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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Photosynthesis : Online introductory course
Vreugdenhil, D. - \ 2017
Wageningen : Wageningen University & Research
photosynthesis - plants - plant physiology - biomass - fotosynthese - planten - plantenfysiologie - biomassa
The aim of this online course is to explain the basic mechanisms of photosynthesis.
Physiological responses of rice to increased day and night temperatures
Shi, Wanju - \ 2017
University. Promotor(en): Paul Struik, co-promotor(en): Xinyou Yin. - Wageningen : Wageningen University - ISBN 9789463437110 - 202
crops - rice - oryza sativa - plant physiology - temperature - crop yield - grain - agronomy - gewassen - rijst - plantenfysiologie - temperatuur - gewasopbrengst - graan - agronomie

A more rapid increase in night-time temperature compared with day-time temperature and the increased frequency of heat waves associated with climate change present a serious threat to rice (Oryza sativa L.) production and food security. This thesis aims to understand the impact of high night-time temperature (HNT) and high day-time temperature (HDT) on rice grain yield and grain quality and to examine adaptation strategies to cope with high-temperature stresses.

Grain yield and quality of a susceptible indica genotype (Gharib) and all tested hybrids, when exposed to HNT in the field, were significantly reduced across seasons, with less average reduction in the dry season than in the wet season, indicating that other environmental factors under field conditions may contribute to impacts of HNT on yield. Among the different yield components, a reduced number of spikelets m−2 significantly contributed to yield loss under HNT followed by the consistently lower single-grain weight across all genotypes, while the impact of the decrease in percentage seed-set was less and season-specific. Lower grain yield and poorer grain quality in susceptible cultivar Gharib were associated with a significant reduction in non-structural carbohydrate translocation after flowering, resulting in reduced grain-filling duration. Increased total nitrogen application did not alleviate the negative impact of HNT. The proposed model approach showed that there were significant differences among cultivars in their changes in source-sink relationships in response to HNT. Given that rice grain yield and quality are challenged by a rise in HDT and HNT, in particular at flowering and during grain filling, differential impacts of HNT and HDT during these critical stages were observed. For the single-grain growth during grain filling, HDT either independently or in combination with HNT exerted greater influences than HNT on the grain filling dynamics, activities of starch metabolism enzymes, temporal starch accumulation patterns, and the process of chalk formation. During flowering, HDT increased spikelet sterility in tested hybrids and hybrids were less tolerant to high temperatures than high-yielding inbred varieties. Moreover, in contrast with HNT, HDT played a dominant role in determining spikelet fertility. Novel observations with a series of snapshots of dynamic fertilization processes demonstrated that disturbances in the pre-fertilization phase were the primary causes for heat-induced spikelet sterility, indicating the effectiveness of employing the early-morning flowering trait for mitigating the impact of heat stress at flowering on rice.

The hot, the cold and the tulip : the regulation of flowering time and dormancy release
Leeggangers, Hendrika A.C.F. - \ 2017
University. Promotor(en): Richard Immink, co-promotor(en): Henk Hilhorst. - Wageningen : Wageningen University - ISBN 9789463430289 - 244
tulipa - lilium - tulips - flowering date - flowering - dormancy - plant development - temperature - plant physiology - vegetative propagation - tulpen - bloeidatum - bloei - slaaptoestand - plantenontwikkeling - temperatuur - plantenfysiologie - vegetatieve vermeerdering

The ornamental geophyte Tulipa gesneriana is the most cultivated bulbous species in the Netherlands. It is widely grown in the field for vegetative propagation purposes and in greenhouses for the production of high quality cut flowers. Over the last decade, the tulip bulb industry is affected by the rapid climate change the world is facing. Temperature is rising and influences the vegetative to reproductive phase change (floral induction) inside the tulip bulbs in spring and processes that are occurring during winter, such as dormancy release.

In this thesis the two temperature-dependent processes related to tulip flowering, being floral induction and dormancy release, were investigated in detail with a special focus at the molecular level. Flowering time has been studied in a broad range of species, including the model species Arabidopsis thaliana and Oryza sativa. The current understanding of this process can be translated to non-model species, such as tulip, through a ‘bottom-up’ and ‘top-down’ approach (Chapter 2). For the ‘bottom-up’ approach conservation of molecular pathways is assumed and researchers make use of sequence homology searches to identify candidate genes. The ‘top-down’ approach starts from large scale data mining, such as RNA-sequencing (RNA-seq) data or microarrays, followed by the association between phenotypes, genes and gene expression patterns. Here, a comparison with data from model plant species is made at the end of the process and this also leads to the identification of candidate genes for a particular process.

Large scale genomics data mining in tulip is only possible via transcriptome analysis with RNA-seq derived data, because no full genome-sequence is present at this moment. Genome sequencing remains a challenge for species with a large and complex genome, containing probably a large number of repetitive sequences, which is the case for tulip and lily. In chapter 3 a high quality transcriptome of tulip and lily is presented, which is derived from a collection of different tissues. In order to obtain good transcriptome coverage and to facilitate effective data mining, different filtering parameters were used. This analysis revealed the limitations of commonly applied methods used in de novo transcriptome assembly. The generated transcriptome for tulip and lily is made publicly available via a user friendly database, named the ‘Transcriptome Browser’.

The molecular regulation of the temperature-dependent floral induction was studied through the use of RNA-seq (Chapter 4). A better understanding of this process is needed to prevent floral bud blasting (dehydration of the flower) in the future. The development at the shoot apical meristem (SAM) was morphologically investigated in two contrasting temperature environments, high and low. Meristem-enriched tissues were collected before and during the start of flower development. The start of flower development is morphologically visible by rounding of the SAM and correlates with the up-regulation of TGSQA, an AP1-like gene. A ‘top-down’ approach was used to identify possible regulators of the floral induction in tulip. However, Gene ontology (GO)-enrichment analysis of the differentially expressed genes showed that the floral induction, maturation of the bulb and dormancy establishment are occurring around the same period in time. Therefore a ‘bottom-up’ approach was followed to identify specific flowering time regulators based on knowledge obtained from other species. Expression analysis in tulip, heterologous analysis in Arabidopsis and yeast two hybrid-based protein-protein interaction studies revealed that Tulipa gesneriana TERMINAL FLOWER 1 (TgTFL1) is likely a repressor of flowering, whereas Tulipa gesneriana SUPPRESSOR OF OVEREXPRESSION OF CONSTANS-LIKE2 (TgSOC1L2) acts probably as a floral activator.

