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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    Transcriptome and Metabolite Profiling Show That APETALA2a Is a Major Regulator of Tomato Fruit Ripening
    Karlova, R.B. ; Rosin, F.M.A. ; Busscher-Lange, J. ; Parapunova, V.A. ; Do, P.T. ; Fernie, A.R. ; Fraser, P.D. ; Baxter, C. ; Angenent, G.C. ; Maagd, R.A. de - \ 2011
    The Plant Cell 23 (2011)3. - ISSN 1040-4651 - p. 923 - 941.
    homeotic gene apetala2 - ethylene biosynthesis - flower development - 1-aminocyclopropane-1-carboxylate synthase - chromoplast differentiation - lycopersicon-esculentum - expression analysis - arabidopsis flower - seed development - organ identity
    Fruit ripening in tomato (Solanum lycopersicum) requires the coordination of both developmental cues as well as the plant hormone ethylene. Although the role of ethylene in mediating climacteric ripening has been established, knowledge regarding the developmental regulators that modulate the involvement of ethylene in tomato fruit ripening is still lacking. Here, we show that the tomato APETALA2a (AP2a) transcription factor regulates fruit ripening via regulation of ethylene biosynthesis and signaling. RNA interference (RNAi)-mediated repression of AP2a resulted in alterations in fruit shape, orange ripe fruits, and altered carotenoid accumulation. Microarray expression analyses of the ripe AP2 RNAi fruits showed altered expression of genes involved in various metabolic pathways, such as the phenylpropanoid and carotenoid pathways, as well as in hormone synthesis and perception. Genes involved in chromoplast differentiation and other ripening-associated processes were also differentially expressed, but softening and ethylene biosynthesis occurred in the transgenic plants. Ripening regulators RIPENING-INHIBITOR, NON-RIPENING, and COLORLESS NON-RIPENING (CNR) function upstream of AP2a and positively regulate its expression. In the pericarp of AP2 RNAi fruits, mRNA levels of CNR were elevated, indicating that AP2a and CNR are part of a negative feedback loop in the regulation of ripening. Moreover, we demonstrated that CNR binds to the promoter of AP2a in vitro
    Genome composition of 'Elatior'-begonias hybrids analyzed by genomic in situ hybridisation
    Marasek Ciolakowska, A.R. ; Ramanna, M.S. ; Laak, W.A. ; Tuyl, J.M. van - \ 2010
    Euphytica 171 (2010)2. - ISSN 0014-2336 - p. 273 - 282.
    hordeum-vulgare-l - lycopersicon-esculentum - chromosome elimination - cytogenetic analysis - bulbosum l - plant dna - differentiation - extraction - nicotiana - progenies
    Interspecific hybridization of various tuberous Begonia species hybrids with Begonia socotrana results in so-called 'Elatior'-begonias hybrids (B. x hiemalis Fotsch). In our study, genomic in situ hybridization (GISH) has been employed to assess the genome composition in eleven 'Elatior'-begonias hybrids and their ancestor genotypes. Genomic DNA of tuberous Begonia was sonicated to 1-10-kb fragments, labelled by nick translation with digoxigenin-11-dUTP and used as a probe whereas B. socotrana DNA was autoclaved to 100 bp fragments and used as block. The genome of tuberous Begonia was clearly pronounced in 'Elatior'-begonias when the probe concentration was similar to 3.75 ng/mu l (150 ng/slide), with 30 times the excess of B. socotrana blocking DNA and stringency of post hybridization washings at 73% (0.1x SSC at 42A degrees C). In 'Elatior'-begonias hybrids GISH distinguished two groups comprising short (0.6-1.03 mu m in length) and relatively longer chromosomes (1.87-3.88 mu m) which represent B. socotrana and tuberous Begonia genomes, respectively. The number of chromosomes derived from tuberous Begonia ranged from 14 to 56 and for B. socotrana from 7 to 28 which suggest the presence of different ploidy levels in analyzed 'Elatior'-begonia hybrids. Intergenomic recombination has not been detected through GISH in hybrids analyzed. Genomic in situ hybridization turned out to be useful to identify the genome constitution of 'Elatior'-begonia hybrids and thus gain an insight into the origins of these cultivars. This knowledge on the ploidy level and genome composition is essential for further progress in breeding Begonias.
