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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    The TIR-NB-LRR pair DSC1 and WRKY19 contributes to basal immunity of Arabidopsis to the root-knot nematode Meloidogyne incognita
    Warmerdam, Sonja ; Sterken, Mark G. ; Sukarta, Octavina C.A. ; Schaik, Casper C. Van; Oortwijn, Marian E.P. ; Lozano-Torres, Jose L. ; Bakker, Jaap ; Smant, Geert ; Goverse, Aska - \ 2020
    BMC Plant Biology 20 (2020)1. - ISSN 1471-2229
    Background
    Root-knot nematodes transform vascular host cells into permanent feeding structures to withdraw nutrients from the host plant. Ecotypes of Arabidopsis thaliana can display large quantitative variation in susceptibility to the root-knot nematode Meloidogyne incognita, which is thought to be independent of dominant major resistance genes. However, in an earlier genome-wide association study of the interaction between Arabidopsis and M. incognita we identified a quantitative trait locus harboring homologs of dominant resistance genes but with minor effect on susceptibility to the M. incognita population tested.
    Results
    Here, we report on the characterization of two of these genes encoding the TIR-NB-LRR immune receptor DSC1 (DOMINANT SUPPRESSOR OF Camta 3 NUMBER 1) and the TIR-NB-LRR-WRKY-MAPx protein WRKY19 in nematode-infected Arabidopsis roots. Nematode infection studies and whole transcriptome analyses using the Arabidopsis mutants showed that DSC1 and WRKY19 co-regulate susceptibility of Arabidopsis to M. incognita.
    Conclusion
    Given the head-to-head orientation of DSC1 and WRKY19 in the Arabidopsis genome our data suggests that both genes may function as a TIR-NB-LRR immune receptor pair. Unlike other TIR-NB-LRR pairs involved in dominant disease resistance in plants, DSC1 and WRKY19 most likely regulate basal levels of immunity to root-knot nematodes.
    Morphological and physiological responses of the potato stem transport tissues to dehydration stress
    Aliche, Ernest B. ; Prusova-Bourke, Alena ; Ruiz-Sanchez, Mariam ; Oortwijn, Marian ; Gerkema, Edo ; As, Henk Van; Visser, Richard G.F. ; Linden, C.G. van der - \ 2020
    Planta 251 (2020)2. - ISSN 0032-0935
    Drought - MRI - Phloem - Potato - Sugar transport - Xylem

    Main conclusion: Adaptation of the xylem under dehydration to smaller sized vessels and the increase in xylem density per stem area facilitate water transport during water-limiting conditions, and this has implications for assimilate transport during drought. Abstract: The potato stem is the communication and transport channel between the assimilate-exporting source leaves and the terminal sink tissues of the plant. During environmental stress conditions like water scarcity, which adversely affect the performance (canopy growth and tuber yield) of the potato plant, the response of stem tissues is essential, however, still understudied. In this study, we investigated the response of the stem tissues of cultivated potato grown in the greenhouse to dehydration using a multidisciplinary approach including physiological, biochemical, morphological, microscopic, and magnetic resonance imaging techniques. We observed the most significant effects of water limitation in the lower stem regions of plants. The light microscopy analysis of the potato stem sections revealed that plants exposed to this particular dehydration stress have higher total xylem density per unit area than control plants. This increase in the total xylem density was accompanied by an increase in the number of narrow-diameter xylem vessels and a decrease in the number of large-diameter xylem vessels. Our MRI approach revealed a diurnal rhythm of xylem flux between day and night, with a reduction in xylem flux that is linked to dehydration sensitivity. We also observed that sink strength was the main driver of assimilate transport through the stem in our data set. These findings may present potential breeding targets for drought tolerance in potato.

    Carbon partitioning mechanisms in POTATO under drought stress
    Aliche, Ernest B. ; Theeuwen, Tom P.J.M. ; Oortwijn, Marian ; Visser, Richard G.F. ; Linden, Gerard van der - \ 2020
    Plant Physiology and Biochemistry 146 (2020). - ISSN 0981-9428 - p. 211 - 219.
