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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    Missing heritability and soft inheritance of morphology and metabolism in Arabidopsis
    Kooke, R. - \ 2014
    Wageningen University. Promotor(en): Harro Bouwmeester; Joost Keurentjes, co-promotor(en): Dick Vreugdenhil. - Wageningen University : Wageningen University - ISBN 9789462570412 - 283
    arabidopsis - heritability - overerving - plantenmorfologie - metabolisme - plantenfysiologie - genetica - epigenetica - genetische variatie - arabidopsis - heritability - inheritance - plant morphology - metabolism - plant physiology - genetics - epigenetics - genetic variation

    The plant phenotype is shaped by complex interactions between its genotype and the environment. Although the genotype is stable and determined by the genomic sequence, plants are able to respond flexibly to changes in environmental conditions by orchestrated signal transduction pathways. The genomic sequence may change with each generation through chromosome rearrangements, meiotic recombination and spontaneous mutations. Through natural selection on these randomly induced changes, genotypes become adapted to their local environment. Because different genotypes adapt to different environments, natural variation within species expands in time and gives rise to a wide variety of genotypes and phenotypes. The genetic architecture that specifies the phenotype can be investigated by analyzing different genotypes in the same environment and associate the phenotypic variation with molecular markers that discriminate the genotypes. Recent advances in next-generation sequencing technology enabled the fast sequencing of entire genomes, and in Arabidopsisthalianaalone, more than 1000 different genotypes have been fully resequenced. The sequencing allows the association of phenotypic variation with large numbers of single nucleotide polymorphisms (SNPs) that greatly enhance resolution in genome-wide association studies (GWAS).

    GWAS on human diseases suffer from missing heritability that is most likely caused by the genetic architecture of the disease traits. Many variants of small effect or rare variants most likely determine a large part of the genetic variation and these variants are difficult to identify in GWAS due to lack of statistical power. In plants, several GWAS have been performed and they have identified previously validated genes and genes involved in monogenic disease resistance, but elucidating quantitative traits such as many agronomic important traits might be problematic in plants as well. Chapter 2 describes a GWA study in which quantitative morphological traits, such as leaf area, flowering time and branching were examined in 350 accessions of Arabidopsis for association with about 200,000 SNPs. The morphological traits showed extensive variation and were highly heritable, but GWA mapping could not identify the genetic variants that explain the heritability. Therefore, missing heritability was addressed using genomic selection models and these models confirmed the quantitative complex architecture of the morphological traits. Based upon these results, the heritability was assumed to be hidden below the significance threshold, and indeed lowering the significance threshold enabled the identification of many candidate genes that have been implicated to play a role in the phenotype directly or indirectly, in previous studies. One candidate gene was studied in more detail; natural variants of ACS11, an ethylene biosynthesis gene, associated significantly with the petiole to leaf length ratio. ACS11is indeed expressed in petioles and ectopically supplied ethylene abolished the difference in the phenotype of natural variants at this locus, strongly suggesting that ACS11is involved in the regulation of petiole growth.

    However, lowering the significance threshold also increases the number of false-positive associations, non-causal alleles that co-segregate with the trait values. Because regulation of the morphological traits occurs at multiple intermediate levels, increased certainty on the associations can be obtained by performing GWA mapping on the intermediate levels from genotype to phenotype such as gene expression, and protein and metabolite content. Chapter 3 describes a literature survey into the multi-dimensional regulation of metabolic networks that are regulated by inputs from the clock, the communication between cells and between source and sink tissues, and the environment. The metabolic status of the plant can be seen as the final product of the interaction with the environment, and as such, it can serve as a blueprint for growth and development. Chapter 4 describes the abundant variation in enzyme activities and metabolites involved in primary carbon and nitrogen metabolism. The metabolite and enzyme activity data were analyzed together with plant biomass data, and many pleiotropic regulators were identified with opposite effects on primary metabolism and biomass formation. Natural variants in two stress-responsive genes were oppositely associated with biomass and many enzymes and metabolites involved in primary metabolism, suggesting that higher enzyme activities and higher levels of sugars and proteins might be needed to support plant resistance to stress at the expense of growth.

    Some studies indicated that epigenetic variation, independent of the genetic SNPs, may contribute to missing heritability. Epigenetic inheritance is defined as the inheritance of phenotypic variation to future generations without changes in DNA sequence. Epigenetic variation is caused by variation in chromatin marks such as DNA methylation, histone modifications and small RNAs. Recently, a recombinant inbred line (RIL) population was developed in Arabidopsis where the chromosomes are differentially methylated in lines with an otherwise isogenic background by crossing wild-type Col-0 with a hypomethylated ddm1-2mutant. Chapter 5 describes the epigenetic regulation of morphology and phenotypic plasticity by studying morphological variation in 99 epiRILs under control and saline conditions. The morphology and plasticity trait values were associated with differentially methylated regions (DMRs) that were used as molecular markers in QTL mapping. Many QTLs for various morphological traits and phenotypic plasticity parameters co-located, suggesting pleiotropic epigenetic regulation of growth, morphology and plasticity. Furthermore, methylation variation in the promoter of a salt-tolerance gene, HIGH-AFFINITY K+TRANSPORTER1 (HKT1)associated significantly with leaf area, especially under saline conditions.

    To gain more insight into the epigenetic regulation of plant growth and morphology, chapter 6 describes the epigenetic regulation of secondary metabolite levels in leaves and flowers and studies the relationship with the morphological traits determined in chapter 5. Many of the QTLs that were found for growth and morphology overlapped with the QTLs for metabolic traits, and suggest pleiotropic regulation. Furthermore, subsets of the metabolites correlated well with the morphological traits and might thus be regulated by the same loci. The majority of metabolite QTLs was detected for glucosinolates and flavonoids in the flowers, and methylation variation was observed for some of the biosynthetic pathway genes of these compounds when comparing Col-0 and ddm1-2, which indicates a role for epigenetic regulation of these biosynthesis pathways.

    Although stable, natural epialleles have been found in plant species and the environment can induce hypo- and hypermethylation of DNA, it remains elusive whether environmentally-induced epigenetic changes can be inherited to subsequent generations, independent of genetic variation. Chapter 7 describes the transgenerational inheritance of phenotypic variation in progeny derived from a common Arabidopsis founder line. The progeny of stressed parents and grandparents showed variation in morphological traits, metabolite accumulation and gene expression. For example, many salt-responsive genes were up-regulated in progeny of salt-stressed grandparents. The responses to biotic (methyljasmonate) and abiotic (salt) stress differed strongly and this suggests that different environments can cause different transgenerational responses. Because all lines are derived from a single ancestor, epigenetic variation and not DNA variation is most likely causal for the phenotypic variation. Further studies are, however, needed to provide conclusive evidence for transgenerational inheritance.

    Chapter 8 provides a synthesis of the work and discusses the GWA studies in the light of missing heritability, genetic architecture and the verification of candidate genes. The work on epigenetic regulation of phenotypic plasticity, morphology and metabolism is discussed in relation to Lamarckian soft inheritance that gained new enthusiasm after some recent discoveries in the field of epigenetics. And finally, the metabolomics work is discussed in the light of the growth-defense hypothesis that states that investments in defense occur at the expense of growth.