    Development of a locus-specific, co-dominant SCAR marker for assisted-selection of the Sw-5 (Tospovirus resistance) gene cluster in a wide range of tomato accessions
    Dianese, E.C. ; Fonseca, M.E.N. ; Goldbach, R.W. ; Kormelink, R.J.M. ; Inoue-Nagata, A.K. ; Resende, R.O. de; Boiteux, L.S. - \ 2010
    Molecular Breeding 25 (2010)1. - ISSN 1380-3743 - p. 133 - 142.
    spotted-wilt-virus - lycopersicon-esculentum - thrips transmission - tswv resistance - rapd markers - peruvianum - sw5
    The best levels of broad-spectrum Tospovirus resistance reported in tomatoes thus far are conferred by the Sw-5 locus. This locus contains at least five paralogues (denoted Sw-5a through Sw-5e), of which Sw-5b represents the actual resistance gene. Here we evaluated a panel of seven PCR primer pairs matching different sequences within a genomic region spanning the Sw-5a and Sw-5b gene cluster. Primer efficiency evaluation was done employing tomato isolines with and without the Sw-5 locus. One primer pair produced a single and co-dominant polymorphism between susceptible and resistant isolines. Sequence analysis of these amplicons indicated that they were specific for the Sw-5 locus and their differences were due to insertions/deletions. The polymorphic SCAR amplicon encompass a conserved sequence of the promoter region of the functional Sw-5b gene, being located in the position -31 from its open reading frame. This primer pair was also evaluated in field assays and with a collection of accessions known to be either susceptible or resistant to tospoviruses. An almost complete correlation was found between resistance under greenhouse/field conditions and the presence of the marker. Therefore, this primer pair is a very useful tool in marker-assisted selection systems in a large range of tomato accessions.
    Differences in N uptake and fruit quality between organically and conventionally grown greenhouse tomatoes
    Gravel, V. ; Blok, W.J. ; Hallmann, E. ; Carmona-Torres, C. ; Wang, H. ; Peppel, A.C. van de; Condor Golec, A.F. ; Dorais, M. ; Meeteren, U. van; Heuvelink, E. ; Rembialkowska, E. ; Bruggen, A.H.C. van - \ 2010
    Agronomy for Sustainable Development 30 (2010)4. - ISSN 1774-0746 - p. 797 - 806.
    biologische landbouw - stikstof - tomaten - kwaliteit - vruchtgroenten - bemesting - glasgroenten - organic farming - nitrogen - tomatoes - quality - fruit vegetables - fertilizer application - greenhouse vegetables - nutritional-value - lycopersicon-esculentum - plant foods - soil - yield - fertilization - extraction - flavonoids - vegetables
    Soil-bound intensive greenhouse production has been scrutinized for its sustainability due to contamination of ground water by over-fertilization resulting in leaching of nutrients. As environmental guidelines are becoming more restrictive worldwide, and especially in Europe, many greenhouse growers have converted to more sustainable production systems including rockwool culture with recycled water and organic cropping systems in soil. The increase in popularity of organic production systems has amplified the debate whether organically grown produce is healthier than conventional produce. So far, little is known about the variations in fruit quality associated with production systems for greenhouse grown tomatoes. Thus, two organic (organic fertilization with and without straw amendment) and three conventional tomato cropping systems (regular and increased nutrient solution in rockwool and regular fertilization in soil) were compared in order to evaluate differences in nutrient availability and effects on fruit quality over a three-year period. Three modern medium-sized round tomato cultivars and one old cultivar were compared. There were no significant interactions between cropping systems and cultivars, so that main effects of systems and cultivars could be evaluated. Fruit yields in the organic systems were similar to those obtained in the conventional soil-bound system, but 15% lower than in the regular rockwool system, even though nitrogen concentrations in soil were not limiting in any of the production systems. Frequent organic amendments resulted in higher soil contents in the organic system without straw than in the other soil-bound systems, indicating that the organic systems were not yet stable in terms of nutrient availability after three years. A fruit quality index, based on the contents of compounds such as lycopene, ß-carotene and vitamin C, was similar in all cropping systems. The old cultivar had a significantly higher quality index, but a lower yield than the other cultivars. According to this study, high quality tomatoes can be obtained through proper adjustment of the quantity and the source of nitrogen fertilizers in organic and conventional cropping systems and the use of selected cultivars with a high nutrient use efficiency for organic systems.
