ; Oygarden, Lilian ; Kvaerno, Sigrun ; Keizer, Jacob ; Verheijen, Frank ; Panagos, Pano ; Ballabio, Cristiana ; Hessel, R. - \ 2016
European Commission DG Joint Research Centre (JRC Technical reports ) - ISBN 9789279540189 - 207 p.
SNP-markers in Allium species to facilitate introgression breeding in onion
Scholten, Olga E. ; Kaauwen, Martijn P.W. van; Shahin, Arwa ; Hendrickx, Patrick M. ; Keizer, Paul ; Burger-Meijer, Karin ; Heusden, Sjaak van; Linden, Gerard van der; Vosman, Ben - \ 2016
BMC Plant Biology 16 (2016). - ISSN 1471-2229 - 10 p.
A. fistulosum - A. roylei - Allium cepa - Botrytis squamosa - Interspecific hybrids - Transcriptome sequencing

Background: Within onion, Allium cepa L., the availability of disease resistance is limited. The identification of sources of resistance in related species, such as Allium roylei and Allium fistulosum, was a first step towards the improvement of onion cultivars by breeding. SNP markers linked to resistance and polymorphic between these related species and onion cultivars are a valuable tool to efficiently introgress disease resistance genes. In this paper we describe the identification and validation of SNP markers valuable for onion breeding. Results: Transcriptome sequencing resulted in 192 million RNA seq reads from the interspecific F1 hybrid between A. roylei and A. fistulosum (RF) and nine onion cultivars. After assembly, reliable SNPs were discovered in about 36 % of the contigs. For genotyping of the interspecific three-way cross population, derived from a cross between an onion cultivar and the RF (CCxRF), 1100 SNPs that are polymorphic in RF and monomorphic in the onion cultivars (RF SNPs) were selected for the development of KASP assays. A molecular linkage map based on 667 RF-SNP markers was constructed for CCxRF. In addition, KASP assays were developed for 1600 onion-SNPs (SNPs polymorphic among onion cultivars). A second linkage map was constructed for an F2 of onion x A. roylei (F2(CxR)) that consisted of 182 onion-SNPs and 119 RF-SNPs, and 76 previously mapped markers. Markers co-segregating in both the F2(CxR) and the CCxRF population were used to assign the linkage groups of RF to onion chromosomes. To validate usefulness of these SNP markers, QTL mapping was applied in the CCxRF population that segregates for resistance to Botrytis squamosa and resulted in a QTL for resistance on chromosome 6 of A. roylei. Conclusions: Our research has more than doubled the publicly available marker sequences of expressed onion genes and two onion-related species. It resulted in a detailed genetic map for the interspecific CCxRF population. This is the first paper that reports the detection of a QTL for resistance to B. squamosa in A. roylei.

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