    CO2 niet meer dan genoeg: Teelt van Tomaat in 2012 bij Improvement Centre met lichtafhankelijk doseren van CO2
    Gelder, A. de; Warmenhoven, M.G. ; Dieleman, J.A. ; Klapwijk, P. ; Baar, P.H. van - \ 2014
    Bleiswijk : Wageningen UR Glastuinbouw (Rapport / Wageningen UR Glastuinbouw 1290)
    glastuinbouw - tomaten - solanum lycopersicum - energiegebruik - kooldioxide - plantenmorfologie - kennisoverdracht - plantenontwikkeling - cultuurmethoden - proeven op proefstations - lichtsterkte - greenhouse horticulture - tomatoes - solanum lycopersicum - energy consumption - carbon dioxide - plant morphology - knowledge transfer - plant development - cultural methods - station tests - light intensity
    Wageningen UR Glastuinbouw heeft met financiering van Kas als Energiebron en Samenwerken aan Vaardigheden onderzoek gedaan naar efficienter gebruik van CO2. In een kasproef bij GreenQ/Improvement Centre is een CO2 doseerstrategie getest, waarbij iets meer CO2 wordt gegeven dan er op basis van de hoeveelheid licht wordt opgenomen. Dit zorgt ervoor dat de CO2 concentratie in de kas bij open luchtramen net iets boven de buitenwaarde uit komt. Met deze doseerstrategie is met 17 kg/m² CO2 een productie gerealiseerd van 62.5 kg/m² tomaat (cultivar Komeett). Het energie gebruik was 26 m3/m². Uit de literatuur blijkt dat de weerstand die CO2 ondervindt vanuit de omgeving tot in de chloroplast, bij huidmondjes die voldoende openstaan, voor 40% bepaald wordt door het transport van CO2 door de celwand en het celvocht en voor 60% door de diffusie weerstand van kaslucht naar de intercellulaire ruimte. Een dun blad met veel sponsparenchym is daarom gunstig voor de CO2 binding. Het aantal huidmondjes per cm2 blad is daarbij minder maatgevend. Sluiting van de huidmondjes remt de fotosynthese binnen een minuut omdat de CO2 in het blad snel wordt opgebruikt. Vergelijking van de bladstructuur op twee hoogtes in het gewas met planten van hetzelfde ras in een andere proef lieten geen verschillen zien, niet in hoogte en niet in behandeling. Wageningen UR Greenhouse Horticulture developed a CO2 supply strategy in which slightly more CO2 is given than is taken up based on the amount of light. A test at GreenQ Improvement Centreresulted in a CO2 concentration in the greenhouse with open windows slightly above the outside value. With this supply strategy, 17 kg/m² CO2 supply resulted in a production level of 62.5 kg/m² tomato (cultivar Komeett). The energy consumption is 26 m3/m². When the stomata are open, the resistance of CO2 on the way from the environment into the chloroplast is for 40% determined by the transport of CO2 through the cell wall and the cytosol and for 60% by the diffusion resistance of greenhouse air to the intercellular space . A thin leaf with lots of spongy parenchym is therefore beneficial for CO2 binding. The number of stomata per cm2 leaf is therefore less important. Closing of the stomata inhibits photosynthesis within a minute because the CO2 in the leaf is then depleted. Comparison of the leaf structure at two heights in the crop with plants of the same variety in another compartment did not show differences, neither in height nor in treatment. This project was financed by Kas als Energiebron and Samenwerken aan Vaardigheden.
    Characterization of African Bush Mango trees with emphasis on the differences between sweet and bitter trees in the Dahomey Gap (West Africa)
    Vihotogbe, R. - \ 2012
    Wageningen University. Promotor(en): Marc Sosef; B. Sinsin, co-promotor(en): Ronald van den Berg. - [S.l. : S.n. - ISBN 9789461734129 - 189
    irvingia - domesticatie - bomen - plantenmorfologie - plantengeografie - genetische diversiteit - taxonomie - smaken - benin - west-afrika - irvingia - domestication - trees - plant morphology - phytogeography - genetic diversity - taxonomy - tastes - benin - west africa

     African bush mango trees (ABMTs) are economically the most important species within the family of Irvingiaceae. They are priority trees producing non-timber forest products (NTFPs) and widely distributed in the humid lowland forests of West and Central Africa. To boost their production and develop them towards a major crop for rural communities in Africa, a domestication program was initiated in the 2000s which is being coordinated by the World Agroforestry Centre. ABMTs belong to two taxa, one with sweet and one with bitter fruits which are morphologically difficult to distinguish. The fresh mesocarp of the sweet bush mangoes are consumed, while the seed of both bitter and sweet fruits are an important component of the African diet. The high oil content of this seed further increases their potential use.

     Apart from the overlap of their morphological characters, the ecological and phenological distinction between sweet and bitter ABMTs is unclear due to: (i) the lack of comparative quantitative data and (ii) the lack of centralizing the existing country-level databases. Therefore, their taxonomic status is still not clear. Do they represent distinct species or varieties or are they mere forms within the same gene pool? It is also unclear whether the occurrence of ABMTs in traditional agroforestry systems in the Dahomey Gap, the dry savannah corridor between the Upper and Lower Guinean rain forest blocks, forms part of the natural distribution or not . Moreover, genetic studies addressing ABMTs diversity have been geographically restricted, and conclusions regarding the taxonomic status of sweet and bitter trees were not unanimous.

    This study was conducted in a perspective of developing suitable strategies for the conservation and use of ABMTs, mostly in the Dahomey Gap. First, differences in ethnobotanical knowledge of the major socio-cultural groups in the Dahomey Gap were linked to the agroforestry status of ABMTs. This was used to explain the characteristics of the spatial pattern of ABMTs abundance and the anthropogenic factors that govern this spatial structure as well as population survival in the Dahomey Gap. Second, occurrence data of wild and cultivated ABMTs were used in a species distribution modelling algorithm to calculate the niche space and potential distribution of bitter and sweet trees in Tropical Africa. The differences in the obtained distribution patterns were compared using ENM-Tools. Third, detailed monthly phenological data and morphological characteristics (qualitative as well as quantitative measurements on the leaves, bark, fruits, and seeds) were used to analyse the diversity of ABMTs and to discover differences between them in order to be able to identify bitter and sweet trees in the field. Finally, the molecular markers AFLP and cpSSR were used in order to map the genetic diversity of ABMTs and to discriminate sweet and bitter trees across Togo, Benin, Nigeria and Cameroon.

    The consumption of mesocarp and seed of bush mangoes is widely known throughout the Dahomey Gap. The level of knowledge within local communities of other types of uses (medical, social-cultural) is generally poor and decreases towards the western part of this region. This suggests that ABMTs (mostly the sweet trees) were introduced in this eco-region through the migration of human populations from the Lower Guinean forest block (Southeast Nigeria) to the West. In the Dahomey Gap, bitter trees are confined to the Volta forest region, a small-sized ecological area in south-western Togo. While low densities (< 462 trees per 25 ha) were recorded for wild bitter trees occurring in the Volta forest region, higher densities (up to 1020 trees per 25 ha) were found for sweet trees in human made agro-systems. This implies a clear difference in cultivation methods between bitter and sweet ABMTs. The intensive cultivation of ABMTs in the Dahomey Gap is influenced by farmland status, farmer’s socio-cultural group and type of ABMT. Small and exhausted farmlands are converted into sweet ABMT orchards indicating that their development is a small-scale process lead by individual farmers. Slash and burn agriculture and intensive collection of fruits for seed commercialization jeopardize bitter trees, while traditional fishing systems (using twigs), traditional mass selection strategy, and intensive land commercialization severely threaten sweet trees genetic resources.

    Using species distribution modelling, the potential distribution of wild sweet trees was predicted in the wetter zones of the Guinean-Congolian phytogeographical region, while that of bitter trees extended to drier zones in the Guineo-Congolia/Sudania and Lake Victoria regions. This difference is significant, supporting the idea that bitter and sweet trees belong to two different species. In the Dahomey Gap, bitter trees occur in the wild in the wettest ecological region of the Volta forest region which is a very small part of the Dahomey Gap. This region is ecologically particular among the ecosystems in which wild bitter trees generally occur. We also conclude that in the Dahomey Gap sweet trees occur only in cultivation.

    Within the Dahomey Gap, clear phenological differences exist between sweet and bitter ABMTs, mostly in their reproduction phases. Moreover, their reproductive success significantly depends on the type of ABMT, soil, climate and season and we conclude there is a low probability of hybridization between sweet and bitter trees in the area where they co-occur.

    The qualitative morphological characters, the type of bark, colour of the mature fruit exocarp and mesocarp, and fruit roughness, do not consistently discriminate bitter and sweet trees in the field. We strongly recommend broadening the geographic area of this study by increasing more bitter trees as well as the wild samples of both taxa to validate this conclusion. The bitter trees in the Volta forest region produce the heaviest seeds and this consistently distinguishes them from all the sweet trees sampled in the Dahomey Gap. However, a combination of quantitative morphological characters (from fruits, mesocarp, and seeds) failed to discriminate populations. On the other hand this indicates the presence of a high diversity and thus high potential for selection across all phytogeographical regions. However, domestication and climate appear to be playing a key role in the morphological differentiation of Dahomey Gap populations, and evidence of success in the traditional domestication and selection of sweet trees is proven.

     Low genetic diversity was found for the bitter trees occurring in the Volta forest region in the Dahomey Gap due to the high fragmentation of the small-sized forest ecosystem in which they occur and the continuous reduction of the population size. The higher polymorphism and genetic diversity observed in the sweet tree population in Benin and Togo indicate the effect of domestication of material from different geographical origins as well as a frequent long distance transfer of genetic material. When used separately, the AFLP and cpSSR data failed to consistently discriminate geographical populations and bitter from sweet trees. But a combined dataset of both markers tends to differentiate such populations as well as tree types. Our results also provide evidence that the suitability of AFLPs and cpSSRs to assess genetic diversity patterns in Irvingia material needs to be thoroughly reassessed.

    Finally, although admitting that a broader study remains necessary, based on the presence of a consistent gap between both taxa regarding their reproductive periods, their different ecology and, of course, the consistent difference in taste of the fruit, we advise to treat the sweet and bitter ABMTs as two taxonomically different entities at species level: Irvingia gabonensis (Aubry-LeComte ex O’Rorke) Baill. and I. wombolu Vermoesen, respectively.