    FISH applications for genomics and plant breeding strategies in tomato and other Solanaceous crops
    Szinay, D. ; Bai, Y. ; Visser, R.G.F. ; Jong, J.H. de - \ 2010
    Cytogenetic and Genome Research 129 (2010)1-3. - ISSN 1424-8581 - p. 199 - 210.
    in-situ hybridization - high-resolution fish - extended dna fibers - lycopersicon-esculentum - recombination nodules - heterochromatic genes - chromosome identification - synaptonemal complexes - pachytene chromosomes - sequence-analysis
    This paper describes the use of advanced fluorescence in situ hybridization (FISH) technologies for genomics and breeding of tomato and related Solanum species. The first part deals with the major determinants of FISH technology: (1) spatial resolution, which depends on the diffraction limit of the microscope and the type of chromosome, chromatin or isolated DNA fibres as target for the hybridisation; (2) the detection sensitivity, which is limited by the sensitivity and dynamic range of the CCD camera and the quality of the microscope, and the amplification system of the weak signals from tiny probe molecules; (3) simultaneous detection of multiple probes labelled directly or indirectly with up to 5 different fluorophores, whether or not in different combinations and/or mixed at different ratios. The power and usability of such multicolour FISH is indispensable when large numbers of bacterial artificial chromosomes (BACs) or other vectors with genomic DNA are available. Mapping of multiple BACs on chromosomes are powerful instruments confirming their assumed genetic position, whereas pooled BACs for a given chromosome arm will reveal the gaps between the BACs or derived contigs of their physical maps. Tandem and dispersed repeats, which are abundant in the genomes of most species, can be analysed in repeat bar coding FISH, showing the major blocks of repeats in heterochromatin and euchromatin areas. Repeat-rich areas of the chromosomes can also be demonstrated by hybridisation of probed Cot fractions of sheared genomic DNA; a powerful method to elucidate the heterochromatin domains for genomic studies. In addition, unlabelled Cot DNA, as blocking agent in BAC-FISH painting, suppresses repetitive sequences from the BACs to hybridise on the chromosomes. Cross-species BAC-FISH painting with labelled probes from tomato and potato BACs and hybridised on the chromosomes of related species, under appropriate conditions, is a powerful instrument to demonstrate chromosomal rearrangements, including inversions and translocations. The technology not only supports phylogenetic studies between the taxa under study but can also be helpful in breeding programs with crops containing introgressed regions from related species when linkage drag or meiotic pairing disturbances between the homoeologues are assumed. In the next steps in comparative genomics, we now can detect smaller chromosomal and DNA rearrangements, diminutions and amplifications of repeats and changes of the epigenetic status of introgressed regions
    Emerging Viral Diseases of Tomato Crops
    Hanssen, I.M. ; Lapidot, M. ; Thomma, B.P.H.J. - \ 2010
    Molecular Plant-Microbe Interactions 23 (2010)5. - ISSN 0894-0282 - p. 539 - 548.
    pepino-mosaic-virus - leaf-curl-virus - infectious-chlorosis-virus - zonate spot virus - complete nucleotide-sequence - picorna-like virus - torrado-virus - 1st report - plant-viruses - lycopersicon-esculentum
    Viral diseases are an important limiting factor in many crop production systems. Because antiviral products are not available, control strategies rely on genetic resistance or hygienic measures to prevent viral diseases, or on eradication of diseased crops to control such diseases. Increasing international travel and trade of plant materials enhances the risk of introducing new viruses and their vectors into production systems. In addition, changing climate conditions can contribute to a successful spread of newly introduced viruses or their vectors and establishment of these organisms in areas that were previously unfavorable. Tomato is economically the most important vegetable crop worldwide and many viruses infecting tomato have been described, while new viral diseases keep emerging. Pepino mosaic virus is a rapidly emerging virus which has established itself as one of the most important viral diseases in tomato production worldwide over recent years. Begomovirus species and other whitefly-transmitted viruses are invading into new areas, and several recently described new viruses such as Tomato torrado virus and new Tospovirus species are rapidly spreading over large geographic areas. In this article, emerging viruses of tomato crops are discussed.
    A role for differential glycoconjugation in the emission of phenylpropanoid volatiles from tomato fruit discovered using a metabolic data fusion approach.
    Tikunov, Y.M. ; Vos, C.H. de; Gonzalez Paramas, A.M. ; Hall, R.D. ; Bovy, A.G. - \ 2010
    Plant Physiology 152 (2010). - ISSN 0032-0889 - p. 55 - 70.
    methyl salicylate - lycopersicon-esculentum - bahd acyltransferase - solanum-lycopersicon - clitoria-ternatea - aroma components - flavor compounds - plant volatiles - glycosides - identification
    A role for differential glycoconjugation in the emission of phenylpropanoid volatiles from ripening tomato fruit (Solanum lycopersicum) upon fruit tissue disruption has been discovered in this study. Application of a multiinstrumental analytical platform for metabolic profiling of fruits from a diverse collection of tomato cultivars revealed that emission of three discriminatory phenylpropanoid volatiles, namely methyl salicylate, guaiacol, and eugenol, took place upon disruption of fruit tissue through cleavage of the corresponding glycoconjugates, identified putatively as hexose-pentosides. However, in certain genotypes, phenylpropanoid volatile emission was arrested due to the corresponding hexose-pentoside precursors having been converted into glycoconjugate species of a higher complexity: dihexose-pentosides and malonyl-dihexose-pentosides. This glycoside conversion was established to occur in tomato fruit during the later phases of fruit ripening and has consequently led to the inability of red fruits of these genotypes to emit key phenylpropanoid volatiles upon fruit tissue disruption. This principle of volatile emission regulation can pave the way to new strategies for controlling tomato fruit flavor and taste.