Another well-known flowering time regulator is FLOWERING LOCUS T (FT), which is a member of the PEBP gene family found in Arabidopsis and many more plant species. In tulip and lily, a total of four highly similar sequences to FT and HEADING DATA 3A (Hd3a) were identified (Chapter 5). Overexpression of Lilium longiflorum FT (LlFT) and TgFT2 in Arabidopsis resulted in an early flowering phenotype, but upon overexpression of TgFT1 and TgFT3 a late flowering phenotype was observed. The tulip PEBP genes TgFT2 and TgFT3 have a similar expression pattern during development, but show a different behaviour in Arabidopsis. Therefore the difference within the amino acid sequence was investigated, which resulted in the identification of two important amino acids for the FT function, which appeared to be mutated in TgFT3. Interchanging of these amino acids between TgFT2 and TgFT3 resulted in conversion of the phenotype, showing the potential importance of these positions in the protein and these specific amino acids for the molecular mode of action of these two proteins. Based on all the data, LlFT is considered to play a role in creating meristem competency to flowering related cues and TgFT2 to act as a florigen involved in the floral induction. The function of TgFT3 is not clear, but phylogenetic analysis suggests a bulb specific function.

After the floral induction and completion of flower development inside the tulip bulb, a period of prolonged cold is required for proper flowering in spring. Low temperature stimulates the re-mobilization of carbohydrates from the scale tissues to the sink organs, such as the floral stem, floral bud and leaves. Not many details are known about the molecular and metabolic changes during this cold period. In chapter 6, first insights are shown on the development of the different tissues inside the bulbs. The floral bud appears to be the least active tissue in comparison with the floral stem and leaves, suggesting a type of floral bud dormancy in tulip. However, metabolic changes are suggesting that the floral bud is still showing active cell division and/or preparation for elongation by turgor-driven cell wall extension. Dormancy of all tissues seems to be released ten weeks after planting and is correlated with the increase of glucose levels. In the leaves, from this same moment, photosynthesis related genes are up-regulated suggesting that the leaves are preparing for photosynthesis while still beneath the soil surface.

At the end of the thesis a glance is given at different perspectives of the tulips life cycle, categorizing tulip as a perennial, biennial or annual plant species, respectively. The perennial way of life is applicable when growing bulbs from seeds, while biennial and annual are more in relation to vegetative propagation. Also the importance of bulb size is highlighted, because it will determine if the bulbs are able to flower or not the following spring. Two scenarios are discussed related to availability of energy in the presence of carbohydrates and meristem incompetency to floral inducing signals. Throughout all research done for this thesis, it became clear that tulip bulbs and seeds have a lot in common. By combining the knowledge of processes in different plant species or developmental systems it is possible to understand how flowering and dormancy release are regulated and this provides us with novel insights how these processes are regulated in bulbous plant species, such as tulip.

Kennisclip Telen op afstand: Grafieken
Looman, B.H.M. ; Ende, Wim van der - \ 2016
Groen Kennisnet
biobased economy - lesmaterialen - teeltsystemen - tuinbouw - glastuinbouw - gewassen, groeifasen - plantenfysiologie - teaching materials - cropping systems - horticulture - greenhouse horticulture - crop growth stage - plant physiology
Deze kennisclip maakt onderdeel uit van de lesmodule Biobased economy van het Centrum voor Innovatief Vakmanschap Tuinbouw en Uitgangsmaterialen (CIV T&U). De productie is tot stand gekomen door financiering met BOGO middelen van het Ministerie van EZ en van CBBE. In samenwerking met Wageningen UR PPO, Delphy, Prinsenbeekcollege, Ontwikkelcentrum en het CIV T&U.
Nitrogen use efficiency in potato : an integrated agronomic, physiological and genetic approach
Ospina Nieto, C.A. - \ 2016
University. Promotor(en): Paul Struik; Edith Lammerts van Bueren, co-promotor(en): Gerard van der Linden. - Wageningen : Wageningen University - ISBN 9789462576469 - 177 p.
solanum tuberosum - potatoes - nitrogen - nutrient use efficiency - plant breeding - crop physiology - plant physiology - quantitative trait loci - cultivars - aardappelen - stikstof - nutriëntengebruiksefficiëntie - plantenveredeling - gewasfysiologie - plantenfysiologie - loci voor kwantitatief kenmerk