    Carbon partitioning - Drought - Gene expression - Potato - Sugar metabolism

    Potato (Solanum tuberosum) is an important food crop consumed all over the world, but it is generally sensitive to drought conditions. One of the major physiological processes affected by drought stress is carbon partitioning: the plant's choice of where to allocate its photoassimilates. Our aim was to investigate the molecular factors and possible bottlenecks affecting carbon partitioning during drought. We studied potato cultivars with contrasting drought responses in the greenhouse in the years 2013–2015, and further investigated the expression of genes involved in carbon partitioning and metabolite levels. Our results indicate that one of the most severe effects of drought stress on potato is the arrest of stolon differentiation and formation of tubers. We also identified some physiological traits like stomatal conductance and chlorophyll content as affecting carbon assimilation, partitioning and eventual tuber yield. The gene expressions and biochemical analyses highlight the various tissues prioritized by the plant for assimilate transport during drought stress, and give indications of what distinguishes drought tolerance and sensitivity of cultivated potato. Some of the key genes studied (like Sucrose synthase and Sucrose transporters) may be inclusive breeding targets for drought tolerance in potato.

    Genetic mapping of tuber size distribution and marketable tuber yield under drought stress in potatoes
    Aliche, Ernest B. ; Oortwijn, Marian ; Theeuwen, Tom P.J.M. ; Bachem, Christian W.B. ; Eck, Herman J. van; Visser, Richard G.F. ; Linden, Gerard van der - \ 2019
    Euphytica 215 (2019)11. - ISSN 0014-2336
    Association panel - Drought - Marketable tubers - Modelling - Size - Yield

    Drought sensitivity of potato leads to a reduction in total tuber yield and marketable yield. An investigation of drought effects on tuber yield attributes will facilitate our understanding of how to reduce such huge yield losses. We have evaluated tuber yield, tuber size distribution and marketable yield of a set of 103 European commercial potato cultivars under irrigated and non-irrigated conditions in the field. The multi-year results from two locations, Connantre, France (2013–2015) and Nieuw-Namen in Zeeland, The Netherlands (2013–2014), were analysed. We used Normal and Gamma Distribution models to describe the tuber size distribution of tuber fresh weight and tuber number, respectively. The interactions among parameters of tuber size distribution and total/marketable tuber yield traits were analysed using correlation matrices and biplots. Finally, we used a 14K Infinium SNP marker array to find associations between the parameters or traits and genetic loci on the potato genome. Late foliage maturity facilitated a wider spread of tuber size distribution in favour of larger-sized tubers. Drought effects on total yield were representative of their impact on marketable yield, however, absolute values of total tuber number may not be indicative of marketable number of tubers. We found significant marker-trait associations between a region on chromosome 3 and the spread of tuber number distribution, size class with maximum tuber number and marketable fractions of tuber number and tuber weight. These findings will contribute to improvement and selection for drought tolerance in potato.

    Resistance-gene independent variation in susceptibility to the root-knot nematode Meloidogyne incognita in Solanum lycopersicum
    Sterken, M.G. ; Warmerdam, S. ; Guarneri, Nina ; Schaik, C.C. van; Oortwijn, M.E.P. ; Steenbrugge, Joris van; Lozano Torres, J.L. ; Goverse, A. ; Smant, G. - \ 2019
    Three genes identified by genome wide association mapping of root-knot nematode susceptibility in Arabidopsis
    Sterken, M.G. ; Warmerdam, S. ; Schaik, C.C. van; Oortwijn, M.E.P. ; Lozano Torres, J.L. ; Bakker, J. ; Smant, G. - \ 2019
    Root-knot nematodes are devastating plant-pathogens affecting agricultural productivity of major food crops world-wide. Current control strategies depend on a limited supply of nematode resistance genes. Hence, there is need for alternative control strategies. Here, we show that more subtle quantitative trait loci could be used as additional genetic resource for nematode control.