    Rpi-vnt1.1, a Tm-2(2) Homolog from Solanum venturii, Confers Resistance to Potato Late Blight
    Foster, S.J. ; Park, T.H. ; Pel, M. ; Brigneti, G. ; Sliwka, J. ; Jagger, L. ; Vossen, E.A.G. van der; Jones, J.D.G. - \ 2009
    Molecular Plant-Microbe Interactions 22 (2009)5. - ISSN 0894-0282 - p. 589 - 600.
    broad-spectrum resistance - race-specific resistance - phytophthora-infestans mont - disease-resistance - chromosome-ix - lycopersicon-esculentum - r-gene - hypersensitive resistance - united-states - aflp markers
    Despite the efforts of breeders and the extensive use of fungicide control measures, late blight still remains a major threat to potato cultivation worldwide. The introduction of genetic resistance into cultivated potato is considered a valuable method to achieve durable resistance to late blight. Here, we report the identification and cloning of Rpi-vnt1.1, a previously uncharacterized late-blight resistance gene from Solanum venturii. The gene was identified by a classical genetic and physical mapping approach and encodes a coiled-coil nucleotide-binding leucine-rich repeat protein with high similarity to Tm-22 from S. lycopersicum which confers resistance against Tomato mosaic virus. Transgenic potato and tomato plants carrying Rpi-vnt1.1 were shown to be resistant to Phytophthora infestans. Of 11 P. infestans isolates tested, only isolate EC1 from Ecuador was able to overcome Rpi-vnt1.1 and cause disease on the inoculated plants. Alleles of Rpi-vnt1.1 (Rpi-vnt1.2 and Rpivnt1.3) that differed by only a few nucleotides were found in other late-blight-resistant accessions of S. venturii. The late blight resistance gene Rpi-phu1 from S. phureja is shown here to be identical to Rpi-vnt1.1, suggesting either that this strong resistance gene has been maintained since a common ancestor, due to selection pressure for blight resistance, or that genetic exchange between S. venturii and S. phureja has occurred at some time.
    C22 Isomerization in a-Tomatine-to-Esculeoside A Conversion during Tomato Ripening Is Driven by C27 Hydroxylation of Triterpenoidal Sekeleton
    Yamanaka, T. ; Vincken, J.P. ; Zuilhof, H. ; Legger, A. ; Takada, N. ; Gruppen, H. - \ 2009
    Journal of Agricultural and Food Chemistry 57 (2009)9. - ISSN 0021-8561 - p. 3786 - 3791.
    steroidal alkaloid glycosides - pulsed amperometric detection - lycopersicon-esculentum - fruits - plant - dehydrotomatine - glycoalkaloids - performance - maturation - hplc
    Compositional analysis by liquid chromatography/mass spectrometry of triterpenoid glycosides in different tomato cultivars, ripening stages, and parts of fruits showed that alpha-tomatine was generally most abundant in the flesh of the mature green stage, whereas esculeoside A was predominant in that of the red ripe stage. The sum of these glycoalkaloids was more or less constant, suggesting that alpha-tomatine is converted to esculeoside A during ripening. Besides various substitutions, the C22alphaN -> C22ßN isomerization is an important step in this transformation. By quantum chemical calculations it was shown that hydroxylation at C27 of the triterpenoidal skeleton is the driving force behind the isomerization. For the protonated form of the glycoalkaloid (predominant at the pH of tomato tissue), the C22ßN configuration becomes more favorable than that of C22alphaN, through the extra energy provided by the hydrogen bond between the protonated nitrogen and the lone pair of the oxygen of the C27-OH
    Mapping and Cloning of Late Blight Resistance Genes from Solanum venturii Using an Interspecific Candidate Gene Approach
    Pel, M. ; Foster, S.J. ; Park, T.H. ; Rietman, H. ; Arkel, G. van; Jones, J.D.G. ; Eck, H.J. van; Jacobsen, E. ; Visser, R.G.F. ; Vossen, E.A.G. van der - \ 2009
    Molecular Plant-Microbe Interactions 22 (2009)5. - ISSN 0894-0282 - p. 601 - 615.