Nitrogen (N) fertilizers increased food production over the last 60 years, but also contributed significantly to the use of fossil energy and the total amount of reactive N in the environment. Agriculture needs to reduce N input and increase nitrogen use efficiency (NUE). Legislation like the Nitrate Directive (91/767/EEC) and the Water Framework Directive (2000/60/EC) forces a reduction in N supply in crop production. The effects of this constraint on yield and quality of potato are expected to be significant since N plays an important role in the vegetative development and production of potato. Considerable amounts of N are needed as N recovery is notoriously low due to the small and shallow roots. The overall aim of this thesis is to improve the nitrogen use efficiency of potato under low nitrogen supply. Specific aims are i) to understand the N effects on potato performance, especially under low N input, ii) to quantify the genotypic variation under contrasting N inputs, iii) to identify quantitative trait loci associated with the crop’s response to nitrogen. We used ecophysiological models to dissect the canopy development into biological meaningful parameters as phenotyping tools. Two potato populations (a set of tetraploid cultivars and a biparental diploid population) were phenotyped in the field under two contrasting N levels. Additionally, a set of 6 cultivars from three maturity groups (early, middle and late) were phenotyped in more detail under 5 nitrogen conditions combining two input levels and two fertilizers types plus a control without nitrogen fertilisation. The curve-fit parameters were, together with other agronomical traits, used in the agronomic and genetic analysis. Our approach using the ecophysiological models captured the phenotypic response to N, enhancing the interpretation of the nitrogen effects and of the differences among maturity types. The nitrogen effects on canopy development resulted in large differences in light interception, tuber yield, tuber size distribution and nitrogen uptake. There were differences in the response to nitrogen between the diploid biparental population and the set of tetraploid cultivars. In general, in the diploid population, having less vigour and therefore less potential to respond to the extra nitrogen, the time required to complete each phase of the canopy development was longer than in the set of tetraploids. In the set of cultivars the rate of early vegetative growth was higher, the onset of the phase with maximum canopy cover was earlier, and the duration of maximum canopy was longer than for the diploid population. However, in both the diploid and the tetraploid population maturity was the major factor accounting for genetic variation in canopy development and tuber development traits. The genotypic differences were reflected in quantitative trait loci that were either N dependent or N independent, with pleiotropic regions affecting most of the maturity-related traits. Few traits showed quantitative trait loci on common regions that were not maturity related like those on chromosomes 2 and 6 (association mapping) or linkage groups ma_VI, pa_VIII pa_XI. Maturity obscures other genotype-dependent physiological traits; therefore it is imperative to find traits that are responsible for genotypic variation, but not related to maturity type. Moreover the results showed that nitrogen use efficiency under low nitrogen input is higher than under high nitrogen input, and higher for late cultivars than for early cultivars. Therefore, breeding for nitrogen use efficiency under low input requires direct selection combined with good response to extra nitrogen and should be done within each maturity group. Finally in a broader context we discussed the need of high-throughput phenotyping in breeding for complex traits, like those involving efficiency, to make the most of the large amount of genetic data, all possible based on advances in technology in remote sensing and images analysis.

Keywords: Association mapping, Breeding for low input, Canopy development, Maturity type, Nitrogen use efficiency, Potato, Solanum tuberosum, Quantitative trait loci.

Desiccation tolerance in seeds and plants
Dias Costa, M.C. - \ 2016
University. Promotor(en): Harro Bouwmeester; Henk Hilhorst; Wilco Ligterink. - Wageningen : Wageningen University - ISBN 9789462576278 - 183 p.
desiccation tolerance - tolerance - plants - seeds - plant physiology - stress tolerance - drought resistance - abscisic acid - uitdrogingstolerantie - tolerantie - planten - zaden - plantenfysiologie - stresstolerantie - droogteresistentie - abscisinezuur

The interest of research groups in desiccation tolerance (DT) has increased substantially over the last decades. The emergence of germinated orthodox seeds and resurrection plants as main research models has pushed the limits of our knowledge beyond boundaries. At the same time, new questions and new challenges were posed. The work presented in this thesis aims at shedding light on some of these questions, deepening our understanding of DT and providing relevant information to improve stress resistance in crops.

Chapter 2 is a survey of the literature and discusses the ecological and evolutionary significance for seeds to be able to re-acquire DT after germination. This chapter also discusses recent progress in DT studies using developing and germinated seeds of the model plants Arabidopsis thaliana and Medicago truncatula.

In Chapter 3 I used microarray data from a time series of DT re-acquisition, together with network analysis of gene expression, to gain temporal resolution and identify relevant genes involved in the re-acquisition of DT in germinated A. thaliana seeds by incubation in abscisic acid (ABA). Overall, genes related to protection, response to stresses, seed development and seed dormancy were up-regulated, whereas genes related to cell growth and photosynthesis were down-regulated with time. Genes that respond early to exogenous ABA were related to wax biosynthetic processes, lipid storage, seed development and response to ABA stimulus. Genes that respond late to exogenous ABA were related to syncytium formation and response to abiotic stimulus (mainly light stimulus). The robustness of the network was confirmed by the projection of sets of genes – related to the acquisition of DT, seed dormancy, drought responses of adult plants and re-induction of DT by polyethylene glycol – on this network.

In Chapter 4 the relation between DT in germinated seeds and drought resistance in adult plants is analysed, using rice (Oryza sativa) as experimental model. Considering the predictions of a future with lower availability of fresh water, efforts to increase rice drought tolerance without reducing yield are increasingly important. The results presented in this chapter suggest that the intrinsic mechanisms of drought tolerance in adult plants are part of the mechanisms used by seeds to tolerate desiccation, but the molecular nature of these mechanisms remains elusive.

Chapter 5 explores the relation between DT and longevity in germinated seeds of the Brazilian tree species Sesbania virgata as experimental model. DT and longevity are acquired by orthodox seeds during the maturation phase of development and lost upon germination. DT can be re-induced in germinated seeds by an osmotic and/or ABA treatment, but there is no information on how these treatments affect seed longevity. S. virgata seeds lose DT slowly upon radicle growth. The radicle appeared to be the most sensitive organ and the cotyledons the most resistant. The ability to produce lateral roots was key for whole seedling survival. An osmotic treatment improved DT in germinated S. virgata seeds, but not longevity. This implies that DT and seed longevity can be uncoupled.

Xerophyta viscosa is one of the best studied resurrection species. Despite the fact that adult plants and mature seeds display DT, young X. viscosa seedlings are sensitive to fast drying. A treatment with ABA can induce DT early in shoots of these seedlings, but not in roots. Chapter 6 addresses the changes in the transcriptome and proteome of X. viscosa seedlings during induction of DT. A draft genome sequence of X. viscosa was used to improve transcript and protein identification and annotation. Differences in ABA signalling and the cross talk between ABA and ethylene were presented as determinant for shoot and root responses. Moreover, differences in the accumulation of late embryogenesis abundant proteins were also shown as being key for DT in shoots and roots.