    An ecogeographic analysis of Oryza series Sativae in Asia and the Pacific
    Banaticla-Hilario, M.C.N. - \ 2012
    Wageningen University. Promotor(en): Marc Sosef, co-promotor(en): Ronald van den Berg; K.L. McNally. - S.l. : s.n. - ISBN 9789461733788 - 237
    oryza - oryza sativa - oryza nivara - genetische bronnen van plantensoorten - plantengeografie - plantenecologie - diversiteit - in-situ conservering - plantenmorfologie - taxonomie - genetica - genenbanken - azië - oryza - oryza sativa - oryza nivara - plant genetic resources - phytogeography - plant ecology - diversity - in situ conservation - plant morphology - taxonomy - genetics - gene banks - asia

    The non-cultivated speciesof the genus Oryza can provide a genetic arsenal of useful traits for improving the widely cultivated and consumed Asian rice (O. sativa). The diversity of these valuable plant resources must be well understood to ensure their effective in- and ex-situ conservation. In this thesis, we examined the ecogeographic variations within and between the three species of Oryza series Sativae in Asia and the Pacific. We looked at species differentiation from different spatial scales by analysing sympatric accession pairs of O. meridionalis and O. rufipogon and of O. nivara and O. rufipogon.

    We conducted phenotypic analyses in Chapter 2. The strong influence of ecology on species morphology was demonstrated in the ordination and cluster analyses results where O. meridionalis and O. nivara grouped together and were separated from O. rufipogon. We detected greater differentiation of O. nivara and O. rufipogon in South Asia and positive correlations between spatial and intraspecific (interpopulation) morphological distances in continental Asia. We found significant correlations between geoclimatic factors and certain character measurements within species and observed that seedling height, culm number and diameter, leaf size, and anther length exhibit contrasting responses for O. nivara and O. rufipogon. We confirmed significant morphological differences between the three species, between the South and Southeast Asian populations of O. nivara, and between the Australasian and the non-Australasian populations of O. rufipogon and provided botanical descriptions to delineate O. meridionalis, O. nivara and O. rufipogon morphologically.

    In Chapter 3, we genotyped the same set of accessions with 29 SSR markers and applied a variety of methods for genetic diversity analysis. Based on ordination and phylogenetic results, we verified that O. meridionalis is a genetically distinct species and that O. nivara and O. rufipogon overlap genetically across their geographic distribution. However, Bayesian clustering analysis recognized local-scale species separation of O. nivara and O. rufipogon implying stronger interspecific gene flow barriers in smaller spatial units. Concurrently, AMOVA indicated that the bulk (64%) of genetic variation in Asia Pacific series Sativae can be found among accessions and the lesser portions within accessions (26%) and among species (10%). We captured contrasting intraspecific variation patterns for O. nivara and O. rufipogon where the former exhibited low diversity, high population differentiation and isolation by distance mainly in South Asia while the latter displayed high diversity, low population differentiation and isolation by distance primarily in continental Southeast Asia. We established that altitude is correlated negatively to accession diversity and positively to local-scale species differentiation. Using Bayesian inference, we identified eight genetically distinct population groups: C1) Indian and Bangladeshi O. nivara; C2) Cambodian O. nivara; C3) Southeast Asian O. rufipogon; C4) O. meridionalis; C5) Nepalese O. nivara; C6) non-Cambodian Southeast Asian O. nivara; C7) Australasian O. rufipogon; and C8) South Asian O. rufipogon. Cluster analysis grouped the aromatic and japonica cultivar groups of O. sativa with O. rufipogon in South Asia and the indica and aus groups with O. nivara from Thailand and Cambodia, respectively. O. nivara from Nepal seemed genetically isolated from the other population groups. We also detected variation patterns that agreed with the results in Chapter 1 such as the South and Southeast Asian divisions of O. nivara, the divergence of Australasian populations from the rest of O. rufipogon and the greater differentiation of O. nivara and O. rufipogon in South Asia.

    In Chapter 4, we conducted artificial crossing experiments to 15 selected parental accessions of O. meridionalis, O. nivara, and O. rufipogon and assessed the extent of several post-pollination isolating mechanisms in Oryza series Sativae. We observed reproductive incompatibility within and between the inbreeding species O. meridionalis and O. nivara and high intraspecific crossability of the outcrossing O. rufipogon where viable and non-sterile F1 hybrids were produced only by combinations with a parental distance that ranged from 1062 to 3813 kilometers. Insular Southeast Asian and/or Australasian accessions of O. rufipogon were the most reproductively successful parents. O. rufipogon exhibited significant pre-zygotic species isolation (in terms of seed set) and reduced post-zygotic isolation, and seemed symmetrically compatible with O. nivara and asymmetrically compatible with O. meridionalis. We obtained few annual hybrids with relatively high fertilities from crosses between O. rufipogon and O. nivara and numerous perennial hybrids with low fertilities from crosses between O. rufipogon and O. meridionalis. Crossability estimates did not show significant correlations with geographic distance between parents. However, we discerned reduced seed set and F1 fertility in interspecific combinations with sympatric parents compared to crosses with non-sympatric parents, indicative of reinforced species isolation in sympatry. We evaluated the F1 offspring of different cross combinations and found a mixture of intermediate and parental character traits in interspecific hybrids.

    We discussed the taxonomic implications of the research results in Chapter 5 where we specifically dealt with the opposing views of lumping or splitting of O. nivara and O. rufipogon. We concluded that these two taxadeserve to be treated as separate species based on the following biosystematic evidence obtained from the thesis: 1) ecological distinction; 2) considerable prezygotic barriers; 3) opposing patterns of gene flow and genetic variation; 4) local-scale genetic divergence and 5) enhanced reproductive barriers under sympatric conditions. We identified ecogeography as a major driving force in the diversification of Oryza series Sativae in Asia and the Pacific and suggested that ecological speciation gave rise to O. nivara and O. rufipogon. We also presented recognizable geographic races within species.

    Ultimately in Chapter 6, we emphasized the importance of our study in several aspects of rice science and identified results that agreed with prior Oryza diversity studies. At the same time, we presented previously unreported morphological and genetic variation patterns that were established in this thesis. We discussed the possible applications of the research results to wild rice conservation, covering in situ strategies as well as gene bank practices. We also highlighted the potential role of O. nivara in Asian rice domestication where it could have either directly given rise to the indica cultivar group or hybridized/introgressed with migrated japonica cultivars in India, eventually leading to the development of indica.