    quantitative trait locus - race-specific resistance - nbs-lrr proteins - phytophthora-infestans - disease-resistance - r-gene - nucleotide-binding - field-resistance - lycopersicon-esculentum - nicotiana-benthamiana
    Late blight, caused by the oomycete Phytophthora infestans, is one of the most devastating diseases of potato. Resistance (R) genes from the wild species Solanum demissum have been used by breeders to generate late-blight-resistant cultivars but resistance was soon overcome by the pathogen. A more recent screening of a large number of wild species has led to the identification of novel sources of resistance, many of which are currently being characterized further. Here, we report on the cloning of dominant Rpi genes from S. venturii. Rpi-vnt1.1 and Rpi-vnt1.3 were mapped to chromosome 9 using nucleotide binding site (NBS) profiling. Subsequently, a Tm-22-based allele mining strategy was used to clone both genes. Rpi-vnt1.1 and Rpi-vnt1.3 belong to the coiled-coil NBS leucine-rich repeat (LRR) class of plant R genes and encode predicted peptides of 891 and 905 amino acids (aa), respectively, which share 75% amino acid identity with the Tomato mosaic virus resistance protein Tm-22 from tomato. Compared with Rpi-vnt1.1, Rpi-vnt1.3 harbors a 14-aa insertion in the N-terminal region of the protein and two different amino acids in the LRR domain. Despite these differences, Rpi-vnt1.1 and Rpi-vnt1.3 genes have the same resistance spectrum
    Changes in gene and protein expression during tomato ripening - consequences for the safety assessment of new crop plant varieties
    Kok, E.J. ; Lehesranta, S.J. ; Dijk, J.P. van; Helsdingen, J.R. ; Dijksma, W.T.P. ; Hoef, A.M.A. van; Koistinen, K.M. ; Karenlampi, S.O. ; Kuiper, H.A. ; Keijer, J. - \ 2008
    Food Science and Technology International 14 (2008)6. - ISSN 1082-0132 - p. 503 - 518.
    lycopersicon-esculentum - fruit maturation - transcriptome - translation - cloning
    An important part of the comparative approach to assess the safety of new crop plant varieties is an extensive compositional analysis, including the measurement of all key nutrients and antinutrients in a specific crop. The study described here investigates the applicability of `omics' technologies, transcriptomics and proteomics, as additional tools in this comparative safety assessment. The aim of the work was to assess the extent of the natural variation in ripening tomato fruits as a model crop and to determine whether it is possible to develop simple `ripening stage' criteria for the sampling of fruits for `omics' analyses. It is shown that the set-up of an `omics' study is of crucial importance. Samples under scrutiny should be well-matched with relation to environmental conditions during growth and harvest, including the stage of ripening, as is stipulated in international guidance documents for the nutritional and toxicological assessment of genetically modified plants
    Isolation, Characterization, and Surfactant Properties of the Major Triterpenoid Glycosides from Unripe Tomato Fruits
    Yamanaka, T. ; Vincken, J.P. ; Waard, P. de; Sanders, M.G. ; Takada, N. ; Gruppen, H. - \ 2008
    Journal of Agricultural and Food Chemistry 56 (2008)23. - ISSN 0021-8561 - p. 11432 - 11440.
    steroidal alkaloid glycosides - tandem mass-spectrometry - lycopersicon-esculentum - electrospray-ionization - liquid-chromatography - glycoalkaloids - saponins - plant - dehydrotomatine - soyasaponins
    Various triterpenoid glycosides were extracted from whole unripe tomato fruits (Lycopersicon esculentum cv. Cedrico), using aqueous 70% (v/v) ethanol to study their surfactant properties. Cation-exchange chromatography using a Source 15S column and subsequent semipreparative HPLC using an XTerra RP18 were employed to purify individual triterpenoid glycosides from the extract. The structure of the purified compounds was established by mass spectrometry and nuclear magnetic resonance spectroscopy. The furostanol glycoside tomatoside A (749 mg/kg of DW) and the glycoalkaloids ¿-tomatine (196 mg/kg of DW) and esculeoside A (427 mg/kg of DW) were the major triterpenoid glycosides present. Furthermore, minor amounts of a new dehydrofurostanol glycoside, dehydrotomatoside, were found. The critical micelle concentrations of the major triterpenoid glycosides, ¿-tomatine, tomatoside A, and esculeoside A, were determined as 0.099, 0.144, and 0.412 g/L, respectively. The results show that tomatoside A, and not the more well-known ¿-tomatine, is the predominant triterpenoidal surfactant in unripe tomato fruits.