    We mapped the genetic architecture of susceptibility in 340 natural isolates of Arabidopsis thaliana to Meloidogyne incognitia. We found ample genetic variation in M. incognita reproduction on these plants, with a narrow-sense heritability of 0.52. By genome wide association 19 associated loci were identified. Three loci were investigated by characterizing nine T-DNA knock-out mutants of candidate genes, identifying three (co-)regulators of nematode susceptibility in Arabidopsis: BZR1, FRNI1, and ERF6.

    Our results suggest that allelic variation in susceptibility genes could be used to improve nematode resistance of plants, paving the way to investigate these traits in food-crops.
    Three genes identified by genome wide association mapping of root-knot nematode susceptibility in Arabidopsis
    Sterken, M.G. ; Warmerdam, S. ; Schaik, C.C. van; Oortwijn, M.E.P. ; Lozano Torres, J.L. ; Bakker, J. ; Goverse, A. ; Smant, G. - \ 2019
    Root-knot nematodes are devastating plant-pathogens affecting the agricultural productivity of major food crops world-wide. The major control strategy nowadays is through incorporating major-effect resistance-genes in food-crops. However, the supply of nematode resistance genes available for breeding is very limited. Hence, there is need for alternative control strategies. Here, we show that more subtle quantitative trait loci could be used as an additional genetic resource for nematode control.We mapped the genetic architecture of susceptibility of the model plant Arabidopsis thaliana to Meloidogyne incognitia using a set of 340 natural isolates. These isolates represent the world-wide genetic variation in this plant. Each of these isolates was tested in at least four technical replicates, the average number of egg-masses per plant ranged from five to 45. We found ample genetic variation in M. incognita reproduction on these plants, with a narrow-sense heritability of 0.52. Subsequently, we mapped quantitative trait loci by genome wide association, explaining genetic variation in nematode reproduction. At a permissive significance threshold of LOD > 4, we identified 19 associated loci. We investigated three loci by characterizing nine T-DNA knock-out mutants of candidate genes. This way, three genes that function as (co-)regulators of nematode susceptibility in Arabidopsis were identified: BRASSINAZOLE RESISTANT1, an F-box familiy protein, and ETHYLENE RESPONSE FACTOR 6. Our results show that there is quantitative genetic variation in the host-plant affecting nematode reproduction. Furthermore, our results suggest that allelic variation in these susceptibility genes could be used to improve the resistance of crops to root-knot nematodes. Our results pave the way to investigate these traits in food-crops.
    Source-Sink Regulation Is Mediated by Interaction of an FT Homolog with a SWEET Protein in Potato
    Abelenda Vila, J.A. ; Bergonzi, S. ; Oortwijn, M.E.P. ; Sonnewald, S. ; Du, Miru ; Visser, R.G.F. ; Sonnewald, U. ; Bachem, C.W.B. - \ 2019
    Current Biology 29 (2019)7. - ISSN 0960-9822 - p. 1176 - 1186.
    Potato plants form tuberous storage organs on underground modified stems called stolons. Tubers are rich in starch, proteins, and other important nutrients, making potato one of the most important staple food crops. The timing of tuber development in wild potato is regulated by day length through a mechanism that is closely related to floral transition [1, 2]. Tuberization is also known to be regulated by the availability of assimilates, in particular sucrose, the transported form of sugar, required for starch synthesis. During the onset of tuber development, the mode of sucrose unloading switches from apoplastic to symplastic [3]. Here, we show that this switch may be mediated by the interaction between the tuberization-specific FT homolog StSP6A and the sucrose efflux transporter StSWEET11 [4]. The binding of StSP6A to StSWEET11 blocked the leakage of sucrose to the apoplast, and is therefore likely to promote symplastic sucrose transport. The direct physical interaction between StSWEET11 and StSP6A proteins represents a link between the sugar and photoperiodic pathways for the regulation of potato tuber formation. Our data suggest that a previously undiscovered function for the FT family of proteins extends their role as mobile signals to mediators of source-sink partitioning, opening the possibility for modifying source-sink interactions.