    Plant Resources of Tropical Africa 16 Fibres
    Brink, M. ; Achigan-Dako, E.G. - \ 2012
    Wageningen, Netherlands : PROTA Foundation/CTA (Plant resources of tropical Africa 16) - ISBN 9789290814818 - 602
    vezelgewassen - plantenvezels - soorten - genetische bronnen van plantensoorten - plantengeografie - plantenmorfologie - biologische naamgeving - taxonomie - plantenvermeerdering - tropisch afrika - fibre plants - plant fibres - species - plant genetic resources - phytogeography - plant morphology - biological nomenclature - taxonomy - propagation - tropical africa
    This volume deals with the fibres of Tropical Africa. 515 ‘primary use’ fibres are described in 248 review articles. Many of the articles are illustrated with a geographic distribution map and a line drawing of the habit.
    MADS on the move : a study on MADS domain protein function and movement during floral development in Arabidopsis thaliana
    Urbanus, S.L. - \ 2010
    Wageningen University. Promotor(en): Gerco Angenent, co-promotor(en): Richard Immink. - S.l. : S.n. - ISBN 9789085856245 - 138
    arabidopsis thaliana - biologische ontwikkeling - bloemen - eiwitten - transcriptie - transcriptiefactoren - genexpressie - plantenmorfologie - eiwittransport - arabidopsis thaliana - biological development - flowers - proteins - transcription - transcription factors - gene expression - plant morphology - protein transport
    In this thesis we investigated the behaviour of fluorescently-tagged MADS domain proteins during floral development in the model plant Arabidopsis thaliana, and explored the importance of intercellular transport via plasmodesmata for MADS domain transcription factor functioning. The MADS domain transcription factor family plays an important regulatory role in the development of flowers, among others by establishing the identities of the different floral organs. Although genetic screens and in vitro and in vivo studies on protein-protein and protein-DNA interactions provide important information on how MADS domain transcription factor complexes are able to regulate downstream target genes, understanding of the behaviour of MADS domain transcription factors in planta is still limited. Also, the extent to which intercellular movement of MADS domain transcription factors via plasmodesmata plays a role in developmental processes is poorly understood. Since the discovery of the GREEN FLUORESCENT PROTEIN (GFP) and the subsequent development of similar fluorescent tags, it has become possible to observe the subcellular localisation and behaviour of fluorescently-tagged proteins in living tissues with confocal laser scanning microscopy.
    In Chapter 2 of this thesis, different methods of tagging the MADS domain transcription factors AGAMOUS (AG), SEPALLATA3 (SEP3), and FRUITFULL (FUL) for chromatin immunoprecipitation, chromatin affinity purification and in planta imaging are described. This research shows that the addition of a small peptide tag or a fluorescent tag to MADS domain proteins easily leads to transgene silencing and specific loss-of-function mutant phenotypes, especially when the tagged MADS box genes are expressed under the control of the constitutive CaMV35S promoter. Plants that express tagged MADS box genes from genomic fragments that include all or most of the regulatory elements, and therefore mimic the natural expression pattern as much as possible, show lower levels of loss-of-function phenotypes. In addition, these plants are also more useful for investigating biological relevant behaviour of the MADS domain proteins.
    In Chapter 3, the spatio-temporal localisation patterns of GFP-tagged MADS domain transcription factors AG, SEP3, FUL and APETALA1 (AP1) during floral development are reported. These analyses demonstrate that there are several tissues, often epidermal cell layers, where MADS domain proteins could be detected, while the available literature describes an absence of mRNA in those tissues. This could indicate that there is intercellular transport of MADS domain proteins in meristematic tissues during floral development. The implications of the observed behaviour of the different MADS domain proteins for MADS domain protein functioning are discussed in this chapter.
    In Chapters 4 and 5 we describe the different methods that were used to investigate whether MADS domain proteins are indeed able to transport between cells during floral development. The difficulties that we encountered in our attempts to investigate intercellular MADS domain protein transport with microinjection techniques and by using the photoconvertible fluorescent mEosFP-tag are discussed. In plants that specifically overexpress GFP-tagged MADS domain transcription factors AG, SEP3, APETALA3 (AP3), or PISTILLATA (PI) in the epidermis, we demonstrated with a photobleaching technique that all tested proteins were able to move within the epidermal cell layer. This mechanism of lateral epidermal movement provides an explanation for most of the unexpected MADS domain protein localisations that we found in the spatio-temporal localisation analyses in Chapter 3. Additionally, we demonstrate that epidermis-expressed GFP-tagged AG is able to move from the epidermis to the subepidermis in the centre of the floral meristem, which provides proof for the suggestions that AG acts non-cell-autonomously in the floral meristem. In these plants we also analyzed the effects of epidermal MADS domain protein expression on the plant phenotype. This showed, among others, that epidermis-expressed AG is able to fully complement its own mutant background, while epidermis-expressed AP3 is not.
    In Chapter 6, we explore the mechanisms underlying the behaviour of GFP-tagged SEP3 during petal and stamen development that was observed in the spatio-temporal localisation studies described in Chapter 3. Just prior to the initiation of petal and stamen primordia GFP-tagged SEP3 proteins change their subcellular localisation from predominantly nuclear to more cytoplasmic, and at later stages GFP-tagged SEP3 protein seems to disappear in the middle of the primordia without the loss of SEP3 mRNA expression. These two processes could be regulated at a post-transcriptional level by two mechanisms that are discussed, namely 26s proteasome mediated SEP3 protein degradation and epidermal-oriented intercellular transport of SEP3 proteins. Additionally, we demonstrate that there are no clear indications that the observed GFP-tagged SEP3 behaviour is due to the presence of F-box protein UNUSUAL FLORAL ORGANS (UFO), which regulates petal and stamen development.
    In Chapter 7, this thesis finishes with some concluding remarks on in planta imaging of MADS domain transcription factors and the possible mechanisms of MADS domain protein movement in the floral meristem. Furthermore, we speculate on the importance of MADS domain protein movement in establishing MADS box gene expression patterns and MADS domain protein gradients, and on the need for symplastically isolated domains for proper floral development.

    LEDs en energiebesparing bij paprika: onderzoek in de praktijk bij VOF Dingemans
    Nederhoff, E.M. ; Boer-Tersteeg, P.M. de; Schapendonk, A.H.C.M. ; Pot, C.S. ; Dueck, T.A. ; Bruins, M.A. ; Uenk, D. ; Steenhuizen, J.W. ; Snel, J.F.H. ; Marcelis, L.F.M. ; Kempkes, F.L.K. ; Sapounas, A. ; Driever, S.M. ; Verkerke, W. ; Warmenhoven, M.G. ; Janssen, H.J.J. - \ 2009
    Bleiswijk : Wageningen UR Glastuinbouw (Rapport / Wageningen UR Glastuinbouw 285) - 106
    teelt onder bescherming - kassen - kunstlicht - licht - lichtgevende dioden - morfologie - plantenmorfologie - lichtsterkte - plantenontwikkeling - paprika - glastuinbouw - led lampen - protected cultivation - greenhouses - artificial light - light - light emitting diodes - morphology - plant morphology - light intensity - plant development - sweet peppers - greenhouse horticulture - led lamps
    In een praktijkproef met met LED belichting, zijn stuurlichteffect op paprika (ras Derby) niet onomstotelijk bewezen, want lichtkleur en lichtintensiteit waren gekoppeld. Echter, belichtingen met een laag intensiteit (blauw licht, 20 µmol/m2/s, en rood licht, 46 µmol/m2/s) suggereren wel een aantal stuurlicht effecten. Bij rood licht waar belichting startte voor zonsopgang raakte de planten uit balans. De zetting was goed bij rood licht en slecht bij blauw licht. Halverwege het seizoen waren de planten onder blauw licht langer en hadden een groter bladoppervlak dan onbelichte planten, maar dit zou ook te danken kunnen zijn aan grotere beschikbaarheid van assimilaten onder blauw licht. Op basis van hetzelfde hoeveelheid licht (gram per mol), werd een verglijkbare productie berekend onder rood licht en SONT. Met de juiste gewassturing wordt verondersteld dat potentieel 5-10% meer productie kan worden bereikt door belichting met LEDs in vergelijking met SON-T lampen
    Growth and development of true sago palm (Metroxylon sagu Rottbøll) : with special reference to accumulation of starch in the trunk : a study on morphology, genetic variation and ecophysiology, and their implications for cultivation
    Schuiling, D.L. - \ 2009
    Wageningen University. Promotor(en): Paul Struik. - [S.l.] : S.n. - ISBN 9789085858546 - 259
    metroxylon sagu - sago - arecaceae - starch crops - plant development - growth analysis - plant morphology - agronomy - maluku - indonesia - ecophysiology - economic botany - metroxylon sagu - sago - arecaceae - zetmeelgewassen - plantenontwikkeling - groeianalyse - plantenmorfologie - agronomie - molukken - indonesië - ecofysiologie - economische botanie
    Keywords: Metroxylon sagu, Arecaceae, starch crops, plant growth and development, plant morphology, inflorescence structure, electron microscopy, phenological scale, genetic variation, plant taxonomy, folk taxonomy, ethnobotany, leaf area, leaf area index, starch accumulation, starch distribution, plant ecophysiology, tropical lowlands, wetlands, traditional processing, estate cultivation, agronomy, Moluccas, Maluku.

    True sago palm (Metroxylon sagu Rottbøll) is a stout, clustering palm adapted to swampy tropical lowland conditions. Each axis in a sago palm clump flowers once at the end of its life after having amassed a large amount of starch in its trunk. Man can harvest this starch by felling the trunk, pulverizing the pith and leaching the starch out with water, and use it like other starches for food or non-food purposes. It is a staple food mainly in eastern Indonesia and in Papua New Guinea where it is harvested mostly from semi-managed stands. For establishing sago palm as a full-fledged plantation crop, desirable because of its envisaged large yield potential as a perennial, its niche habitat, and its potential as a raw material provider for bio-ethanol production, the scientific base for establishing the right felling time to harvest the starch needed strengthening.

    Between October 1988 and November 1990, 27 sago trunks in the Adult Vegetative (AV) or Generative (G) phase belonging to six varieties were selected from semi wild sago stands in the Moluccas, eastern Indonesia: 23 trunks (4 varieties) on the alluvial coastal plain near Hatusua village, Seram Island, and 4 trunks (2 varieties) on hilly terrain near Siri Sori Serani village, Saparua Island. These trunks were felled, dissected, morphologically described and sampled for the amount and distribution of starch they contained. The leafless parts of the trunks were 4.45 to 19.65 m long, had a mean starch density of 4.6 to 254 kg/m3 and contained five to 777 kg of starch (maximum found in a whole trunk: 819 kg).

    To link starch content to age, the ages of the sampled trunks had to be estimated. To enable age estimation by counting leaf scars on the trunk, the leaf unfolding rate of 36 AV-phase palms around Hatusua (31 palms) and Siri-Sori Serani (5 palms) was monitored for varying periods between 1989 and 1992. Probably due to large variation in habitat and genetic make up, this rate varied from 2 to 14 leaves per year (mean 7.85), rendering number of leaf scars unfit as accurate age estimator. Also trunk height proved unfit for this purpose. From monitoring 5 G-phase palms, the G-phase could be subdivided into 3 sub-phases (G1, G2, G3), recognizable from the ground by the phased development of the successive orders of inflorescence branches. By combining gathered morphological and monitoring data, a phenological scale of a model palm was composed consisting of two parallel timelines of hidden and outwardly visible events: two years after the start of the Establishment (E) phase, the first AV-phase leaf is initiated in the apical growing point, to unfold only 2.5 years later; the initiation of the first AV-phase tissues is followed 12.5 to 14.5 years later by the initiation of the first G-phase tissues, followed 4 to 5.5 years later by the shedding of fruits, and finally by a 2- to 5-year Recycling phase (name proposed here) in which the axis decays and collapses. This scale, which accounts for the large time gap between initiation of trunk parts and their becoming visible, may help to correctly time cultural measures. The 27 sampled trunks could tentatively be ranked according to physiological age into 4 AV phase classes and 9 G phase classes.

