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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Identification, cloning and characterization of the tomato TCP transcription factor family
Parapunova, V.A. ; Busscher, M. ; Busscher-Lange, J. ; Lammers, M. ; Karlova, R.B. ; Bovy, A.G. ; Angenent, G.C. ; Maagd, R.A. de - \ 2014
BMC Plant Biology 14 (2014). - ISSN 1471-2229
mads-box gene - arabidopsis-thaliana - fruit-development - leaf development - high-throughput - plant-growth - dna-binding - expression - time - interference
Background: TCP proteins are plant-specific transcription factors, which are known to have a wide range of functions in different plant species such as in leaf development, flower symmetry, shoot branching, and senescence. Only a small number of TCP genes has been characterised from tomato (Solanum lycopersicum). Here we report several functional features of the members of the entire family present in the tomato genome. Results: We have identified 30 Solanum lycopersicum SlTCP genes, most of which have not been described before. Phylogenetic analysis clearly distinguishes two homology classes of the SlTCP transcription factor family - class I and class II. Class II differentiates in two subclasses, the CIN-TCP subclass and the CYC/TB1 subclass, involved in leaf development and axillary shoots formation, respectively. The expression patterns of all members were determined by quantitative PCR. Several SlTCP genes, like SlTCP12, SlTCP15 and SlTCP18 are preferentially expressed in the tomato fruit, suggesting a role during fruit development or ripening. These genes are regulated by RIN (RIPENING INHIBITOR), CNR (COLORLESS NON-RIPENING) and SlAP2a (APETALA2a) proteins, which are transcription factors with key roles in ripening. With a yeast one-hybrid assay we demonstrated that RIN binds the promoter fragments of SlTCP12, SlTCP15 and SlTCP18, and that CNR binds the SlTCP18 promoter. This data strongly suggests that these class I SlTCP proteins are involved in ripening. Furthermore, we demonstrate that SlTCPs bind the promoter fragments of members of their own family, indicating that they regulate each other. Additional yeast one-hybrid studies performed with Arabidopsis transcription factors revealed binding of the promoter fragments by proteins involved in the ethylene signal transduction pathway, contributing to the idea that these SlTCP genes are involved in the ripening process. Yeast two-hybrid data shows that SlTCP proteins can form homo and heterodimers, suggesting that they act together in order to form functional protein complexes and together regulate developmental processes in tomato.
Metabolomics reveals organ-specific metabolic rearrangements during early tomato seedling development
Gomez-Roldan, M.V. ; Engel, B. ; Vos, R.C.H. de; Vereijken, P.F.G. ; Astola, L. ; Groenenboom, M.A.C. ; Geest, H.C. van de; Bovy, A.G. ; Molenaar, J. ; Eeuwijk, F.A. van; Hall, R.D. - \ 2014
Metabolomics 10 (2014)5. - ISSN 1573-3882 - p. 958 - 974.
transcriptome coexpression analysis - mass-spectrometry - fruit-development - integrated analysis - network analysis - systems biology - arabidopsis - pathway - expression - tool
Tomato seedlings (Solanum lycopersicum cv.MoneyMaker), grown under strictly controlled conditions, have been used to study alterations occurring in secondary metabolite biosynthetic pathways following developmental and environmental perturbations. Robustness and reproducibility of the system were confirmed using detailed statistical analyses of the metabolome. LCMS profiling was applied using whole germinated seeds as well as cotyledons, hypocotyls and roots from 3 to 9 days old seedlings to generate relative levels of 433 metabolites, of which 62 were annotated. Initial focus was given to the polyphenol pathway and several additional mass signals have been putatively annotated using high mass resolution fragmentation. Clear organ and developmental stage—specific differences were observed. Seeds accumulated saponin-like compounds; roots accumulated mainly alkaloids; cotyledons contained mainly glycosylated flavonols and; hypocotyls contained mainly anthocyanins. For each organ, the developmental changes in metabolite profiles were described by using linear mixed models. Across three independent experiments, 85 % of the metabolites showed similar developmental trends. This tomato seedling system has given us valuable additional insights into the complexity of seedling secondary metabolism. How metabolic profiles reflect an interplay between depletion of stored molecules and de novo synthesis and how the overall picture for this important crop plant contrasts to e.g. Arabidopsis are emphasised.