In Chapter 7, DT-transcriptomes of distantly related organisms are compared and surveyed for a core set of genes representing the signatures of critical adaptive DT mechanisms. A shortlist of 260 genes emerged, with a significant number of genes under the control of ABI3 and related to dormancy. The results reinforced the idea that core mechanisms and key regulators involved in DT developed early in the history of life and were carried forward by diverse species and life forms in a conserved manner and in conjunction with dormancy.

In Chapter 8, the findings of this thesis are integrated, showing how they can contribute to future improvement of stress tolerance in crops. The ability of germinated seeds to re-acquire DT is discussed in combination with dormancy and longevity and related to seed survival under unfavourable environmental conditions. The relationship between drought- and desiccation tolerance and the role of ABA are presented briefly. Possible approaches to mine for new genes for crop improvement, such as searching for conserved genes and analysing new genome sequences, are addressed. Finally, a new perspective of the way to consider the evolution of DT is proposed.

Planten sturen met groen of blauw licht is mogelijk
Hoogstraten, K. van; Dieleman, J.A. ; Meinen, E. - \ 2015
Onder Glas 12 (2015)10. - p. 17 - 19.
tuinbouw - glastuinbouw - belichting - led lampen - plantenfysiologie - gewaskwaliteit - landbouwkundig onderzoek - groenten - tomaten - gewassen, groeifasen - horticulture - greenhouse horticulture - illumination - led lamps - plant physiology - crop quality - agricultural research - vegetables - tomatoes - crop growth stage
De toepassing van LED-belichting in de glastuinbouw staat nog in de kinderschoenen. Enkele bedrijven zetten al LED’s in, vooral rode en blauwe. Over hoe de verschillende lichtkleuren precies uitwerken op de fysiologie van de plant, is nog maar weinig bekend. Een onderzoek van Wageningen UR Glastuinbouw laat zien dat blauwe en groene LED’s kunnen worden gebruikt als stuurlicht. Een grotere kasproef moet inzicht geven hoe dit praktisch toe te passen is.
Multi-level analysis of the impact of temperature and light on tomato fruit growth
Okello, R.C.O. - \ 2015
University. Promotor(en): Paul Struik; Leo Marcelis, co-promotor(en): Ep Heuvelink; Pieter de Visser. - Wageningen : Wageningen University - ISBN 9789462571648 - 166
solanum lycopersicum - tomaten - groei - temperatuur - licht - plantenfysiologie - celdeling - cyclinen - genexpressie - tomatoes - growth - temperature - light - plant physiology - cell division - cyclins - gene expression

Keywords: cell division, endoreduplication, cell expansion, cyclin, cyclin dependent kinase, growth theory, systems biology.

Okello, R.C.O (2015) Multi-level analysis of the impact of temperature and light on tomato fruit growth. PhD thesis, Wageningen University, Wageningen, The Netherlands, 166 pp, with English and Dutch summaries.

Tomato fruit growth commences with an increase in cell number followed by cell expansion. Upon cessation of cell division, a spectacular increase in nuclear DNA content without cell division (endoreduplication) occurs, which is positively correlated with cell size. Evaluation of the relative importance of each cellular process during fruit growth is important for attempts aimed at manipulating fruit size.

In this thesis, the genetic and physiological basis for the differences in fruit size between cultivars and their response to fruit temperature was studied. In addition, the effects of darkness, white, blue, and red light around the fruits on tomato fruit growth were investigated. Temperature or light treatments were applied at the fruit level in all experiments in order to separate plant and fruit level responses. Fruit phenotype was assessed at whole fruit, cell and gene level. Expression patterns of 20 different genes encoding regulators of cell division, endoreduplication or cell expansion were analysed. Besides the experimental work, a literature review of the role of light in the regulatory networks of cell division, endoreduplication and cell expansion was conducted. Results from experiments were then placed into context of other studies in order to identify processes that drive fruit growth.

Experiments showed that differences in fruit size between cultivars can result from differences in both cell number and cell size. Increased cell number in the larger fruited cultivar was corroborated by an increase in the expression of three cell division promoters (CDKB2, CycA1 and E2Fe) and a decrease in the expression of an inhibitor (fw2.2) of cell division. The observed smaller fruit size in heated compared with non-heated fruits appeared to stem from a reduction in cell size even when cell number tended to increase. The expression of three promoters (CDKB1, CDKB2, and CycA1) and one inhibitor (fw2.2) of cell division increased when fruits were heated. However, the expression of genes encoding proteins known to regulate endoreduplication and cell expansion did not corroborate observations on cell size in the temperature experiment. Fruits subjected to different light treatments did not differ in either fruit size or carbohydrate content. However, cell division was strongly stimulated at the expense of cell expansion by light. This thesis shows that cell division is stimulated by light irrespective of the organ under consideration while endoreduplication and cell expansion responses are organ specific. It is proposed that light effects on cell division, endoreduplication and cell expansion stem from either degradation of transcription factors or inhibitory competition between transcription factors for promoter regions of target genes. It is also argued here that the commonly observed positive correlation between cell number and fruit size does not imply a causal relationship. In addition, the thesis argues that fruit growth is dependent on cell-autonomous and non-cell-autonomous regulatory mechanisms as well as a global coordinator, the target-of-rapamycin and, consequently, the increase in fruit size follows the neo-cellular theory of fruit growth.

This thesis provides clues on the link between gene expression and cell and fruit level observations. It also provides in depth knowledge on the role of environmental factors on the regulation of cell division, endoreduplication and cell expansion. Further studies at the level between genes and the cells will be necessary to quantify the relationship between gene expression and cell and fruit phenotype.