    Since the examined palms belonged to 6 different local varieties, their relative rareness or commonness had to be established to assess the validity of the findings. Based on literature and on interviews with informants, an overview of locally recognised sago palm varieties is presented. The number of unique variety names in 32 localities in Indonesia and Papua New Guinea totalled 325, ranging from 2 (spined vs unspined only) to 34 per locality. On the basis of this survey, the Hatusua varieties were considered average. The nomenclatural category folk variety (fovar, fv.) is proposed to unambiguously name local varieties by adding to the variety name an indication of the location where, and (if known) the ethnic/linguistic group by which that name is used.


    Leaf area estimation methods were devised to enable investigation of the relationship between leaf area and starch content. In the AV-phase the Total leaf area (TLA) of a sago palm axis ranged from 200 m2 to 325 m2, one axis having an exceptional TLA of 388 m2. The TLA in the G-phase before fruiting mostly remained within the same range, possibly exceeding it for a short period early in that stage. The Leaf area index (LAI) of an individual axis showed an upward trend from 1 - 1.5 in the E-phase to 1.25 - 1.75 in the AV-phase, to more than 2 in the early G-phase, followed by a decrease to about 1.5 again in the late G-phase before fruiting. No fruiting palms were available for analysis. The TLA and LAI of a single trunk could not be linked to the mean starch density of its pith, nor to the total amount of starch the pith contained.
    Generally, starch density in the trunk first increased with height above ground level, reached a maximum about half-way to two-thirds up the leafless part of the trunk, and then sharply dropped towards the top of the trunk. From the late AV phase onward the maximum starch density ranged from 238 to 284 kg/m3. The four trunks with the highest maximum starch densities, all closely around 280 kg/m3, belonged to three different varieties, suggesting that 280 kg/m3 may be considered the maximum starch storage capacity in the pith of any variety.
    The starch distribution pattern in the leafless part of the trunk showed a tendency to evolve with age from two tailed (density gradually increasing from base, gradually decreasing towards top) to one tailed (density gradually increasing from base, sharply decreasing towards top). The differences in distribution pattern found strongly suggested that there must be other factors besides age and development phase affecting starch accumulation. Attempts to determine the effect of palm variety and of the environment mostly failed.

    Potential yield of a model palm based on the maximum starch density of 280 kg/m3 was estimated at 840 kg of dry starch. That this amount is much higher than generally found may partly be due to poor recovery ratios, as the results of a traditionally processed trunk demonstrated: only 47% of the starch in the processed trunk part was recovered, and if the unharvested starch present in the traditionally discarded basal and top part of the trunk is taken into account, recovery drops to 44%.

    In an attempt to establish the point in time at which a sago palm starts to be a nett consumer of its own starch, the course of the energy producing and consuming capacity of an axis during its life time was modelled based on the assumption that by the end of the AV-phase the existing TLA of the axis produces just the amount of energy needed to maintain existing biomass, to keep up the normal regular growth, and to fill new trunk with starch. Using this model, assimilate requirements for building and maintaining the inflorescence and the fruits could not be met by the production capacity of the leaves plus the starch reserves in the trunk. For this modelling approach to succeed in predicting the turning point from nett production to nett consumption of starch by a sago palm axis, additional data on chemical composition of its parts and on assimilation rate are needed.

    Lack of precise data on the age of the sampled trunks and lack of uniformity of their genetic make up and growing conditions made it impossible to arrive at the sought-after detailed timetable of the evolution of trunk starch accumulation and depletion to base the right felling time of a sago palm on. The high starch density found in the trunk of a palm with half-grown fruits indicated that depletion of starch reserves by the palm itself may set in much later than generally assumed.
    Once the course of starch accumulation in time in a single axis is unravelled, the next research question should be how this adds up in a clump - the actual production unit in a plantation - with axes of different age. Timing felling in such a situation should be aimed at maintaining a maximum starch accumulation rate for the plantation as a whole rather than at harvesting a maximum amount of starch per trunk.

    Data sheets of each palm examined containing all primary and some secondary data, and including photographs, are appended in digital form.


    Functional-structural plant modelling in crop production
    Vos, J. ; Marcelis, L.F.M. ; Visser, P.H.B. de; Struik, P.C. ; Evers, J.B. - \ 2007
    Dordrecht : Springer (Wageningen UR Frontis series vol. 22) - ISBN 9781402060335 - 269
    gewasproductie - modellen - plantenfysiologie - plantenmorfologie - meting - planten - gewassen - concurrentie tussen planten - planteninteractie - crop production - models - plant physiology - plant morphology - measurement - plants - crops - plant competition - plant interaction
    Functional-structural plant models (FSPMs) describe in quantitative terms the development over time of the three-dimensional (3D) structure of plants as governed by physiological processes and affected by environmental factors. FSPMs are particularly suited to analyse problems in which the spatial structure of the plant or its canopy is an essential factor to explain, e.g., plant competition (intra-plant, inter-plant, inter-species) and the effects of plant configuration and plant manipulation (e.g., pruning and harvesting) on yield and produce quality. This book describes the philosophy of functional-structural plant modelling and several tools for making FSPMs; it outlines methods for measuring essential parameters, including those pertaining to plant structure.
    Lianas and trees in tropical forests in south China
    Cai, Z.Q. - \ 2007
    Wageningen University. Promotor(en): Frans Bongers, co-promotor(en): K.F. Cao. - [S.l.] : S.n. - ISBN 9789085046530 - 162
    klimplanten - bosbomen - bomen - tropische bossen - biodiversiteit - plantenecologie - plantenmorfologie - china - ecofysiologie - climbing plants - forest trees - trees - tropical forests - biodiversity - plant ecology - plant morphology - china - ecophysiology
    Lianas (woody climbers) and trees are the most important life-forms in most tropical forests. In many of these forests lianas are abundant and diverse and their presence is often a key physiognomic feature. Lianas contribute substantially to the floristic, structural and functional diversity of tropical forests, and have both positive (providing valuable food resources, habitat, and connections among tree canopies that are used as pathways by arboreal animals) and negative (reducing tree growth, fecundity and survivorship) effects on forests.

    Lianas are increasingly well studied in many areas around the world, but in southeast Asia they are relatively unknown. This PhD dissertation describes liana communities in selected but well distributed tropical forests in Xhishuangbanna, southwest China. In addition the question what makes lianas functionally different from trees is addressed. A number of structural-functional characteristics of lianas are analysed, comparative to trees. Special attention is put to growth performance and ecophysiological leaf and plant characters in a framework of adaptive ecology. The last part of the dissertation addresses adaptive behavior, both within one liana species as across a number of species differing in adult stature.

    Liana communities in different forests

    The liana communities of three common forest types are analysed: seasonally wet. montane forest and evergreen broad-leaved forest. In each forest five 0.1 ha (20 x 50 m) plots were established. The density of lianas varied significantly among the three forests, with on average 445, 276 and 301 individuals per plot in the seasonally wet, montane, and evergreen forests,respectively. All three forests combined consisted of a total of 147 liana species, representing 48 families and 75 genera. A plot had on average 40, 26, and 21 species in the seasonally wet, montane, and evergreen forest, respectively. The forests were rather different as similarity between their liana assemblages was low. In all three forests, most lianas were stem twiners and scramblers, with relatively few hook, tendril and root climbers. Liana species were mostly wind dispersed in the evergreen forest, but animal and gravity dispersed in the other two forests.

    The higher liana abundance in the seasonal forest is consistent with the documented pattern that lianas peak in abundance with increasing seasonality. Compared to other tropical Asian tropical forests, the diversity and abundance of lianas is relatively high in Xishuangbanna, which may be due to the relatively warm climate, as well as its high seasonal rainfall and its high rates of disturbance and forest fragmentation.

    How different are lianas from trees?

