Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Continuous-light tolerance in tomato is graft-transferable
Vélez Ramírez, A.I. ; Ieperen, W. van; Vreugdenhil, D. ; Millenaar, F.F. - \ 2015
Planta 241 (2015)1. - ISSN 0032-0935 - p. 285 - 290.
lycopersicon-esculentum - plants - temperature - photosynthesis - rootstock - increase - growth - injury - xylem - fruit
Continuous light induces a potentially lethal injury in domesticated tomato (Solanum lycopersicum) plants. Recently, continuous-light tolerance was reported in several wild tomato species, yet the molecular mechanisms underpinning tolerance/sensitivity are still elusive. Here, we investigated from which part of the plant continuous-light tolerance originates and whether this trait acts systemically within the plant. By exposing grafted plants bearing both tolerant and sensitive shoots, the trait was functionally located in the shoot rather than the roots. Additionally, an increase in continuous-light tolerance was observed in sensitive plants when a continuous-light-tolerant shoot was grafted on it. Cultivation of greenhouse tomatoes under continuous light promises high yield increases. Our results show that to pursuit this, the trait should be bred into scion rather than rootstock lines. In addition, identifying the nature of the signal/molecule(s) and/or the mechanism of graft-induced, continuous-light tolerance can potentially result in a better understanding of important physiological processes like long-distance signaling.
Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome
Shearer, L.A. ; Anderson, L.K. ; Jong, H. de; Smit, S. ; Goicoechea, J.L. ; Roe, B.A. ; Hua, A. ; Giovannoni, J.J. ; Stack, S.M. - \ 2014
G3 : Genes Genomes Genetics 4 (2014)8. - ISSN 2160-1836 - p. 1395 - 1405.
extended dna fibers - zea-mays l. - lycopersicon-esculentum - pachytene chromosomes - synaptonemal complexes - 2-dimensional spreads - solanaceous plants - solanum pennellii - multicolor fish - linkage maps
The order and orientation (arrangement) of all 91 sequenced scaffolds in the 12 pseudomolecules of the recently published tomato (Solanum lycopersicum, 2n = 2x = 24) genome sequence were positioned based on marker order in a high-density linkage map. Here, we report the arrangement of these scaffolds determined by two independent physical methods, bacterial artificial chromosome–fluorescence in situ hybridization (BAC-FISH) and optical mapping. By localizing BACs at the ends of scaffolds to spreads of tomato synaptonemal complexes (pachytene chromosomes), we showed that 45 scaffolds, representing one-third of the tomato genome, were arranged differently than predicted by the linkage map. These scaffolds occur mostly in pericentric heterochromatin where 77% of the tomato genome is located and where linkage mapping is less accurate due to reduced crossing over. Although useful for only part of the genome, optical mapping results were in complete agreement with scaffold arrangement by FISH but often disagreed with scaffold arrangement based on the linkage map. The scaffold arrangement based on FISH and optical mapping changes the positions of hundreds of markers in the linkage map, especially in heterochromatin. These results suggest that similar errors exist in pseudomolecules from other large genomes that have been assembled using only linkage maps to predict scaffold arrangement, and these errors can be corrected using FISH and/or optical mapping. Of note, BAC-FISH also permits estimates of the sizes of gaps between scaffolds, and unanchored BACs are often visualized by FISH in gaps between scaffolds and thus represent starting points for filling these gaps
Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome
Tang, X. ; Datema, E. ; Olortegui Guzman, M.C. ; Boer, J.M. de; Eck, H.J. van; Bachem, C.W.B. ; Visser, R.G.F. ; Jong, H. de - \ 2014
Molecular Genetics and Genomics 289 (2014)6. - ISSN 1617-4615 - p. 1307 - 1319.
ty1-copia group retrotransposons - species-specific sequences - repeated dna-sequences - in-situ hybridization - somatic hybrids - lycopersicon-esculentum - satellite repeat - repetitive dna - transposable elements - metaphase chromosomes
One of the most powerful technologies in unraveling the organization of a eukaryotic plant genome is high-resolution Fluorescent in situ hybridization of repeats and single copy DNA sequences on pachytene chromosomes. This technology allows the integration of physical mapping information with chromosomal positions, including centromeres, telomeres, nucleolar-organizing region, and euchromatin and heterochromatin. In this report, we established chromosomal positions of different repeat fractions of the potato genomic DNA (Cot100, Cot500 and Cot1000) on the chromosomes. We also analysed various repeat elements that are unique to potato including the moderately repetitive P5 and REP2 elements, where the REP2 is part of a larger Gypsy-type LTR retrotransposon and cover most chromosome regions, with some brighter fluorescing spots in the heterochromatin. The most abundant tandem repeat is the potato genomic repeat 1 that covers subtelomeric regions of most chromosome arms. Extensive multiple alignments of these repetitive sequences in the assembled RH89-039-16 potato BACs and the draft assembly of the DM1-3 516 R44 genome shed light on the conservation of these repeats within the potato genome. The consensus sequences thus obtained revealed the native complete transposable elements from which they were derived
The Tomato spotted wilt virus cell-to-cell movement protein (NSM) triggers a hypersensitive response in Sw-5 containing resistant tomato lines and Nicotiana benthamiana transformed with the functional Sw-5b resistance gene copy.