Biochemical, physiological and molecular responses of Ricinus communis seeds and seedlings to different temperatures: a multi-omics approach
Ribeiro de Jesus, P.R. - \ 2015
University. Promotor(en): Harro Bouwmeester, co-promotor(en): Henk Hilhorst; Wilco Ligterink. - Wageningen : Wageningen University - ISBN 9789462574700 - 203
ricinus communis - zaden - zaailingen - plantenfysiologie - temperatuur - moleculaire biologie - genexpressie - zaadkieming - zaadopkomst - seeds - seedlings - plant physiology - temperature - molecular biology - gene expression - seed germination - seedling emergence

Biochemical, physiological and molecular responses of Ricinus communis seeds and seedlings to different temperatures: a multi-omics approach

by Paulo Roberto Ribeiro de Jesus

The main objective of this thesis was to provide a detailed analysis of physiological, biochemical and molecular-genetic responses of Ricinus communis to temperature during seed germination and seedling establishment.

In Chapter 2, I describe the assessment of 17 candidate reference genes across a diverse set of samples, including several tissues, various developmental stages and environmental conditions, encompassing seed germination and seedling growth in R. communis. These genes were tested by RT-qPCR and ranked according to the stability of their expression using two different approaches: GeNorm and NormFinder. Both GeNorm and Normfinder indicated that ACT, POB and PP2AA1 represent the optimal combination for normalization of gene expression data in inter-tissue studies. I also describe the optimal combination of reference genes for a subset of samples from root, endosperm and cotyledonary tissues. The selection of reference genes was validated by normalizing the expression levels of three target genes involved in energy metabolism with the identified optimal reference genes. This approach allowed me to identify stably expressed genes, and, thus, reference genes for use in RT-qPCR studies in seeds and seedlings of R. communis.

In Chapter 3, a thermo-sensitive window is identified during seed germination in which high temperatures compromise subsequent seedling development. I assessed the biochemical and molecular requirements of R. communis germination for successful seedling establishment at varying temperatures. For that, I performed metabolite profiling (GC-TOF-MS) and measured transcript levels of key genes involved in several energy-generating pathways such as storage oil mobilization, β-oxidation of fatty acids and gluconeogenesis of seeds germinated at three different temperatures. Transient overexpression of genes encoding for malate synthase (MLS) and glycerol kinase (GK) resulted in higher starch levels in N. benthamiana leaves, which highlights the likely importance of these genes in energy-generating pathways for seedling establishment. Additionally, I showed that γ-aminobutyric acid (GABA), which is a stress-responsive metabolite, accumulated in response to the water content of the seeds during the initial phase of imbibition.

In Chapter 4 I undertook a genomics approach using microarray analysis to determine transcriptome changes in three distinct developmental stages during seed germination at 20, 25 and 35ºC that could explain the thermo-sensitive window that is described in Chapter 3. Most of the differences in the R. communis transcriptome occurred between 6 hours of imbibition and the commencement of germination, i.e. radicle protrusion. This coincides with the thermo-sensitive window identified during seed germination in which high temperatures compromise seedling development. The transcriptome data was used to identify heat-stress responsive genes that might be involved in thermotolerance of R. communis during germination. Temperature had a major effect on genes involved in energy generating pathways, such as the Calvin-Benson-Bassham cycle, gluconeogenesis, and starch- and triacylglycerol degradation. Transcripts coding for ATP binding proteins, DNA binding proteins, RNA binding proteins, DNA-directed RNA polymerases I, II, and III, heat shock factor proteins, multiprotein-bridging factor proteins, and zinc finger proteins were also affected by temperature suggesting the whole transcriptional regulatory machinery was altered in response to temperature. Among the downregulated transcripts under high temperature, only three were shared by all three stages: an oxidation-related zinc finger 2, an F-box and wd40 domain protein, and a DNA binding protein/MYB-like transcription factor. Among the upregulated transcripts, nine were shared by all three stages: a BET1P/SFT1P-like protein, 14BB, a low-molecular-weight cysteine-rich protein LCR78, a WD-repeat protein, a GAST1 protein, an adenylate kinase 1/P-loop containing nucleoside triphosphate hydrolases superfamily protein, and four conserved hypothetical proteins. These genes constitute good candidates for further characterization of temperature-responsive genes in R. communis.

In Chapter 5, I studied the genetic variation in the effect of temperature on growth of young R. communis seedlings and measured primary and secondary metabolites in roots and cotyledons of three R. communis genotypes, varying in stress tolerance. Seedling biomass was strongly affected by the temperature, with the lowest total biomass observed at 20ºC. The response in terms of biomass production for the genotype MPA11 was clearly different from the other two studied genotypes: genotype MPA11 produced heavier seedlings at all temperatures but the root biomass of this genotype decreased with increasing temperature, reaching the lowest value at 35ºC. In contrast, root biomass of genotypes MPB01 and IAC80 was not affected by temperature, suggesting that the roots of these genotypes are less sensitive to changes in temperature. A shift in carbon-nitrogen metabolism towards the accumulation of nitrogen-containing compounds seems to be the main biochemical response to support growth at higher temperatures. Carbohydrate content was reduced in response to increasing temperature in both roots and cotyledons, whereas amino acids accumulated to higher levels. The results in this chapter show that a specific balance between amino acids, carbohydrates and organic acids in the cotyledons and roots of genotype MPA11 seems to be an important trait for faster and more efficient growth of this genotype at higher temperatures.

In Chapter 6, I decided to focus on the differential ability of genotypes MPA11 and IAC80 to sustain root biomass production at higher temperatures. Biomass allocation was assessed by measuring dry weight of roots, stems, and cotyledons of seedlings grown at three different temperatures. Seedlings grown at 25ºC and 35ºC showed greater biomass than seedlings grown at 20ºC. Cotyledon and stem dry weight increased for both genotypes with increasing temperature, whereas root biomass allocation showed a genotype-dependent behaviour. Genotype MPA11 showed a continuous increase in root dry weight with increasing temperature, while genotype IAC80 was not able to sustain further root growth at higher temperatures. Metabolite and gene expression profiles of genotype MPA11 demonstrated an increase in the levels of osmoprotectant molecules, such as galactinol and transcripts of genes encoding antioxidant enzymes and heat shock proteins, to a higher extent than in genotype IAC80.