    In two studies a large number of liana and tree species were compared for selected leaf structural and physiological characteritics. Chapter 3 focusses on differences in adaptation to climate seasonality. Most organisms decrease in abundance with decreasing annual precipitation and increasing seasonality. However, lianas are an exception to this general rule: they increase in abundance with increasing seasonality (Schnitzer 2005). In this chapter the hypothesis is tested that lianas are physiologically more robust than trees during the dry season, thus contributing to an explanation of their relatively high abundance in seasonal forests. We compared a range of leaf-level physiological attributes of 18 co-occurring liana and 16 tree species during the wet and dry seasons in a tropical seasonal rainforest in Xishuangbanna. During the wet season, lianas (liana leaves) had significantly higher nitrogen concentrations ( Nmass ), δ13 Cvalues, and lower leaf mass per area (LMA) than trees, indicating that lianas have higher water-use efficiency (WUE) and lower structural investments. However, liana and tree species did not differ significantly in photosynthesis ( Aarea ), dark respiration (R darea ), chlorophyll content (Chl mass ), carotenoid to chlorophyll ratio (Car/Chl), phosphorus concentration ( Pmass ), N:P ratios, and photosynthetic nitrogen- and phosphorus- use effeciency (PNUE, PPUE). During the dry season, the decrease in Aarea and Nmass was far lower in lianas than in trees, suggesting that lianas fix more carbon and suffer less from water stress during this season. From the wet to the dry season, average Aarea decreased by 30.1% in tree species, compared with only 12.8 % in liana species. Nmass , Pmass and PNUE changed little for lianas, while these factors decreased strongly for tree species. The δ13 C, LMA and Car/Chl values for both lianas and trees did not vary significantly with the season.

    These results show that lianas are less negatively effected by a dry season than trees, providing eco-physiological evidences as to why lianas are abundant in the seasonally rainforest. The leaf-level physiological characteristics show that lianas tend to fix more carbon, have a higher resource capture efficiency (water and nitrogen) in the dry season, and have lower cost of resource capture, compared to trees, thus confirming the hypothesis that differences in photosynthetic attributes may contribute to the competitive advantage of lianas over trees in seasonal forests.

    Chapter 4 addresses the question whether lianas are more efficient than trees in nutrient resorption during leaf senescence. This would give an additional advantage in nutrient poor environments as many tropical forests are. The chapter presents changes in leaf size, leaf mass and foliar nutrient concentrations during leaf senescence in 12 liana and 14 tree species in a tropical strongly phosporus-limited montane rain forest in Xishuangbanna. The relative leaf shrinkage and mass loss during senescence did not differ significantly between lianas and trees. Nutrient concentrations in mature leaves and nitrogen resorption efficiency of liana species were similar to those of tree species, but the phosphorus concentrations of liana litter were higher, and liana's phosphorus resorption efficiencies were lower. These results therefore provide clear evidence in favour of a novel mechanism whereby lianas may influence the ecosystems in which they occur. Through the production of nutrient-rich litter, they have the potential to greatly enhance the availability of nutrients in areas where they are abundant, and thus they may have significant effects on small-scale biodiversity.

    Another important difference between lianas and trees is the larger growth rate of lianas, as has been often postulated. To examine this hypothesis more closely, a range of physiological, morphological, and biomass parameters at the leaf and whole plant level were compared in seedlingsof five Bauhinia species of different life form and light demand: two light-demanding lianas, one shade-tolerant liana, and two light-demanding trees. Seedlings of these five species were grown in a shadehouse with 25% of full sunlight. Compared to trees, the two light-demanding lianas had lower photosynthetic rates per unit area (Aarea ) and similar photosynthetic rates per unit mass (Amass ). High specific leaf area (SLA) and leaf mass fraction (leaf mass/plant mass, LMF) in the two light-demanding lianas were reflected in a higher leaf area ratio (LAR). The two light-demanding liana species had higher relative growth rate (RGR), allocated more biomass to leaf production (higher LMF and LAR) and stem mass fraction (SMF), and less biomass to the roots (root mass fraction, RMF) than the two tree species. The shade-tolerant liana had the lowest RGR of all five species, and had a higher RMF, lower SMF, and similar LMF than the two light-demanding liana species. Across species, RGR was positively related toSLA, but not to LAR and Aarea. The faster growth of light-demanding lianas compared to light-demanding trees is based on morphological parameters (SLA, LMF, and LAR), and cannot be attributed to higher photosynthetic rates at the leaf level. The shade-tolerant liana exhibited a different growth strategy from the light-demanding species. Our study shows that, even within a genus (in this case Bauhinia), plant growth is rather variable, and that this variation is related to life form (lianas vs trees) and to light demand (light-demanding vs shade tolerant).

    Seasonal acclimation of a liana

    Under natural conditions, photosynthesis is biochemically regulated to maintain a balance between the rates of its component processes and the concentrations of metabolites, and is affected by continuously changing environmental variables, such as light, water availability, and temperature. Xishuangbanna, biogeographically located in the transitional zone between tropical Southeast Asia and subtropical East Asia, has a rich tropical flora and typical tropical rain forests in the lowland area. It has been hypothesized that the vegetation there is likely to be affected by the seasonal drought and chilling because it is far from the Equator and at a relatively high altitude. To test this hypothesis, Chapter 6 addresses the photosynthetic adaptation and growth responses in seedlings of a local liana species (Zizyphus attopensis Pierre) in three contrasting natural microhabitats: understory, a small gap and a large gap. Photosynthetic capacity(light-saturated photosynthetic rate, Amax ), maximum rate of carboxylation (Vcmax ) and electron transport ( Jmax ), and partitioning of leaf nitrogen into carboxylation ( Pc ) and electron light transport ( Pb ) differed significantly between seasons and microhabitats. Specific leaf area (SLA) did not change seasonally, but was different between plants grown in each of the three microhabitats and was negatively linear related to the daily integrated photon flux density (PPFD i ). In contrast, nitrogen content per unit area (Na ) changed seasonally but did not differ among microhabitats. Measurements of maximum photosystem II (PSII) photochemical efficiency showed that no chronic photoinhibition occurred for all microhabitats throughout the experimental period. Photosynthetic capacity was greatest in the wet season and lowest in the cool season. During the cool and dry seasons, the reduction in Amax was greater in seedlings grown in the large gap than in those grown in understory and small gap. Close logarithmic relationships were detected between PPFD, leaf Na and photosynthetic capacity. Stem mass ratio decreased and root mass ratio increased in the dry season. These results show that seasonal acclimation in growth and photosynthesis of the seedlings was due to changes in biochemical features (particularly Na and partitioning of total leaf nitrogen between the different photosynthetic pools) and biomass allocation, rather than to changes in leaf morphological features (such asSLA). The local light level is the main factor driving seasonal variations in growth and photosynthesis in the study area due to the presence of heavy fog during the cool and dry seasons which reduces irradiance and supplies water to the soil surface layers.

    Light acclimation, adult stature and shade tolerance

    Finally, Chapter 7 addresses light acclimation of seedlings of six late-successional common woody species differing in adult stature and shade tolerance. Especially morphological and physiological leaf and whole-plant features are analysed. After 1 year of growth in low light (4.5% full sun), seedlings were transferred to high light (24.5% full sun) to investigate acclimation responses of existing leaves to forest gap opening and to determine whether seedling capacity for acclimation is a limiting factor in its natural regeneration. Leaves of the small shrub species are shade-adapted, as indicated by their low photosynthetic capacity, efficiency in using sunflecks, low stomatal density, low Chl a/b ratio and high spongy/palisade mesophyll ratio. The shrub species utilized sunflecks efficiently because of a short photosynthetic induction time and low induction loss. In all species, transfer of seedlings to high light resulted in a substantial initial reduction in the dark-adapted quantum yield of photosystem II ( Fv / Fm ) atmidday. Predawn Fv / Fm of the taller species did not change greatly, but predawn Fv / Fm of the short species (shrubs) decreased significantly without complete recovery within 25 days of transfer to high light, indicating chronic photoinhibition and damage to the previously shade-adapted leaves. Maximum net photosynthetic rate and dark respiration of the four taller species increased considerably after transfer to high light, but not in the shrub species. Similar trends were observed for the number of newly formed leaves and relative height growth rate. We conclude that the short species have limited potential for developmental and physiological acclimation to high light, which explains their absence from forest gaps. Compared with shrub species, the taller tree species, which are more likely to experience high light during their life span, showed a greater potential for light acclimation. Physiological differences among the four tree species were not consistent with differences in adult stature.

    Lianas versus trees: are differences adaptive?