    FISH mapping and molecular organization of the major repetitive sequences of tomato
    Chang, S.B. ; Yang, T.J. ; Datema, E. ; Vugt, J. van; Vosman, B. ; Kuipers, A. ; Meznikova, M. ; Szinay, D. ; Klein Lankhorst, R.M. ; Jacobsen, E. ; Jong, J.H.S.G.M. de - \ 2008
    Chromosome Research 16 (2008)7. - ISSN 0967-3849 - p. 919 - 933.
    in-situ hybridization - ty1-copia group retrotransposons - repeated dna-sequences - high-resolution fish - lycopersicon-esculentum - pachytene chromosomes - metaphase chromosomes - centromeric region - genome - genes
    This paper presents a bird's-eye view of the major repeats and chromatin types of tomato. Using fluorescence in-situ hybridization (FISH) with Cot-1, Cot-10 and Cot-100 DNA as probes we mapped repetitive sequences of different complexity on pachytene complements. Cot-100 was found to cover all heterochromatin regions, and could be used to identify repeat-rich clones in BAC filter hybridization. Next we established the chromosomal locations of the tandem and dispersed repeats with respect to euchromatin, nucleolar organizer regions (NORs), heterochromatin, and centromeres. The tomato genomic repeats TGRII and TGRIII appeared to be major components of the pericentromeres, whereas the newly discovered TGRIV repeat was found mainly in the structural centromeres. The highly methylated NOR of chromosome 2 is rich in [GACA](4), a microsatellite that also forms part of the pericentromeres, together with [GA](8), [GATA](4) and Ty1-copia. Based on the morphology of pachytene chromosomes and the distribution of repeats studied so far, we now propose six different chromatin classes for tomato: (1) euchromatin, (2) chromomeres, (3) distal heterochromatin and interstitial heterochromatic knobs, (4) pericentromere heterochromatin, (5) functional centromere heterochromatin and (6) nucleolar organizer region
    High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6
    Szinay, D. ; Chang, S.B. ; Khrustaleva, L.I. ; Peters, S.A. ; Schijlen, E.G.W.M. ; Bai, Y. ; Stiekema, W. ; Ham, R.C.H.J. van; Jong, H. de; Klein Lankhorst, R.M. - \ 2008
    The Plant Journal 56 (2008)4. - ISSN 0960-7412 - p. 627 - 637.
    molecular linkage maps - lycopersicon-esculentum - root-knot - genome sequence - pachytene chromosomes - metaphase chromosomes - arabidopsis-thaliana - meiotic pachytene - dna-sequences - rice genome
    Within the framework of the International Solanaceae Genome Project, the genome of tomato (Solanum lycopersicum) is currently being sequenced. We follow a 'BAC-by-BAC' approach that aims to deliver high-quality sequences of the euchromatin part of the tomato genome. BACs are selected from various libraries of the tomato genome on the basis of markers from the F2.2000 linkage map. Prior to sequencing, we validated the precise physical location of the selected BACs on the chromosomes by five-colour high-resolution fluorescent in situ hybridization (FISH) mapping. This paper describes the strategies and results of cytogenetic mapping for chromosome 6 using 75 seed BACs for FISH on pachytene complements. The cytogenetic map obtained showed discrepancies between the actual chromosomal positions of these BACs and their markers on the linkage group. These discrepancies were most notable in the pericentromere heterochromatin, thus confirming previously described suppression of cross-over recombination in that region. In a so called pooled-BAC FISH, we hybridized all seed BACs simultaneously and found a few large gaps in the euchromatin parts of the long arm that are still devoid of seed BACs and are too large for coverage by expanding BAC contigs. Combining FISH with pooled BACs and newly recruited seed BACs will thus aid in efficient targeting of novel seed BACs into these areas. Finally, we established the occurrence of repetitive DNA in heterochromatin/euchromatin borders by combining BAC FISH with hybridization of a labelled repetitive DNA fraction (Cot-100). This strategy provides an excellent means to establish the borders between euchromatin and heterochromatin in this chromosome.
    Map - vs. homology - based cloning for the recessive gene ol-2 conferring resistance to tomato powdery mildew
    Pavan, S.N.C. ; Zheng, Z. ; Borisova, M. ; Berg, P.M.M.M. van den; Lotti, C. ; Giovanni, C. de; Lindhout, P. ; Jong, J.H. de; Ricciardi, L. ; Visser, R.G.F. ; Bai, Y. - \ 2008
    Euphytica 162 (2008)1. - ISSN 0014-2336 - p. 91 - 98.