Hallwass, M. ; Silva de Oliveira, A. ; Dianese, E.C. ; Lohuis, D. ; Boiteux, L.S. ; Inoue-Nagata, A.K. ; Resende, R.O. de; Kormelink, R.J.M. - \ 2014
Molecular Plant Pathology 15 (2014)9. - ISSN 1464-6722 - p. 871 - 880.
mosaic-virus - lycopersicon-esculentum - nonstructural protein - capsicum-chinense - coat protein - plant-cells - rna segment - tswv - tospovirus - tobacco
Although the Sw-5 gene cluster has been cloned, and Sw-5b has been identified as the functional gene copy that confers resistance to Tomato spotted wilt virus (TSWV), its avirulence (Avr) determinant has not been identified to date. Nicotiana tabacum SR1 plants transformed with a copy of the Sw-5b gene are immune without producing a clear visual response on challenge with TSWV, whereas it is shown here that N.benthamiana transformed with Sw-5b gives a rapid and conspicuous hypersensitive response (HR). Using these plants, from all structural and non-structural TSWV proteins tested, the TSWV cell-to-cell movement protein (NSM) was confirmed as the Avr determinant using a Potato virus X (PVX) replicon or a non-replicative pEAQ-HT expression vector system. HR was induced in Sw-5b-transgenic N.benthamiana as well as in resistant near-isogenic tomato lines after agroinfiltration with a functional cell-to-cell movement protein (NSM) from a resistance-inducing (RI) TSWV strain (BR-01), but not with NSM from a Sw-5 resistance-breaking (RB) strain (GRAU). This is the first biological demonstration that Sw-5-mediated resistance is triggered by the TSWV NSM cell-to-cell movement protein.
A single locus confers tolerance to continuous light and allows substantial yield increase in tomato
Vélez Ramírez, A.I. ; Ieperen, W. van; Vreugdenhil, D. ; Poppel, P.M.J.A. van; Heuvelink, E. ; Millenaar, F.F. - \ 2014
Nature Communications 5 (2014). - ISSN 2041-1723
differential expression analysis - photosystem-ii - lycopersicon-esculentum - greenhouse tomato - dependent phosphorylation - chlorophyll fluorescence - arabidopsis-thaliana - gene-expression - air humidity - plants
An important constraint for plant biomass production is the natural day length. Artificial light allows for longer photoperiods, but tomato plants develop a detrimental leaf injury when grown under continuous light—a still poorly understood phenomenon discovered in the 1920s. Here, we report a dominant locus on chromosome 7 of wild tomato species that confers continuous light tolerance. Genetic evidence, RNAseq data, silencing experiments and sequence analysis all point to the type III light harvesting ¿chlorophyll a/b binding protein 13 (¿CAB-13) gene as a major factor responsible for the tolerance. In Arabidopsis thaliana, this protein is thought to have a regulatory role balancing light harvesting by photosystems I and II. Introgressing the tolerance into modern tomato hybrid lines, results in up to 20% yield increase, showing that limitations for crop productivity, caused by the adaptation of plants to the terrestrial 24-h day/night cycle, can be overcome.
Capturing flavors from Capsicum baccatum by introgression in sweet pepper
Eggink, P.M. ; Tikunov, Y.M. ; Maliepaard, C.A. ; Haanstra, J.P.W. ; Rooij, H. de; Vogelaar, A. ; Gutteling, E.W. ; Freymark, G. ; Bovy, A.G. ; Visser, R.G.F. - \ 2014
Theoretical and Applied Genetics 127 (2014)2. - ISSN 0040-5752 - p. 373 - 390.