    Phenotypic changes that we see over evolutionary time, across diverse environments and among taxa, often reflect adaptive evolution. In the broad sense adaptations are phenotypic traits that have been favored by natural selection, and can be identified by being variable, heritable and responsible for variation in fitness. The evolution of growth forms since the early terrestrial radiations is a complex history of innovation, complexification, simplification, conservatism, radiation and extinction (Rowe and Speck 2003, 2005). Trees and lianas have different ecological preferences and different attributes, but we are far from being able to link this directly to evolutionary differences. In more general terms we are confronted with questions like: are certain types of growth form highly constrained and immovable in evolutionary terms? Are some plant groups more 'flexible' in their capacity to evolve widely differing growth forms and is this capacity related to the evolutionary age or complexity of the group? What are the ecological factors that coerce to either canalise or facilitate growth form variation and evolution? Much more work is needed to be able to answer these questions. It is clear that lianas have growth strategies different from trees, as shown for some aspects in this thesis, but lianas do not always follow expected patterns. Additionally, for some characteristics lianas are far less different from trees than expected, as has been showed by a number of recent studies (Gilbert et al. 2006, Santiago and Wright 2007, Selaya 2007, this thesis). These new results shed new light on patterns of adaptive ecology of lianas versus trees in tropical forests. Together, these results force us to re-evaluate the broad generalizations that we sometimes use. This warrants further studies on the ecological differences between lianas and trees, including variations therein among forest types in different climates.
    A European reference collection of rose varieties : final report
    Vosman, B. ; Barendrecht, C.J. ; Esselink, D. ; Jones, H. ; Scott, E. ; Spellerberg, B. ; Tams, S. - \ 2006
    Wageningen : Plant Research International - 59
    rozen - rosa - cultivars - rassen (planten) - databanken - moleculaire biologie - foto's - gegevens verzamelen - plantenmorfologie - gegevensbeheer - roses - rosa - cultivars - varieties - databases - molecular biology - photographs - data collection - plant morphology - data management
    An integrated pilot database was constructed containing administrative, morphological and molecular data as well as pictures of each variety. In spite of some encountered difficulties, it was demonstrated that two laboratories can produce substantially equivalent data and that the molecular data produced is useful as a tool for managing reference collections, prescreening and quality assurance
    Contribution to the biosystematics of Celtis L. (Celtidaceae) with special emphasis on the African species
    Sattarian, A. - \ 2006
    Wageningen University. Promotor(en): Jos van der Maesen, co-promotor(en): Freek Bakker. - [S.l. ] : S.n. - ISBN 9789085044451 - 142
    celtis - ulmaceae - biosystematiek - soorten - taxonomie - plantenmorfologie - fylogenie - taxonomische revisies - biologische naamgeving - moleculaire taxonomie - afrika - celtis - ulmaceae - biosystematics - species - taxonomy - plant morphology - phylogeny - taxonomic revisions - biological nomenclature - molecular taxonomy - africa
    CeltisL. (Celtidaceae, earlier part of the Ulmaceae) is a genus mainly of tree species, which has its natural distribution in Africa, the Mediterranean region, Asia, North and South America, and northernAustralia. Outside this natural distribution various species are planted in temperate areas, but they occur in many different ecological habitats, tropical and temperate regions in all continents. Some species are ornamental; some are used for timber and reforestation.

    This thesis is focused on African Celtis with general objectives such as providing a phylogeny of the Celtidaceae, understanding the relationships of African Celtis , preparation of a revision of the African Celtis species, a study of the main morphological characters, and a conspectus containing all names and synonyms in the genus.

    This thesis provided results, such as: Ulmaceae s.l. is not monophyletic and we confirm that this family has to be split into two families, Ulmaceaes.s. and Celtidaceae; the Celtidaceae should merge with Cannabaceae; in general Celtis is monophyletic but for more support we need to add more markers and taxa. In the relationships of Celtis , a few clades can be seen especially for South American species, which have thorns and by this morphological character that clade is distinguished from the rest of the genus Celtis. African and Asian Celtis form a mixed clade, this clade could havebeeninfluenced by the dispersal of these species.

    In total 12 African Celtis are identified in Africa andMadagascar: Celtis adolfi-friderici, C. africana , C.australis, C. mildbraedii, C. gomphophylla, C. prantlii, C. tessmannii, C. toka, C. wightii, and C. zenkeri. OnMadagascarthere are two endemic species: C. bifida and the newly described species Celtis malagasica . ForAustraliaa new species was separated from the " Celtis philippensis complex": Celtis australiensis . The main morphological characters in African Celtis instrumental for the distinction of species include leaf shape, venation, indumentum, stomata, inflorescences, flowers, pollen, fruits and their endocarps. Two pollen types could be distinguished based on the feature of the apertures, also two types of hairs are distinguished (glandular and non-glandular); stomata include three types: paracytic, cyclocytic and anisocytic; inflorescences are cymose and fruit shape are drupes, the endocarp of Celtis differs from globose ellipsoid to ovoid with different sizes, colours, and texture.

    The conspectus contains about 500 names of specific and infraspecific rank, many of which remain to be verified to complete publication and typification details. Generally for getting better relationship patterns of this genus revision of the Asian Celtis is recommended.

    Tillering in spring wheat : a 3D virtual plant modelling study
    Evers, J.B. - \ 2006
    Wageningen University. Promotor(en): Paul Struik, co-promotor(en): Jan Vos; B. Andrieu. - Wageningen : s.n. - ISBN 9789085043775 - 159
    triticum aestivum - tarwe - plantenontwikkeling - uitstoeling - plantenmorfologie - modellen - licht - verrood licht - lichtrelaties - optische eigenschappen - bladoppervlakte-index - grondbedekking - triticum aestivum - wheat - plant development - tillering - plant morphology - models - light - far red light - light relations - optical properties - leaf area index - ground cover - cum laude
    cum laude graduation (with distinction)
    Teelthandleiding vezelvlas : morfologie
    Paauw, J.G.M. - \ 2005
    Kennisakker.nl 2005 (2005)15 april.
    teelt - linum usitatissimum - vlas - plantenmorfologie - plantenanatomie - plantenfysiologie - vezelgewassen - akkerbouw - teelthandleidingen - cultivation - linum usitatissimum - flax - plant morphology - plant anatomy - plant physiology - fibre plants - arable farming - cultivation manuals
    In deze teelthandleiding wordt ingegaan op de kieming, vlasstengel, vertakking, de bloem, zaadbollen, zaad, afrijping en de vezel- en bladvorming bij vezelvlas.
    Manipulating transplant morphology to advance post-transplant growth and yield in strawberry
    Reekie, J.Y. - \ 2005
    Wageningen University. Promotor(en): Paul Struik. - Wageningen : S.n. - ISBN 9789085042617 - 126
    fragaria ananassa - aardbeien - plantenmorfologie - verplanten - maaien - wortel spruit ratio - fragaria ananassa - strawberries - plant morphology - transplanting - mowing - root shoot ratio
    Two methods were developed to enhance transplant success and minimize water use of strawberry transplants harvested in Canadian nurseries for use in the annual strawberry production system in the Southern United States: mechanical leaf removal by mowing, and chemical control of growth and development using prohexadione-calcium (ProCa). 'Camarosa' and 'Sweet Charlie', two cultivars used in the annual strawberry production system with contrasting growth patterns were chosen for this study. Treatment in Canadian nurseries resulted in several morphological changes in the transplants: reduced plant height and total leaf area, increased root to shoot ratio, and decreased specific leaf area (with ProCa application). Physiological changes in response to treatment included: a higher rate of photosynthesis, an increase in root initials, an increase in fruit number, and osmotic adjustment that pre-adapted transplants to water stress. Production changes caused by treatments included: an increase in the number of harvestable daughter transplants produced in the nurseries with ProCa application, decreased irrigation requirement, and increased early or seasonal fruit yield in mowed and ProCa-treated plants in some but not all years. Mowing and ProCa are useful tools to manipulate strawberry plant morphology in the northern nurseries to produce more robust transplants, resulting in better post-transplant growth, higher fruit yields, earlier fruit production and lower irrigation costs. This has the potential to significantly improve profitability for nursery and fruit producers.
    Molecular analysis of plant architecture in Arabidopsis thaliana using activation tagging.
    Chalfun Junior, A. - \ 2004
    Wageningen University. Promotor(en): Maarten Koornneef; Gerco Angenent. - Wageningen : S.n. - ISBN 9789085040361 - 144
    arabidopsis thaliana - transposons - dna - mutanten - plantenontwikkeling - plantenmorfologie - moleculaire genetica - genexpressie - arabidopsis thaliana - transposable elements - dna - mutants - plant development - plant morphology - molecular genetics - gene expression
    Keywords: Arabidopsisthaliana, activation tagging, T-DNA, transposon, mutants, enhancer, DNA methylation, plant architecture, development, forward/reverse genetics, lateral organs, flower, vascular tissue, HLH, transmembrane, transcription factors