    oidium-neolycopersici - lycopersicon-esculentum - rflp analysis - markers - locus - aflp - heterochromatin - identification - defense - plants
    The recessive gene ol-2 confers papilla-associated and race-non-specific resistance to tomato powdery mildew caused by Oidium neolycopersici. In order to facilitate marker assisted selection (MAS) in practical breeding programmes, we identified two simple sequence repeat (SSR) markers and one cleaved amplified polymorphic sequence (CAPS) marker which are linked to the resistance locus and co-dominantly inherited. Aiming to provide a base for ol-2 positional cloning, we used a large segregating F2 population to merge these markers with all the ol-2 linked amplified fragment length polymorphism (AFLP®) markers previously identified in an integrated genetic map. By screening a tomato bacterial artificial chromosome (BAC) library, we detected two BAC clones containing two expressed sequence tags (ESTs) homologous to the gene mlo, responsible for powdery mildew resistance in barley, as well as an ol-2-linked marker. Chromosomal mapping by Fluorescence in situ Hybridization (FISH) revealed major signals of the two BAC DNAs in the pericentromeric heterochromatin of the short arm of chromosome 4, in the same region where the ol-2 gene was previously mapped. The genetic and cytogenetic co-localisation between ol-2 and tomato mlo-homologue(s), in addition to the similarity of ol-2 and mlo resistances for both genetic and phytopathological characteristics, suggests that ol-2 is likely a mlo-homologue. Thus, a homology-based cloning approach could be more suitable than positional cloning for ol-2 isolation.
    Diversity and linkage disequilibrium analysis wihtin a selected set of cultivated tomatoes
    Berloo, R. van; Zhu, A. ; Ursem, R.A. ; Verbakel, H. ; Gort, G. ; Eeuwijk, F.A. van - \ 2008
    Theoretical and Applied Genetics 117 (2008). - ISSN 0040-5752 - p. 89 - 101.
    fragment-length-polymorphism - lycopersicon-esculentum - genetic diversity - rapd markers - aflp markers - software - accessions - stability - inference - map
    Within the Dutch genomics initiative the ¿Centre for Biosystems Genomics¿ (CBSG) a major research effort is directed at the identification and unraveling of processes and mechanisms affecting fruit quality in tomato. The basis of this fruit quality program was a diverse set of 94 cultivated tomato cultivars, representing a wide spectrum of phenotypes for quality related traits. This paper describes a diversity study performed on these cultivars, using information of 882 AFLP markers, of which 304 markers had a known map position. The AFLP markers were scored as much as possible in a co-dominant fashion. We investigated genome distribution and coverage for the mapped markers and conclude that it proved difficult to arrive at a dense and uniformly distributed coverage of the genome with markers. Mapped markers and unmapped markers were used to investigate population structure. A clear substructure was observed which seemed to coincide with a grouping based on fruit size. Finally, we studied amount and decay of linkage disequilibrium (LD) along the chromosomes. LD was observed over considerable (genetic) distances. We discuss the feasibility of marker-trait association studies and conclude that the amount of genetic variation in our set of cultivars is limited, but that there exists scope for association studies
    Mapping and characterization of novel parthenocarpy QTLs in tomato
    Gorguet, B.J.M. ; Eggink, P.M. ; Ocaña, J. ; Tiwari, A. ; Schipper, E.H. ; Finkers, H.J. ; Visser, R.G.F. ; Heusden, A.W. van - \ 2008
    Theoretical and Applied Genetics 116 (2008)6. - ISSN 0040-5752 - p. 755 - 767.
    quantitative trait loci - lycopersicon-esculentum - botrytis-cinerea - resistance - hirsutum - set - auxin-response-factor8 - identification - introgression - chromosomes
    Parthenocarpy is the development of the fruit in absence of pollination and/or fertilization. In tomato, parthenocarpy is considered as an attractive trait to solve the problems of fruit setting under unfavorable conditions. We studied the genetics of parthenocarpy in two different lines, IL5-1 and IVT-line 1, both carrying Solanum habrochaites chromosome segments. Parthenocarpy in IL5-1 is under the control of two QTLs, one on chromosome 4 (pat4.1) and one on chromosome 5 (pat5.1). IVT-line 1 also contains two parthenocarpy QTLs, one on chromosome 4 (pat4.2) and one on chromosome 9 (pat9.1). In addition, we identified one stigma exsertion locus in IL5-1, located on the long arm of chromosome 5 (se5.1). It is likely that pat4.1, from IL5-1 and pat4.2, from IVT-line 1, both located near the centromere of chromosome 4 are allelic. By making use of the microsynteny between tomato and Arabidopsis in this genetic region, we identified ARF8 as a potential candidate gene for these two QTLs. ARF8 is known to act as an inhibitor for further carpel development in Arabidopsis, in absence of pollination/fertilization. Expression of an aberrant form of the Arabidopsis ARF8 gene, in tomato, has been found to cause parthenocarpy. This candidate gene approach may lead to the first isolation of a parthenocarpy gene in tomato and will allow further use in several crop species
    Breeding for a more energy efficient greenhouse tomato: past and future perspectives
    Ploeg, A. van der; Meer, M. van der; Heuvelink, E. - \ 2007
    Euphytica 158 (2007)1-2. - ISSN 0014-2336 - p. 129 - 138.