plastid compartment size - lycopersicon-esculentum - volatile compounds - anthracnose resistance - chemical-composition - gas-chromatography - sensory evaluation - mass-spectrometry - candidate gene - essential oils
The species Capsicum baccatum includes the most common hot peppers of the Andean cuisine, known for their rich variation in flavors and aromas. So far the C. baccatum genetic variation remained merely concealed for Capsicum annuum breeding, due to post-fertilization genetic barriers encountered in interspecific hybridization. However, to exploit the potential flavor wealth of C. baccatum we combined interspecific crossing with embryo rescue, resulting in a multi-parent BC2S1 population. Volatile and non-volatile compounds plus some physical characters were measured in mature fruits, in combination with taste evaluation by a sensory panel. An enormous variation in biochemical composition and sensory attributes was found, with almost all traits showing transgression. A population-specific genetic linkage map was developed for QTL mapping. BC2S1 QTLs were validated in an experiment with near-isogenic lines, resulting in confirmed genetic effects for physical, biochemical and sensory traits. Three findings are described in more detail: (1) A small C. baccatum LG3 introgression caused an extraordinary effect on flavor, resulting in significantly higher scores for the attributes aroma, flowers, spices, celery and chives. In an attempt to identify the responsible biochemical compounds few consistently up- and down-regulated metabolites were detected. (2) Two introgressions (LG10.1 and LG1) had major effects on terpenoid content of mature fruits, affecting at least 15 different monoterpenes. (3) A second LG3 fragment resulted in a strong increase in Brix without negative effects on fruit size. The mapping strategy, the potential application of studied traits and perspectives for breeding are discussed.
Aroma volatile release kinetics of tomato genotypes measured by PTR-MS following artificial chewing
Farneti, B. ; Alarcón, A. ; Cristescu, S.M. ; Costa, G. ; Harren, F.J.M. ; Holthuysen, N.T.E. ; Woltering, E.J. - \ 2013
Food Research International 54 (2013)2. - ISSN 0963-9969 - p. 1579 - 1588.
reaction-mass spectrometry - flavor release - lycopersicon-esculentum - in-vitro - physiological-parameters - quantitative-analysis - model mouth - cultivars - fruit - mastication
The aim of this study was to develop an analytical system to study the tomato aroma profile. An artificial chewing device coupled to a PTR-MS was developed to mimic, as close as possible, the release of volatiles during chewing in the human mouth and the retronasal olfaction perception. VOC profiles of 9 tomato lines, selected based on flavor characteristics by a sensory panel, were acquired by both a PTR-MS system following artificial chewing and by SPME–GC–MS and compared to the quantitative descriptive analysis (QDA) measured by the trained sensory panel. Based on multivariate statistical analysis, data obtained by the PTR-MS system showed a better correlation to the outcome of the QDA than SPME–GC–MS, especially for the descriptive parameters “tomato fragrance” and “tomato flavor”. The great advantage of such an analytical system was the possibility to study the release kinetics of volatiles during eating and the possibility to consider volatile concentration similar to in vivo condition resulting to an improved characterization of the aroma profile.
Screening for new sources of resistance to Clavibacter michiganensis subsp. michiganensis (Cmm) in tomato
Sen, Y. ; Zhu, F. ; Vandenbroucke, H. ; Wolf, J.M. van der; Visser, R.G.F. ; Heusden, A.W. van - \ 2013
Euphytica 190 (2013)2. - ISSN 0014-2336 - p. 309 - 317.
bacterial canker - corynebacterium-michiganense - lycopersicon-esculentum - ssp michiganensis - seeds - pcr - quantification - crosses
Bacterial canker of tomato, caused by Clavibacter michiganensis subsp. michiganensis (Cmm), is considered the most serious bacterial threat, resulting in high damages in production areas. Worldwide, Cmm is subjected to quarantine regulations.There is no cultivar in market containing Cmm resistance genes. This project aimed to screen tomatoes or wild relatives of tomato for resistance to Cmm, to be used for starting breeding programs. We have screened 24 different wild accessions of tomato and found several new tolerant sources: Solanum pimpinellifolium GI.1554, S. parviflorum LA735 and S. parviflorum LA2072. We also confirmed the tolerance which was reported previously in S. peruvianum LA2157, S. peruvianum PI127829, S. peruvianum LA385, S. habrochaites LA407 and S. lycopersicum cv. IRAT L3. No immunity was found. Also accessions showing a low disease score still contained high titers of bacteria as determined by a dilution plating method, using tow selective media. These results were confirmed with a TaqMan real time PCR assay, which was developed to determine and quantify Cmm in planta
Tsw gene-based resistance is triggered by a functional RNA silencing suppressor protein of the Tomato spotted wilt virus
Ronde, D. de; Butterbach, P.B.E. ; Lohuis, H. ; Hedil, M. ; Lent, J.W.M. van; Kormelink, R.J.M. - \ 2013
Molecular Plant Pathology 14 (2013)4. - ISSN 1464-6722 - p. 405 - 415.