    Plant development is one of the most important aspects of plant's life cycle that has extensively been studied at the morphological, genetic and molecular level. It is import for systematic and taxonomic classification, but also for applied agronomic reasons, because it affects the growth and cultivation leading to higher yield and quality of the product.The generation of genetic variants, like mutants may increase genetic pool and gives information about plant processes and their genetic control.Activation tagging is a new powerful tool to generate and identify new mutants, which emerged as an alternative for gene function analysis. This thesis reports the study on the molecular control of plant architecture, using mutants generated by an activation tagging-based approach in the model plant Arabidopsis thaliana . In addition, it also describes experiments that could explain why the low frequencies of mutants were obtained by T-DNA based activation tagging. Based on this comparison, the transposon-based activation tagging strategy was chosen and a screen for flower and silique mutants in a large Arabidopsis population yielded three gain-of-function mutants. These mutants were designated downwards siliques1 ( ds1-D ), needle1 ( ndl1-D ) and twisted1 ( twt1-D ). In the ds1-D mutant, internodes are shorter and the lateral organs such as flowers are bending downwards. Further molecular and genetic studies on this mutant revealed that DS1 is important to control petiole-blade boundary in Arabidopsis petals. In the ndl1-D mutant, the normal formation of valve tissues is altered, resulting in a pin-like structure that replaces the two fused carpels of the wild type pistil. The results suggest that NDL1 is involved in normal carpel development, in which auxin distribution plays an important role. In the third mutant, twt1-D , the overexpression of TWT1 led to twisting of all organs, whichismost pronounced in siliques. This phenotype and the expression pattern of the gene suggest that TWT1 is involved in proper vascular tissue development in Arabidopsis . These studies demonstrate the power of activation tagging and it gains valuable knowledge about the molecular networks that control plant development.
    From signal to form: Nod factor as a morhogenetic signal molecule to induce symbiotic responses in legume root hairs
    Esseling, J.J. - \ 2004
    Wageningen University. Promotor(en): Anne Mie Emons. - [S.l.] : S.n. - ISBN 9789085040552 - 152
    fabaceae - peulgewassen - medicago truncatula - rhizobium - wortelharen - plantenmorfologie - celskelet - symbiose - stikstof - knobbelvorming - signaaltransductie - fabaceae - legumes - medicago truncatula - rhizobium - root hairs - plant morphology - cytoskeleton - symbiosis - nitrogen - nodulation - signal transduction

    In this thesis, research is presented which contributes to a better understanding of nod factor (NF) induced signalling in Iegume root hairs, leading to a successful symbiosis. We mainly use root hairs of the model Iegume Medicago truncatula ('barrel medic') as an experimental system. In the different chapters, different aspects of the NF induced changes in root hair morphology that are required for establishing a successful symbiosis between rhizobia and legumes are covered.

    Chapter 1 is a review article that describes the different roles of the actin cytoskeleton in Iegume root hairs: its different configurations in relation to root hair growth, its function as backbone of cytoplasmic strands and highway for cellular transport, and its target for NF-induced signalling.

    Chapter 2 describes a new experimental assay to test the effects of NF on legume root hairs. The advantage of this assay, in comparison with the classical global application assays, is that it better mimics the natural situation in which rhizobia are locally present on the hosts' root hairs. It tests a theoretical computer model explaining root hair curling around bacteria. With a microinjection needie, a small droplet of purified NF was applied on the side o1 the tip of growing root hairs. The result of this is that the root hair under study reoriented its growth axis - it curls, toward the site of NF application, and i1 expresses the early nodulin gene

    Mutagenesis screens are nowadays widely performed to genetically dissec1 signal transduction pathways. In chapter 3, we studied the root hair phenotype in the non nodulating M. truncatula dmi2/N0RK mutant which was found in such a screen. This mutant, and its two orthologues in alfalfa and Lotus japonicus, appeared to exhibit an enhanced touch response to experimenta handling. When care was taken to not induce this touch response, the mutan1 root hairs responded morphologically like wild-type root hairs to NF application. A global application resulted in root hair deformation and NF spot application induced root hair reorientation or - branching, depending on the position of application on the root hair. In addition, dmi2/N0RK root hairs make 180° curls in the presence of rhizobia, but as soon as the root hair tip touches its own shank, the root hair stops growing/curling, and as such is unable to entrap bacteria in a three-dimensional pocket. Because dmi2 root hairs do not express the ProMtENOon-GUS reporter gene after NF application we propose a split in NF-induced signalling, with one branch to root hair curling, the other to ProutENOon-GUS expression.

    Pea plants can be successfully nodulated by certain strains of rhizobia that oroduce hardly detectable amounts of NF. In addition, very low concentrations of purified NF elicit changes in root hair morphology and gene expression in other legume species. Therefore, we tested what is the lowest NF concentration at which root hair reorientation and ProMtENooii-GUS expression.still occur. In chapter 4, we show the exciting result that one single NF molecule is sufficient to induce root hair reorientation and ProMtENoon-GUS expression,

    In chapter 5 we describe the results that we obtained after spot application of nod factor mixed with pharmacological agonists or antagonists of signal transduction pathways. As such, we show that NF-induced root hair reorientation can be blocked with gadolinium ions, ions that specifically block calcium influxes in plant cells. Moreover, we show that we can induce root hair reorientation in a number of hairs after spot application of a mixture of calcium ions and the ionophore A23187. Pertussis toxin specifically inhibits heterotrimeric G-proteins. Upon spot application of a mixture of NF and pertussis toxin, root hairs do reorient their growth axis, but do not express the ProMtENODii-GUS reporter gene. Spot application of mastoparan, a small peptide from wasp venom that activates heterotrimeric G-proteins, does not result in root hair reorientation, but does induce Pro^tENOon-GUS expression. Heterotrimeric G-proteins activate phospholipase C. Upon spot application of a mixture of NF and neomycin or U~73122, two known antagonists of phospholipase Ct ProMtENOon-GUS expression was inhibited, but root hair reorientation not Phospholipase C is an enzyme that cleaves phosphoinositolbisphosphate (PIP2) into diacylglycerolphosphate (DAG) and inositoltriphosphate (IP3). With microinjection of caged IP3 into growing M. truncatula root hairs and subsequent uncaging with an UV laser, we got expression of ProMtENooirGUS in a number of root hairs. This all shows that heterotrimeric G-protein coupled phosphoinositide signalling is involved in NF-induced Pr0MtEN0Di1-GUS expression in M. truncatula root hairs.

    Chapter 6 is a review which covers the current state of the art in the research of the Rhizobium-\egume symbiosis, with a special focus on signal transduction. It not only compares genetic dissection with pharmacological approaches, but also covers the cell biological aspects that are necessary to fully understand NF induced signal transduction.

    Chapter 7 is a chapter which describes that SHAGGY-kinase signalling is involved in root hair deformation in thale cress (Arabidopsis). This is a small weed that is used as a non~legume model plant. We show that application of lithium ions induces root hair deformation, and that in roots which lack a SHAGGY-kinase, a significant higher percentage of root hairs deform upon lithium application. In plant cells, lithium ions influence ethylene and phosphoinositide signalling, but with the use of specific agonists and antagonists of these pathways, we show that lithium induced root hair deformation in Arabidopsis is not caused by disrupted ethylene or phosphoinositide signalling.

    Teelthandleiding consumptieaardappelen : morfologie (bouw) van de aardappelplant
    Veerman, A. - \ 2003
    Kennisakker.nl 2003 (2003)15 sept.
    solanum tuberosum - aardappelen - landbouwplantenteelt - teeltsystemen - plantkunde - plantenmorfologie - teelthandleidingen - solanum tuberosum - potatoes - crop husbandry - cropping systems - botany - plant morphology - cultivation manuals
    De aardappel maakt, evenals tomaat, aubergine, tabak, Spaanse peper en petunia, deel uit van de Solanaceae-familie. De geslachtsnaam waaronder de aardappel thuishoort, is Solanum. Tot dit geslacht behoren ook tomaat en bitterzoet. De volledige soortnaam van de cultuuraardappel is Solanum tuberosum L. De aardappelplant bestaat uit stengels, wortels en knollen
    Uitgebreid sortiment kattekruid in kaart gebracht
    Hoffman, M.H.A. - \ 2003
    Tuin en Landschap 25 (2003)10. - ISSN 0165-3350 - p. 18 - 21.
    nepeta - rassen (planten) - cultivars - rassenproeven - plantenveredeling - gebruikswaarde - ornamentele waarde - bloemen - bloei - overblijvende planten - tuinplanten - plantenmorfologie - nomenclatuur - taxonomie - biologische naamgeving - inspectie - evaluatie - sierplanten - bloeiende planten - nepeta - varieties - cultivars - variety trials - plant breeding - use value - ornamental value - flowers - flowering - perennials - bedding plants - plant morphology - nomenclature - taxonomy - biological nomenclature - inspection - evaluation - ornamental plants - flowering plants
    PPO heeft van 1997 tot 2002 een groot sortiment Nepeta beoordeeld, d.w.z. het volledige Nederlandse handelssortiment aangevuld met nieuwe cultivars, een aantal botanische soorten, en nog onbenoemde selecties uit het veredelingsonderzoek. De planten zijn gekeurd door de KVBC en de Vereniging van Vasteplantenkwekers. In een tabel de uitslag van de sterrenkeuring van de KVBC en de belangrijkste morfologische en gebruikswaarde-kenmerken. Ook worden voorstellen gedaan voor verbeteringen in de naamgeving
    Studies in Begoniaceae: VII
    Wilde, J.J.F.E. de - \ 2002
    Leiden : Backhuys (Wageningen University papers 2001-2) - 271
    begoniaceae - begonia - taxonomische revisies - taxonomie - voortplanting - geografische verdeling - plantenecologie - identificatie - determinatietabellen - plantenmorfologie - nieuwe soorten - gabon - kameroen - begoniaceae - begonia - taxonomic revisions - taxonomy - reproduction - geographical distribution - plant ecology - identification - keys - plant morphology - new species - gabon - cameroon
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