In Chapter 7 I raised the question whether carbohydrate accumulation in R. communis leaves, roots, and seeds, grown at low temperatures, as compared to higher temperatures, results from up-regulation of biosynthetic pathways, from down-regulation of catabolic pathways, or both. To answer this question, transcript levels were measured of genes encoding enzymes involved in starch biosynthesis, starch catabolism, and gluconeogenesis in leaves, roots, and seeds grown at 20ºC and 35ºC. Transcript levels of genes involved in starch catabolism were higher in leaves grown at 20ºC than at 35ºC, but up-regulation of genes involved in starch biosynthesis seems to compensate for this and, therefore, is the likely explanation for higher levels of starch in leaves grown at 20ºC. Higher levels of soluble carbohydrates in leaves grown at 20ºC may have been caused by a coordinated up-regulation of starch catabolism and gluconeogenesis pathways. In roots, starch catabolism and gluconeogenesis seem to be enhanced at elevated temperatures. Higher levels of starch in seeds germinated at low temperatures is associated with higher transcript levels of genes involved in starch biosynthesis. Similarly, higher transcript levels of RcPEPCK and RcFBPase are most likely causal for fructose and glucose accumulation in seeds germinated at 20ºC.

This thesis provides important insights in the understanding of the plasticity of R. communis in response to temperature. The knowledge obtained may apply to other species as well. Additionally, based on the transcriptomics data, we selected several candidate genes that are potentially involved in, or required for, proper seed germination and seedling establishment under different temperatures, such as a number of transcription factors, a zinc finger protein, heat-shock proteins, malate synthase and glycerol kinase. Overexpressing Arabidopsis lines transformed with these R. communis genes, as well as Arabidopsis T-DNA lines, in which Arabidopsis homologs of these genes are knocked-out, are being generated for further phenotypical analysis. These overexpression and T-DNA lines should help us to understand the molecular requirements for vigorous seedling growth of R. communis under different environmental conditions.

This work was performed at the Laboratory of Plant Physiology, Wageningen University. This research was financially supported by the Brazilian Government through the National Counsel of Technological and Scientific Development (CNPq grant number 200745/2011-5).

Nieuwe inzichten vereist voor goed sturen op onderhoudsademhaling : onderhoud gaat altijd voor de groei
Elings, A. ; Heuvelink, E. ; Kierkels, T. - \ 2015
Onder Glas 12 (2015)3. - p. 16 - 17.
glastuinbouw - cultuurmethoden - plantkunde - plantenfysiologie - fotosynthese - innovaties - landbouwkundig onderzoek - plantenontwikkeling - temperatuur - greenhouse horticulture - cultural methods - botany - plant physiology - photosynthesis - innovations - agricultural research - plant development - temperature
De verschillende soorten ademhaling bij de plant wekken vaak verwarring. De enige soort waar de teler echt vat op heeft, is de onderhoudsademhaling. Om daar goed op te kunnen sturen, zijn wel nieuwe inzichten noodzakelijk, met name in het verloop over het etmaal.
Stuurlicht in de Glastuinbouw : 1. Kansen voor energiebesparing?
Dueck, T.A. ; Hogewoning, S. ; Pot, S. ; Meinen, E. ; Trouwborst, G. ; Kempkes, F.L.K. - \ 2015
Bleiswijk : Wageningen UR Glastuinbouw (Rapport GTB 1349) - 56
teelt onder bescherming - gewasproductie - gewasopbrengst - gewaskwaliteit - gewasfysiologie - kunstlicht - kunstmatige verlichting - plantenfysiologie - aanvullend licht - blauw licht - verrood licht - rood licht - phalaenopsis - kalanchoe - chrysanten - protected cultivation - crop production - crop yield - crop quality - crop physiology - artificial light - artificial lighting - plant physiology - supplementary light - blue light - far red light - red light - chrysanthemums
This report focusses on energy efficient steering light applications by energy efficient lighting systems, but especially with new possibilities to influence crop growth and production with the light spectrum. After an introduction of the physiological background and application of steering light, new applications for steering light in the future are described with respect to energy saving opportunities. Possible scenario’s for steering light are presented for phalaenopsis, chrysanthemum and kalanchoë.
Biologische klok brengt compactheid zonder chemie dichterbij : hoe gaat plant om met zetmeel en suikers in de nacht?
Krol, S. van der; Heuvelink, E. ; Kierkels, T. - \ 2015
Onder Glas 12 (2015)8. - p. 23 - 25.
glastuinbouw - sierplanten - teeltsystemen - plantenontwikkeling - plantkunde - plantenfysiologie - biologische ritmen - landbouwkundig onderzoek - gewasproductie - greenhouse horticulture - ornamental plants - cropping systems - plant development - botany - plant physiology - biological rhythms - agricultural research - crop production
Meer inzicht in hoe de biologische klok van de plant processen aanstuurt, geeft nieuwe mogelijkheden om groei en bloei te sturen. Het brengt compact houden van pot- en perkplanten met teeltmaatregelen dichterbij. Onderdeel hiervan is een beter begrip van hoe de plant omgaat met zetmeel en suikers in de nacht. Het interessante onderzoek op dit terrein krijgt financiële en praktische ondersteuning van ongekend veel tuinbouwbedrijven.
Als het gebrek eenmaal zichtbaar is, is het vaak te laat
Voogt, W. ; Heuvelink, E. ; Kierkels, T. - \ 2015
Onder Glas 12 (2015)5. - p. 13 - 17.
glastuinbouw - bemesting - toediening op blad - bladvoeding - effecten - controle - plantenfysiologie - dosering - potplanten - greenhouse horticulture - fertilizer application - foliar application - foliar nutrition - effects - control - plant physiology - dosage - pot plants
Planten halen nutriënten normaal gesproken binnen via hun wortels. Het opname- en transportsysteem is daar volledig op ingericht. Bij bemesting via het blad is er niet zo’n gestroomlijnde route. Dat maakt het resultaat van bladbemesting erg wisselend. Immobiele elementen blijven snel steken bij de plek waar ze terecht zijn gekomen.
Using natural variation to unravel the dynamic regulation of plant performance in diverse environments
Molenaar, J.A. - \ 2015
University. Promotor(en): Harro Bouwmeester; Joost Keurentjes, co-promotor(en): Dick Vreugdenhil. - Wageningen : Wageningen University - ISBN 9789462573444 - 186
planten - genomen - loci voor kwantitatief kenmerk - warmtestress - genetische kartering - groei - droogte - plantengenetica - plantenfysiologie - plants - genomes - quantitative trait loci - heat stress - genetic mapping - growth - drought - plant genetics - plant physiology