Parthenocarpic potential in Capsicum annuum L. is enhanced by carpelloid structures and controlled by a single recessive gene
Tiwari, A. ; Vivian-Smith, A. ; Voorrips, R.E. ; Habets, M.E.J. ; Xue, L.B. ; Offringa, R. ; Heuvelink, E. - \ 2011
BMC Plant Biology 11 (2011). - ISSN 1471-2229 - 15 p.
mads-box genes - ovule development - fruit-development - sweet-pepper - arabidopsis - tomato - pollen - growth - flower - mutant
Background Parthenocarpy is a desirable trait in Capsicum annuum production because it improves fruit quality and results in a more regular fruit set. Previously, we identified several C. annuum genotypes that already show a certain level of parthenocarpy, and the seedless fruits obtained from these genotypes often contain carpel-like structures. In the Arabidopsis bel1 mutant ovule integuments are transformed into carpels, and we therefore carefully studied ovule development in C. annuum and correlated aberrant ovule development and carpelloid transformation with parthenocarpic fruit set. Results We identified several additional C. annuum genotypes with a certain level of parthenocarpy, and confirmed a positive correlation between parthenocarpic potential and the development of carpelloid structures. Investigations into the source of these carpel-like structures showed that while the majority of the ovules in C. annuum gynoecia are unitegmic and anatropous, several abnormal ovules were observed, abundant at the top and base of the placenta, with altered integument growth. Abnormal ovule primordia arose from the placenta and most likely transformed into carpelloid structures in analogy to the Arabidopsis bel1 mutant. When pollination was present fruit weight was positively correlated with seed number, but in the absence of seeds, fruit weight proportionally increased with the carpelloid mass and number. Capsicum genotypes with high parthenocarpic potential always showed stronger carpelloid development. The parthenocarpic potential appeared to be controlled by a single recessive gene, but no variation in coding sequence was observed in a candidate gene CaARF8. Conclusions Our results suggest that in the absence of fertilization most C. annuum genotypes, have parthenocarpic potential and carpelloid growth, which can substitute developing seeds in promoting fruit development.
Quantifying abortion rates of reproductive organs and effects of contributing factors using time-to-event analysis
Wubs, A.M. ; Heuvelink, E. ; Marcelis, L.F.M. ; Hemerik, L. - \ 2011
Functional Plant Biology 38 (2011)5. - ISSN 1445-4408 - p. 431 - 440.
capsicum-annuum l. - fruit-development - sweet-pepper - survival analysis - yield components - sink strength - heat-stress - seed set - flower - age
Time-to-event analysis, or survival analysis, is a method to analyse the timing of events and to quantify the effects of contributing factors. We apply this method to data on the timing of abortion of reproductive organs. This abortion often depends on source and sink strength. We hypothesise that the effect of source and sink strength on abortion rate can be quantified with a statistical model, obtained via survival analysis. Flower and fruit abortion in Capsicum annuum L., observed in temperature and planting density experiments, were analysed. Increasing the source strength as well as decreasing the sink strength decreased the abortion rate. The effect was non-linear, e.g. source strengths above 6 g CH2O per plant per d did not decrease abortion rates further. The maximum abortion rate occurred around 100 degree-days after anthesis. Analyses in which sink strength was replaced with the number of fruits in a specified age category had an equal or better fit to the data. We discuss the advantages and disadvantages of using survival analyses for this kind of data. The technique can also be used for other crops showing reproductive organ abortion (e.g. soybean (Glycine max L.), cucumber (Cucumis sativus L.)), but also on other event types like bud break or germination.