    Mediator of tolerance to abiotic stress ERF6 regulates susceptibility of Arabidopsis to Meloidogyne incognita
    Warmerdam, Sonja ; Sterken, Mark G. ; Schaik, Casper van; Oortwijn, Marian E.P. ; Lozano-Torres, Jose L. ; Bakker, Jaap ; Goverse, Aska ; Smant, Geert - \ 2019
    Molecular Plant Pathology 20 (2019)1. - ISSN 1464-6722 - p. 137 - 152.
    abiotic stress - Arabidopsis thaliana - ERF6 - genome-wide association mapping - Meloidogyne incognita - root-knot nematodes - transcription factor

    Root-knot nematodes transform vascular host cells into permanent feeding structures to selectively withdraw their nutrients from host plants during the course of several weeks. The susceptibility of host plants to root-knot nematode infections is thought to be a complex trait involving many genetic loci. However, genome-wide association (GWA) analysis has so far revealed only four quantitative trait loci (QTLs) linked to the reproductive success of the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana, which suggests that the genetic architecture underlying host susceptibility could be much simpler than previously thought. Here, we report that, by using a relaxed stringency approach in a GWA analysis, we could identify 15 additional loci linked to quantitative variation in the reproductive success of M. incognita in Arabidopsis. To test the robustness of our analysis, we functionally characterized six genes located in a QTL with the lowest acceptable statistical support and smallest effect size. This led us to identify ETHYLENE RESPONSE FACTOR 6 (ERF6) as a novel susceptibility gene for M. incognita in Arabidopsis. ERF6 functions as a transcriptional activator and suppressor of genes in response to various abiotic stresses independent of ethylene signalling. However, whole-transcriptome analysis of nematode-infected roots of the Arabidopsis erf6-1 knockout mutant line showed that allelic variation at this locus may regulate the conversion of aminocyclopropane-1-carboxylate (ACC) into ethylene by altering the expression of 1-aminocyclopropane-1-carboxylate oxidase 3 (ACO3). Our data further suggest that tolerance to abiotic stress mediated by ERF6 forms a novel layer of control in the susceptibility of Arabidopsis to M. incognita.

    Genome-wide association mapping of the architecture of susceptibility to the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana
    Warmerdam, S. ; Sterken, M.G. ; Schaik, C.C. van; Oortwijn, M.E.P. ; Lozano Torres, J.L. ; Dicke, M. ; Helder, J. ; Kammenga, J.E. ; Goverse, A. ; Bakker, J. ; Smant, G. - \ 2018
    Susceptibility to the root-knot nematode Meloidogyne incognita in plants is thought to be a complex trait based on multiple genes involved in cell differentiation, growth, and defence. Previous genetic analyses of susceptibility to M. incognita have mainly focussed on segregating dominant resistance genes in crops. It is not known if plants harbour significant genetic variation in susceptibility to M. incognita independent of dominant resistance genes. To study the genetic architecture of susceptibility to M. incognita in plants, we analysed nematode reproduction on a highly diverse set of 340 natural inbred lines of Arabidopsis thaliana with genome-wide association mapping. We observed a surprisingly large variation in nematode reproduction among these lines. Genome-wide association mapping revealed thirty-six quantitative trait loci (QTLs) in the genome of A. thaliana significantly associated with reproductive success of M. incognita. Mutant analysis of candidate genes located in four QTLs revealed various novel proteins functioning as (co-)regulators of susceptibility to M. incognita in Arabidopsis. Our data further suggests that breeding for loss-of-susceptibility, based on allelic variants critically involved in nematode feeding, could be used to make crops more resilient to root-knot nematodes.
    Drought response in field grown potatoes and the interactions between canopy growth and yield
    Aliche, Ernest B. ; Oortwijn, Marian ; Theeuwen, Tom P.J.M. ; Bachem, Christian W.B. ; Visser, Richard G.F. ; Linden, Gerard van der - \ 2018
    Agricultural Water Management 206 (2018). - ISSN 0378-3774 - p. 20 - 30.