Summary

All plants are able to respond to changes in their environment by adjusting their morphology and metabolism, but large differences are observed in the effectiveness of these responses in the light of plant fitness. Between and within species large differences are observed in plant responses to drought, heat and other abiotic stresses. This natural variation is partly due to variation in the genetic composition of individuals. Within-species variation can be used to identify and study genes involved in the genetic regulation of plant performance.

Growth of the world population will, in the coming years, lead to an increased demand for food, feed and other natural products. In addition, extreme weather conditions with, amongst others, more and prolonged periods of drought and heat are expected to occur due to climate change. Therefore breeders are challenged to produce stress tolerant cultivars with improved yield under sub-optimal conditions. Knowledge about the mechanisms and genes that underlie tolerance to drought, heat and other abiotic stresses will ease this challenge.

The aim of this thesis was to identify and study the role of genes that are underlying natural variation in plant performance under drought, salt and heat stress. To reach this goal a genome wide association (GWA) mapping approach was taken in the model species Arabidopsis thaliana. A population of 350 natural accessions of Arabidopsis, genotyped with 215k SNPs, was grown under control and several stress conditions and plant performance was evaluated by phenotyping one or several plant traits per environment. Genes located in the genomic regions that were significantly associated with plant performance, were studied in more detail.

Plant performance was first evaluated upon osmotic stress (Chapter 2). This treatment resulted not only in a reduced plant size, but also caused the colour of the rosette leaves to change from green to purple-red due to anthocyanin accumulation. The latter was visually quantified and subsequent GWA mapping revealed that a large part of the variation in anthocyanin accumulation could be explained by a small genomic region on chromosome 1. The analysis of re-sequence data allowed us to associate the second most frequent allele of MYB90 with higher anthocyanin accumulation and to identify the causal SNP. Interestingly MYB75, a close relative of MYB90, was not identified by GWA mapping, although causal sequence variation of this gene for anthocyanin accumulation was identified in the Cvi x Ler and Ler x Eri-1 RIL populations. Re-sequence data revealed that one allele of MYB75 was dominating the population and that the MYB75 alleles of Cvi and Ler were both rare, explaining the lack of association at this locus in GWA mapping. For MYB90, two alleles were present in a substantial part of the population, suggesting balancing selection between them.

Next, the natural population was exposed to short-term heat stress during flowering (Chapter 3). This short-term stress has a large impact on seed set, while it hardly affects the vegetative tissues. Natural variation for tolerance against the effect of heat on seed set was evaluated by measuring the length of all siliques along the inflorescence in both heat-treated and control plants. Because the flower that opened during the treatment was tagged, we could analyse the heat response for several developmental stages separately. GWA mapping revealed that the heat response before and after anthesis involved different genes. For the heat response before anthesis strong evidence was gained that FLC, a flowering time regulator and QUL2, a gene suggested to play a role in vascular tissue development, were causal for two strong associations.

Furthermore, the impact of moderate drought on plant performance was evaluated in the plant phenotyping platform PHENOPSIS. Homogeneous drought was assured by tight regulation of climate cell conditions and the robotic weighing and watering of the pots twice a day. Because plant growth is a dynamic trait it was monitored over time by top-view imaging under both moderate drought and control conditions (Chapter 4 and 5). To characterise growth it was modelled with an exponential function. GWA mapping of temporal growth data resulted in the detection of time-dependent QTLs whereas mapping of model parameters resulted in another set of QTLs related to the entire growth period. Most of these QTLs would not have been identified if plant size had only been determined on a single day. For the QTLs detected under control conditions eight candidate genes with a growth-related mutant or overexpression phenotype were identified (Chapter 4). Genes in the support window of the drought-QTLs were prioritized based on previously reported gene expression data (Chapter 5). Additional validation experiments are needed to confirm causality of the candidate genes.

Next, to search for genes that determine plant size across many environments, biomass accumulation in the natural population was determined in 25 different environments (Chapter 6). Joint analysis of these data by multi-environment GWA mapping resulted in the detection of 106 strongly associated SNPs with significant effects in 7 to 16 environments. Several genes involved in starch metabolism, leaf size control and flowering time determination were located in close proximity of the associated SNPs. Two genes, RPM1 and ACD6, were located in close proximity of SNPs with significant GxE effects. For both genes, alleles have been identified that increase resistance to bacterial infection, but that reduce biomass accumulation. The sign of the allelic effect is therefore dependent on the environmental conditions. Whole genome predictions revealed that most of the GxE interactions observed at the phenotypic level were not the consequence of strong associations with strong QxE effects, but of moderate and weak associations with weak QxE effects.

Finally, in Chapter 7 I discuss the usefulness of GWA mapping in the identification of genes underlying natural variation in plant performance under drought, heat stress and a number of other environments. Strong associations were observed for both environment-specific as well as common plant performance regulators. Some choices in phenotyping and experimental design were crucial for our success, like evaluation of plant performance over time and simplification of the quantification of the phenotype. It is suggested that follow-up work should focus on the functional characterization of the causal genes, because such analyses would be helpful to identify pathways in which the causal genes are involved and to understand why sequence variation results in changes at the phenotype level. Although translation of the findings to applications in crops is challenging, this thesis contributes to the understanding of the genetic regulation of stress response and therefore will likely contribute to the development of stress tolerant and stable yielding crops.