    lycopersicon-esculentum - growth - temperature - fruit - improvement - yield - cultivars - quality - biomass
    Energy efficiency can be increased either by increasing the production per m2 or by reducing the energy input per m2, e.g. by reducing temperature set-points in the greenhouse. So far, in Dutch glasshouse tomatoes energy efficiency was almost exclusively raised by yield increases. To study the role of tomato breeding in this production increase, yield and underlying components of 7 cultivars released between 1950 and 2002 were studied. Furthermore, variation in temperature response between cultivars was studied. In three experiments yield and biomass production of in total 11 cultivars were evaluated at two temperature regimes (17/15°C and 21/19°C day/night temperature set-points). Breeding has resulted in a remarkable increase in production. Under current conditions, yield of modern cultivars was on average 40% higher than yield of `Moneymaker¿, released in 1950. This increase in production resulted from a higher light use efficiency. Although the fraction of assimilates partitioned to the fruits showed small differences between cultivars, this trait was not related to year of release. Furthermore, more recently introduced cultivars produced larger fruits rather than more fruits. All cultivars responded similar to both temperature regimes for all important characteristics, limiting the possibilities of using existing cultivars in a breeding program for improved yield at lower temperatures.
    Domestication and breeding of tomatoes: what have we gained and what can we gain in the future?
    Bai, Y. ; Lindhout, P. - \ 2007
    Annals of Botany 100 (2007)5. - ISSN 0305-7364 - p. 1085 - 1094.
    quantitative trait loci - backcross qtl analysis - lycopersicon-esculentum - fruit size - cultivated tomato - solanum-lycopersicoides - genus lycopersicon - genetic diversity - natural variation - resistance genes
    Background It has been shown that a large variation is present and exploitable from wild Solanum species but most of it is still untapped. Considering the thousands of Solanum accessions in different gene banks and probably even more that are still untouched in the Andes, it is a challenge to exploit the diversity of tomato. What have we gained from tomato domestication and breeding and what can we gain in the future? Scope This review summarizes progress on tomato domestication and breeding and current efforts in tomato genome research. Also, it points out potential challenges in exploiting tomato biodiversity and depicts future perspectives in tomato breeding with the emerging knowledge from tomato-omics. Conclusions From first domestication to modern breeding, the tomato has been continually subjected to human selection for a wide array of applications in both science and commerce. Current efforts in tomato breeding are focused on discovering and exploiting genes for the most important traits in tomato germplasm. In the future, breeders will design cultivars by a process named 'breeding by design' based on the combination of science and technologies from the genomic era as well as their practical skills.
    Three QTLs for Botrytis cinerea resistance in tomato
    Finkers, H.J. ; Berg, P.M.M.M. van den; Berloo, R. van; Have, A. ten; Heusden, A.W. van; Kan, J.A.L. van; Lindhout, P. - \ 2007
    Theoretical and Applied Genetics 114 (2007)4. - ISSN 0040-5752 - p. 585 - 593.
    recombinant inbred lines - lycopersicon-esculentum - linkage maps - backcross - hirsutum - phytoalexins - fungal - plants - aflp - populations
    Tomato (Solanum lycopersicum) is susceptible to grey mold (Botrytis cinerea). Partial resistance to this fungus was identified in accessions of wild relatives of tomato such as S. habrochaites LYC4. In order to identify loci involved in quantitative resistance (QTLs) to B. cinerea, a population of 174 F2 plants was made originating from a cross between S. lycopersicum cv. Moneymaker and S. habrochaites LYC4. The population was genotyped and tested for susceptibility to grey mold using a stem bioassay. Rbcq1, a QTL reducing lesion growth (LG) and Rbcq2, a QTL reducing disease incidence (DI) were identified. Rbcq1 is located on Chromosome 1 and explained 12% of the total phenotypic variation while Rbcq2 is located on Chromosome 2 and explained 15% of the total phenotypic variation. Both QTL effects were confirmed by assessing disease resistance in two BC2S1 progenies segregating for either of the two QTLs. One additional QTL, Rbcq4 on Chromosome 4 reducing DI, was identified in one of the BC2S1 progenies. F2 individuals, homozygous for the Rbcq2 and Rbcq4 alleles of S. habrochaites showed a reduction of DI by 48%. QTLs from S. habrochaites LYC4 offer good perspectives for breeding B. cinerea resistant tomato cultivars.
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