    AUC - Irrigation - Maturity - Rainfall - Stress
    Potato is an important food crop with high yields. However when exposed to drought it suffers major yield losses. Considering its global importance and the increasing incidence of drought due to climate change, research toward drought tolerance in potato remains imperative. We have studied a set of 103 commercial cultivars representing the genetic diversity in the European potato market. The cultivars were grown in different field locations in three subsequent years (2013–2015). Our aim was to understand how different field drought regimes affect canopy growth in potato, and how these effects translate to tuber yield. The field environmental conditions were monitored, and pictures of canopy ground cover during the growing season were taken. Canopy growth parameters were extracted by an iterative method using the beta sigmoid growth function to model canopy growth. At harvest, tuber yield was scored and tuber size was graded. The GGE (Genotype and Genotype-by-Environment) bi-plot and Finlay Wilkinson's Regression were used to investigate Genotype x Environment interactions. We observed that the timing of the drought occurrence differentially affected canopy growth and tuber yield. Under drought stress, fast attainment of exponential growth and maximum canopy cover had negative effects on tuber formation and tuber bulking. Growth rate, maximum canopy cover, and area under the canopy curve (photosynthetic capacity over the growth season) were more important for tuber bulking than they were for tuber formation under drought stress. Cultivars with high yield were identified as potential material for improvement to drought tolerance. These findings will contribute to the breeding for drought-tolerant potato amidst the threats of climate change.
    Genome-wide association mapping of the architecture of susceptibility to the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana
    Warmerdam, S. ; Sterken, M.G. ; Schaik, C.C. van; Oortwijn, M.E.P. ; Sukarta, O.C.A. ; Lozano Torres, J.L. ; Dicke, M. ; Helder, J. ; Kammenga, J.E. ; Goverse, A. ; Bakker, J. ; Smant, G. - \ 2018
    Genome-wide association mapping of the architecture of susceptibility to the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana
    Warmerdam, Sonja ; Sterken, Mark G. ; Schaik, Casper van; Oortwijn, Marian E.P. ; Sukarta, Octavina C.A. ; Lozano-Torres, Jose L. ; Dicke, Marcel ; Helder, Johannes ; Kammenga, Jan E. ; Goverse, Aska ; Bakker, Jaap ; Smant, Geert - \ 2018
    New Phytologist 218 (2018)2. - ISSN 0028-646X - p. 724 - 737.
    Susceptibility to the root-knot nematode Meloidogyne incognita in plants is thought to be a complex trait based on multiple genes involved in cell differentiation, growth and defence. Previous genetic analyses of susceptibility to M. incognita have mainly focused on segregating dominant resistance genes in crops. It is not known if plants harbour significant genetic variation in susceptibility to M. incognita independent of dominant resistance. To study the genetic architecture of susceptibility to M. incognita, we analysed nematode reproduction on a highly diverse set of 340 natural inbred lines of Arabidopsis thaliana with genome-wide association mapping. We observed a surprisingly large variation in nematode reproduction among these lines. Genome-wide association mapping revealed four quantitative trait loci (QTLs) located on chromosomes 1 and 5 of A. thaliana significantly associated with reproductive success of M. incognita, none of which harbours typical resistance gene homologues. Mutant analysis of three genes located in two QTLs showed that the transcription factor BRASSINAZOLE RESISTANT1 and an F-box family protein may function as (co-)regulators of susceptibility to M. incognita in Arabidopsis.
    Our data suggest that breeding for loss-of-susceptibility, based on allelic variants critically involved in nematode feeding, could be used to make crops more resilient to root-knot nematodes.