Atmospheric Boundary Layer, Integrating Air Chemistry and Land Interactions
Vilà-Guerau De Arellano, J. ; Heerwaarden, C.C. van; Stratum, B.J.H. van; Dries, C.L.A.M. van den - \ 2015
New York : Cambridge University Press - ISBN 9781107090941 - 265
atmosferische grenslaag - atmosfeer - fysica - chemie - plantenfysiologie - vegetatie - bodemkunde - meteorologie - agrometeorologie - hydrologie - studieboeken - atmospheric boundary-layer - atmosphere - physics - chemistry - plant physiology - vegetation - soil science - meteorology - agricultural meteorology - hydrology - textbooks
This textbook provides an introduction to the interactions between the atmosphere and the land for advanced undergraduate and graduate students and a reference text for researchers in atmospheric physics and chemistry, hydrology, and plant physiology. The combination of the book, which provides the essential theoretical concepts, and the associated interactive Chemistry Land-surface Atmosphere Soil Slab (CLASS) software, which provides hands-on practical exercises and allows students to design their own numerical experiments, will prove invaluable for learning about many aspects of the soil-vegetation-atmosphere system. This book has a modular and flexible structure, allowing instructors to accommodate it to their own learning-outcome needs.
Framewerk onderzoek en praktijk voor inzet biostimulanten - Bijdrage aan de groei, productiviteit en weerbaarheid
Staalduinen, J. van; Wurff, A.W.G. van der - \ 2015
Onder Glas 12 (2015)5. - p. 50 - 51.
glastuinbouw - plantenfysiologie - plantenontwikkeling - plantgezondheid - groeiregulatoren - gewasproductie - optimalisatiemethoden - plantenvoeding - landbouwkundig onderzoek - tomaten - groenten - greenhouse horticulture - plant physiology - plant development - plant health - growth regulators - crop production - optimization methods - plant nutrition - agricultural research - tomatoes - vegetables
De belangstelling van telers voor biostimulanten neemt gestaag toe. Deze producten bevorderen de groei, productiviteit en weerbaarheid van gewassen. In een gezamenlijk project met de praktijk doet Wageningen UR Glastuinbouw onderzoek naar de invloed van biostimulanten op het afweermechanisme van tomatenplanten. Het einddoel is een framewerk waarmee telers hun gewas effectief en op voorspelbare wijze weerbaarder kunnen maken.
Ecology of lianas
Schnitzer, S.A. ; Bongers, F. ; Burnham, R.J. ; Putz, F.E. - \ 2015
Oxford : Wiley-Blackwell - ISBN 9781118392492 - 504
klimplanten - plantenecologie - plantenanatomie - plantenfysiologie - evolutie - tropische bossen - bossen - climbing plants - plant ecology - plant anatomy - plant physiology - evolution - tropical forests - forests
A liana is a long-stemmed, woody vine that is rooted in the soil at ground level and uses trees to climb up to the canopy to get access to well-lit areas of the forest. The main goal of this book is to present the current status of liana ecology in tropical and temperate forests. In essence, it is a forum to summarize and synthesize the most recent research in liana ecology and to address how this research fits into the broader field of ecology.
Knowledge about plant is basis for successful cultivation : new international standard handbook on plant physiology
Esch, H. van; Heuvelink, E. ; Kierkels, T. - \ 2015
In Greenhouses : the international magazine for greenhouse growers 4 (2015)2. - ISSN 2215-0633 - p. 35 - 35.
glastuinbouw - handboeken - naslagwerken - plantenfysiologie - plantkunde - kennistheorie - kennisoverdracht - greenhouse horticulture - handbooks - reference works - plant physiology - botany - theory of knowledge - knowledge transfer
‘Plant physiology in Greenhouses’ is the new international standard handbook on plant knowledge for the commercial greenhouse grower. It relates the functioning of the plant to the rapid developments in greenhouse cultivation. It is based on a continuing series of plant physiology articles published in the Dutch journal Onder Glas and the international edition In Greenhouses, written by Ep Heuvelink and Tijs Kierkels.
Nitrogen: The most important nutritional element for the plant : complicated balance between vegetative and generative growth
Heuvelink, E. ; Kierkels, T. - \ 2015
In Greenhouses : the international magazine for greenhouse growers 4 (2015)2. - ISSN 2215-0633 - p. 44 - 45.
glastuinbouw - plantenvoeding - voedingsstoffen - voedingsstoffenbeschikbaarheid - opname (uptake) - plantenfysiologie - nitraten - ammonium - cultuurmethoden - greenhouse horticulture - plant nutrition - nutrients - nutrient availability - uptake - plant physiology - nitrates - cultural methods
Nitrogen is found in almost all parts of the plant. It’s one of the plant’s most essential nutritional element. There’s a tendency in greenhouse horticulture to over-fertilise. In most situations it’s difficult to get around this. However, more precise application offers more possibilities to control production.
Production in a factory (the cell) requires high level of organisation : the cell: The plant’s smallest building block
Heuvelink, E. - \ 2015
In Greenhouses : the international magazine for greenhouse growers 4 (2015)2. - ISSN 2215-0633 - p. 18 - 19.
glastuinbouw - plantenfysiologie - plantkunde - celbiologie - cellen - celstructuur - beschrijvingen - greenhouse horticulture - plant physiology - botany - cellular biology - cells - cell structure - descriptions
The cell is the plant’s smallest building block. Many cultivation techniques and climate control measures have an effect at this level. Some knowledge about the functioning of the cell is therefore very useful. Many components of the cell have bizarre names so to understand it all better, for the purpose of this article, we compare it to a factory.
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