In planta localisation patterns of MADS domain proteins during floral development in Arabidopsis thaliana
Urbanus, S.L. ; Folter, S. de; Shchennikova, A. ; Kaufmann, K. ; Immink, G.H. ; Angenent, G.C. - \ 2009
BMC Plant Biology 9 (2009). - ISSN 1471-2229
green-fluorescent protein - box transcription factors - homeotic gene apetala1 - flower development - ovule development - meristem identity - cell-differentiation - negative regulation - fruit-development - organ identity
Background: MADS domain transcription factors play important roles in various developmental processes in flowering plants. Members of this family play a prominent role in the transition to flowering and the specification of floral organ identity. Several studies reported mRNA expression patterns of the genes encoding these MADS domain proteins, however, these studies do not provide the necessary information on the temporal and spatial localisation of the proteins. We have made GREEN FLUORESCENT PROTEIN (GFP) translational fusions with the four MADS domain proteins SEPALLATA3, AGAMOUS, FRUITFULL and APETALA1 from the model plant Arabidopsis thaliana and analysed the protein localisation patterns in living plant tissues by confocal laser scanning microscopy (CLSM). Results: We unravelled the protein localisation patterns of the four MADS domain proteins at a cellular and subcellular level in inflorescence and floral meristems, during development of the early flower bud stages, and during further differentiation of the floral organs. The protein localisation patterns revealed a few deviations from known mRNA expression patterns, suggesting a non-cell autonomous action of these factors or alternative control mechanisms. In addition, we observed a change in the subcellular localisation of SEPALLATA3 from a predominantly nuclear localisation to a more cytoplasmic localisation, occurring specifically during petal and stamen development. Furthermore, we show that the down-regulation of the homeodomain transcription factor WUSCHEL in ovular tissues is preceded by the occurrence of both AGAMOUS and SEPALLATA3 proteins, supporting the hypothesis that both proteins together suppress WUSCHEL expression in the ovule. Conclusion: This approach provides a highly detailed in situ map of MADS domain protein presence during early and later stages of floral development. The subcellular localisation of the transcription factors in the cytoplasm, as observed at certain stages during development, points to mechanisms other than transcriptional control. Together this information is essential to understand the role of these proteins in the regulatory processes that drive floral development and leads to new hypotheses.
Hormonal control of seed development in gibberellin- and ABA-deficient tomato (Lycopersicon esculentum Mill. cv. Moneymaker) mutants
Castro, R.D. de; Hilhorst, H.W.M. - \ 2006
Plant Science 170 (2006)3. - ISSN 0168-9452 - p. 462 - 470.
beta-tubulin accumulation - abscisic-acid - gibberellin-deficient - arabidopsis-thaliana - plant embryogenesis - fruit-development - primary dormancy - sitiens mutant - germination - maize
Developing seeds of tomato gibberellin (GA)-deficient gib1 and abscisic acid (ABA)-deficient sitw mutants enabled us to analyze the role of GA in the regulation of embryo histo-differentiation, and the role of ABA in the regulation of maturation and quiescence. Our data show that DNA synthesis and mitotic microtubule arrays are markers for cell division activity and histo-differentiation during early embryogenesis. Cortical microtubular cytoskeleton alone is a marker for expansion growth during maturation, as seed and embryo gain dry weight and attain their final size. During this phase germinability, desiccation tolerance and dormancy are acquired, and a transient increase in ABA occurs, preceding the achievement of physiological maturity and subsequent quiescence. In the gib1 mutant embryo development was retarded in all parameters studied, except for a transient rise in ABA content. In the sitw mutant embryonic DNA synthesis activity was resumed upon completion of histo-differentiation, the microtubular cytoskeleton network was re-established during maturation and followed by viviparous germination. This suggests that ABA controls the suppression of these events during maturation and quiescence. Induction of full seed germinability, desiccation tolerance and dormancy was related to the completion of embryo histo-differentiation but was independent of the state of the microtubular cytoskeleton during maturation.
Transcript profiling of transcription factor genes during silique development in Arabidopsis
Folter, S. de; Lange, J. ; Colombo, L. ; Losa, A. ; Angenent, G.C. - \ 2004
Plant Molecular Biology 56 (2004)3. - ISSN 0167-4412 - p. 351 - 366.
mads-box genes - shoot apical meristem - fruit-development - ovule development - seed development - domain protein - zinc-finger - plant - expression - thaliana
Flower development is a key process for all angiosperms and is essential for sexual reproduction. The last phase in flower development is fertilization of the ovules and formation of the fruits, which are both biologically and economically of importance. Here, we report the expression profiles of over 1100 unique Arabidopsis genes coding for known and putative transcription factors (TFs) during silique development using high-density filter array hybridizations. Hierarchical cluster analyses revealed distinct expression profiles for the different silique developmental stages. This allowed a functional classification of these expression profiles in groups, namely pistil development, embryogenesis, seed maturation, fruit maturation, and fruit development. A further focus was made on the MADS-box family, which contains many members that are functionally well-characterized. The expression profiles of these MADS-box genes during silique development give additional clues on their functions and evolutionary relationship.
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