    The PIN family of proteins in potato and their putative role in tuberisation
    Roumeliotis, E. ; Kloosterman, B.A. ; Oortwijn, M.E.P. ; Visser, R.G.F. ; Bachem, C.W.B. - \ 2013
    Frontiers in Plant Science 4 (2013). - ISSN 1664-462X
    arabidopsis-thaliana - auxin biosynthesis - root gravitropism - tuber initiation - expression - transport - growth - identification - transformation - tissues
    The PIN family of trans-membrane proteins mediates auxin efflux throughout the plant and during various phases of plant development. In Arabidopsis thaliana, the PIN family comprised of 8 members, divided into ‘short’ and ‘long’ PINs according to the length of the hydrophilic domain of the protein. Based on sequence homology using the recently published potato genome sequence (Solanum tuberosum group Phureja) we identified ten annotated potato StPIN genes. Mining the publicly available gene expression data, we constructed a catalogue tissue specificity of StPIN gene expression, focusing on the process of tuberization. A total of four StPIN genes exhibited increased expression four days after tuber induction, prior to the onset of stolon swelling. For two PIN genes, StPIN4 and StPIN2, promoter sequences were cloned and fused to the GUS reporter protein to study tissue specificity in more detail. StPIN4 promoter driven GUS staining was detected in the flower stigma, in the flower style, below the ovary and petals, in the root tips, in the vascular tissue of the stolons and in the tuber parenchyma cells. StPIN2 promoter driven GUS staining was detected in flower buds, in the vascular tissue of the swelling stolons and in the storage parenchyma of the growing tubers. Based on our results, we postulate a role for the StPINs in redistributing auxin in the swelling stolon during early events in tuber development.
    Down regulation of StGA3ox genes in potato results in altered GA content and affect plant and tuber growth characteristics.
    Roumeliotis, E. ; Kloosterman, B.A. ; Oortwijn, M.E.P. ; Lange, Theo ; Visser, R.G.F. ; Bachem, C.W.B. - \ 2013
    Journal of Plant Physiology 170 (2013)14. - ISSN 0176-1617 - p. 1228 - 1234.
    gibberellin biosynthesis - overexpression - auxin - transformation - arabidopsis - 2-oxidases - metabolism - expression - confers - pea
    GA biosynthesis and catabolism has been shown to play an important role in regulating tuberization in potato. Active GAs are inactivated in the stolon tips shortly after induction to tuberization. Overexpression of a GA inactivation gene results in an earlier tuberization phenotype, while reducing expression of the same gene results in delayed tuberization. In addition, overexpression of genes involved in GA biosynthesis results in delayed tuberization, while decreased expression of those genes results in earlied tuberization. The final step in GA biosynthesis is catalysed by StGA3ox1 and StGA3ox2 activity, that convert inactive forms of GA into active GA1 and GA4. In this study we cloned StGA3ox2 gene in an RNAi construct and used this construct to transform potato plants. The StGA3ox2 silenced plants were smaller and had shorter internodes. In addition, we assayed the concentrations of various GAs in the transgenic plants and showed an altered GA content. No difference was observed on the time point of tuber initiation. However, the transgenic clones had increased number of tubers with the same yield, resulting in smaller average tuber weight. In addition, we cloned the promoter of StGA3ox2 to direct expression of the GUS reporter gene to visualize the sites of GA biosynthesis in the potato plant. Finally, we discuss how changes of several GA levels can have an impact on shoot, stolon and tuber development, as well as the possible mechanisms that mediate feed-forward and feed-back regulation loops in the GA biosynthetic pathway in potato.
    Naturally occurring allele diversity allows potato cultivation in northern latitudes
    Kloosterman, B.A. ; Abelenda, J.A. ; Carretero Gomez, M. ; Oortwijn, M.E.P. ; Boer, J.M. de; Kowitwanich, K. ; Horvath, B.M. ; Eck, H.J. van; Smaczniak, C. ; Prat, S. ; Visser, R.G.F. ; Bachem, C.W.B. - \ 2013
    Nature 495 (2013)7440. - ISSN 0028-0836 - p. 246 - 250.
    flowering-time - arabidopsis - constans - tuberization - gene - plants - fkf1
    Potato (Solanum tuberosum L.) originates from the Andes and evolved short-day-dependent tuber formation as a vegetative propagation strategy. Here we describe the identification of a central regulator underlying a major-effect quantitative trait locus for plant maturity and initiation of tuber development. We show that this gene belongs to the family of DOF (DNA-binding with one finger) transcription factors1 and regulates tuberization and plant life cycle length, by acting as a mediator between the circadian clock and the StSP6A mobile tuberization signal2. We also show that natural allelic variants evade post-translational light regulation, allowing cultivation outside the geographical centre of origin of potato. Potato is a member of the Solanaceae family and isone of the world’s most important food crops. This annual plant originates from the Andean regions of South America3. Potato develops tubers from underground stems called stolons. Its equatorial origin makes potato essentially short-day dependent for tuberization and potato will not make tubers in the long-day conditions of spring and summer in the northern latitudes. When introduced in temperate zones, wild material will form tubers in the course of the autumnal shortening of day-length. Thus, one of the first selected traits in potato leading to a European potato type4 is likely to have been long-day acclimation for tuberization. Potato breeders can exploit the naturally occurring variation in tuberization onset and life cycle length, allowing varietal breeding for different latitudes, harvest times and markets.
    The effects of auxin and strigolactones on tuber initiation and stolon architecture in potato
    Roumeliotis, E. ; Kloosterman, B.A. ; Oortwijn, M.E.P. ; Kohlen, W. ; Bouwmeester, H.J. ; Visser, R.G.F. ; Bachem, C.W.B. - \ 2012
    Journal of Experimental Botany 63 (2012)12. - ISSN 0022-0957 - p. 4539 - 4547.
    gene-expression - solanum-tuberosum - key role - arabidopsis - biosynthesis - transport - tuberization - growth - plant - identification
    Various transcriptional networks and plant hormones have been implicated in controlling different aspects of potato tuber formation. Due to its broad impact on many plant developmental processes, a role for auxin in tuber initiation has been suggested but never fully resolved. Here, auxin concentrations were measured throughout the plant prior to and during the process of tuber formation. Auxin levels increase dramatically in the stolon prior to tuberization and remain relatively high during subsequent tuber growth, suggesting a promoting role for auxin in tuber formation. Furthermore, in vitro tuberization experiments showed higher levels of tuber formation from axillary buds of explants where the auxin source (stolon tip) had been removed. This phenotype could be rescued by application of auxin on the ablated stolon tips. In addition, a synthetic strigolactone analogue applied on the basal part of the stolon resulted in fewer tubers. The experiments indicate that a system for the production and directional transport of auxin exists in stolons and acts synergistically with strigolactones to control the outgrowth of the axillary stolon buds, similar to the control of above-ground shoot branching.
    Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source-sink tissues in a segregating potato population
    Kloosterman, B.A. ; Anithakumari, A.M. ; Chibon, P.Y.F.R.P. ; Oortwijn, M.E.P. ; Linden, C.G. van der; Visser, R.G.F. ; Bachem, C.W.B. - \ 2012
    BMC Plant Biology 12 (2012). - ISSN 1471-2229
    quantitative trait loci - arabidopsis circadian clock - pseudo-response regulators - solanum-tuberosum l. - gene-expression - level variation - genome - identification - architecture - networks
    Background With the completion of genome sequences belonging to some of the major crop plants, new challenges arise to utilize this data for crop improvement and increased food security. The field of genetical genomics has the potential to identify genes displaying heritable differential expression associated to important phenotypic traits. Here we describe the identification of expression QTLs (eQTLs) in two different potato tissues of a segregating potato population and query the potato genome sequence to differentiate between cis- and trans-acting eQTLs in relation to gene subfunctionalization. Results Leaf and tuber samples were analysed and screened for the presence of conserved and tissue dependent eQTLs. Expression QTLs present in both tissues are predominantly cis-acting whilst for tissue specific QTLs, the percentage of trans-acting QTLs increases. Tissue dependent eQTLs were assigned to functional classes and visualized in metabolic pathways. We identified a potential regulatory network on chromosome 10 involving genes crucial for maintaining circadian rhythms and controlling clock output genes. In addition, we show that the type of genetic material screened and sampling strategy applied, can have a high impact on the output of genetical genomics studies. Conclusions Identification of tissue dependent regulatory networks based on mapped differential expression not only gives us insight in tissue dependent gene subfunctionalization but brings new insights into key biological processes and delivers targets for future haplotyping and genetic marker development.
    From QTL to candidate gene: Genetical genomics of simple and complex traits in potato using a pooling strategy
    Kloosterman, B.A. ; Oortwijn, M.E.P. ; Willigen, J. uit de; America, A.H.P. ; Vos, C.H. de; Visser, R.G.F. ; Bachem, C.W.B. - \ 2010
    BMC Genomics 11 (2010). - ISSN 1471-2164
    single-feature polymorphism - microarray experiments - transcriptional regulation - arabidopsis-thaliana - tuber development - locus analysis - messenger-rna - expression - identification - methionine
    Background: Utilization of the natural genetic variation in traditional breeding programs remains a major challenge in crop plants. The identification of candidate genes underlying, or associated with, phenotypic trait QTLs is desired for effective marker assisted breeding. With the advent of high throughput -omics technologies, screening of entire populations for association of gene expression with targeted traits is becoming feasible but remains costly. Here we present the identification of novel candidate genes for different potato tuber quality traits by employing a pooling approach reducing the number of hybridizations needed. Extreme genotypes for a quantitative trait are collected and the RNA from contrasting bulks is then profiled with the aim of finding differentially expressed genes. Results: We have successfully implemented the pooling strategy for potato quality traits and identified candidate genes associated with potato tuber flesh color and tuber cooking type. Elevated expression level of a dominant allele of the ß-carotene hydroxylase (bch) gene was associated with yellow flesh color through mapping of the gene under a major QTL for flesh color on chromosome 3. For a second trait, a candidate gene with homology to a tyrosine-lysine rich protein (TLRP) was identified based on allele specificity of the probe on the microarray. TLRP was mapped on chromosome 9 in close proximity to a QTL for potato cooking type strengthening its significance as a candidate gene. Furthermore, we have performed a profiling experiment targeting a polygenic trait, by pooling individual genotypes based both on phenotypic and marker data, allowing the identification of candidate genes associated with the two different linkage groups. Conclusions: A pooling approach for RNA-profiling with the aim of identifying novel candidate genes associated with tuber quality traits was successfully implemented. The identified candidate genes for tuber flesh color (bch) and cooking type (tlrp) can provide useful markers for breeding schemes in the future. Strengths and limitations of the approach are discussed.
    Differences in regulation of carbohydrate metabolism during early fruit development between domesticated tomato and two wild relatives
    Kortstee, A.J. ; Appeldoorn, N.J.G. ; Oortwijn, M.E.P. ; Visser, R.G.F. - \ 2007
    Planta 226 (2007)4. - ISSN 0032-0935 - p. 929 - 939.
    accumulating lycopersicon-hirsutum - starch accumulation - sucrose synthase - quantitative trait - hexose-phosphate - sink metabolism - esculentum mill - invertase - expression - size
    Early development and growth of fruit in the domesticated tomato Solanum lycopersicum cultivar Money Maker and two of its wild relatives, S. peruvianum LA0385 and S. habrochaites LA1777, were studied. Although small differences exist, the processes involved and the sequence of events in fruit development are similar in all three species. The growth of developing fruits is exponential and the relative growth rate accelerates from 5 days after pollination (DAP 5) to DAP 8, followed by a decline during further development. Growth is positively correlated to the standard ¿Brix plus starch¿¿ in the period DAP 8¿DAP 20. Carbohydrate composition and levels of sugars and organic acids differ in fruits of the wild accessions compared to domesticated tomato. The wild accessions accumulate sucrose instead of glucose and fructose, and ripe fruits contain higher levels of malate and citrate. The enzymes responsible for the accumulation of glucose and fructose in domesticated tomatoes are soluble invertase and sucrose synthase. The regulation of initial carbohydrate metabolism in the domesticated tomato differs from that in the wild species, as could be concluded from measuring activities of enzymes involved in primary carbohydrate metabolism. Furthermore, changes in the activity of several enzymes, e.g., cell wall invertase, soluble invertase, fructokinase and phosphoglucomutase, could be attributed to changes in gene expression level. For other enzymes, additional control mechanisms play a role in the developing tomato fruits. Localization by in-situ activity staining of enzymes showed comparable results for fruits of domesticated tomato and the wild accessions. However, in the pericarp of S. peruvianum, less activity staining of phosphogluco-isomerase, phosphoglucomutase and UDP-glucosepyrophosphorylase was observed.
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