mediated plant transformation - capsicum-chinense - cell-death - disease-resistance - lycopersicon-esculentum - viral suppressors - sw-5 gene - potato - tospovirus - agrobacterium
As a result of contradictory reports, the avirulence (Avr) determinant that triggers Tsw gene-based resistance in Capsicum annuum against the Tomato spotted wilt virus (TSWV) is still unresolved. Here, the N and NSs genes of resistance-inducing (RI) and resistance-breaking (RB) isolates were cloned and transiently expressed in resistant Capsicum plants to determine the identity of the Avr protein. It was shown that the NSsRI protein triggered a hypersensitive response (HR) in Tsw-containing Capsicum plants, but not in susceptible Capsicum, whereas no HR was discerned after expression of the NRI/RB protein, or when NSsRB was expressed. Although NSsRI was able to suppress the silencing of a functional green fluorescence protein (GFP) construct during Agrobacterium tumefaciens transient assays on Nicotiana benthamiana, NSsRB had lost this capacity. The observation that RB isolates suppressed local GFP silencing during an infection indicated a recovery of RNA silencing suppressor activity for the NSs protein or the presence of another RNA interference (RNAi) suppressor. The role of NSs as RNA silencing suppressor and Avr determinant is discussed in the light of a putative interplay between RNAi and the natural Tsw resistance gene
Rapid tomato volatile profiling by using proton-transfer reaction mass spectrometry (PTS-MS)
Farneti, B. ; Cristescu, S.M. ; Costa, G. ; Harren, F.J.M. ; Woltering, E.J. - \ 2012
Journal of Food Science 77 (2012)5. - ISSN 0022-1147 - p. C551 - C559.
electronic nose - lycopersicon-esculentum - quality attributes - organic-compounds - flavor compounds - aroma volatiles - kidney beans - shelf-life - cultivars - harvest
The availability of rapid and accurate methods to assess fruit flavor is of utmost importance to support quality control especially in the breeding phase. Breeders need more information and analytical tools to facilitate selection for complex multigenic traits such as flavor quality. In this study, it is shown that proton-transfer reaction mass spectrometry (PTR-MS) is a suitable method to monitor at high sensitivity the emission of volatiles determining the tomato aromatic profile such as hexanal, hexenals, methanol, ethanol, and acetaldehyde. The volatiles emitted by 14 tomato varieties (at red stage) were analyzed by 2 solvent-free headspace methods: solid-phase microextraction/gas chromatography MS and PTR-MS. Multivariate statistics (principal component analysis and cluster analysis) of the PTR-MS results allow an unambiguous separation between varieties, especially with a clear fingerprinting separation between the different tomato types: round truss, cocktail, and cherry tomatoes. PTR-MS was also successfully used to monitor the changes in volatile profiles during postharvest ripening and storage.
Prediction of sweet pepper (Capsicum annuum) flavour over different harvests
Eggink, P.M. ; Maliepaard, C.A. ; Tikunov, Y.M. ; Haanstra, J.P.W. ; Pohu-Flament, L.M.M. ; Wit-Maljaars, S.C. de; Willeboordse-Vos, F. ; Bos, S. ; Benning-de Waard, C. ; Grauw-van Leeuwen, P.J. de; Freymark, G. ; Bovy, A.G. ; Visser, R.G.F. - \ 2012
Euphytica 187 (2012)1. - ISSN 0014-2336 - p. 117 - 131.
lycopersicon-esculentum - chemical-composition - volatile compounds - metabolomics - tomatoes
To better understand and predict the complex multifactorial trait flavor, volatile and non-volatile components were measured in fresh sweet pepper (Capsicum annuum) fruits throughout the growing season in a diverse panel of 24 breeding lines, hybrids, several cultivated genotypes and one gene bank accession. Biochemical profiles were linked to individual flavor attributes, that were objectively quantified by a trained descriptive expert panel. We used a Random Forest regression approach for prediction of the flavor attributes within and between harvests. Predictions of texture related attributes (juiciness, toughness, crunchiness and stickiness of the skin) and sweetness were good (around 60–65 %in the analyses with the three harvests combined). The predictions of the attributes aroma intensity, sourness and fruity/apple were somewhat lower and more variable between harvests. (E)-2-hexen-1-ol, neopentane, p-menth-1-en-9-al, 3-hepten-2-one, (Z)-b-ocimene, (Z)-2-penten-1-ol, 1-methyl-1,4-cyclohexadiene, glucose, fructose and three unknown volatile compounds were identified as key-metabolites involved in the flavor differences between both genotypes and harvests. The complex nature of flavor is exemplified by the observed masking effect of fructose and other sugars on sourness and sourness related metabolites, like citrate. The knowledge obtained from the overall biochemical, sensory and prediction analyses forms a basis for targeted flavor improvement by breeding.
Auxin-induced Fruit Set in Capsicum annuum L. Requires Downstream Gibberellin Biosynthesis
Tiwari, A. ; Offringa, R. ; Heuvelink, E. - \ 2012
Journal of Plant Growth Regulation 31 (2012)4. - ISSN 0721-7595 - p. 570 - 578.
plant-growth regulators - pisum-sativum - sweet-pepper - lycopersicon-esculentum - unpollinated ovaries - tomato fruits - pod wall - parthenocarpy - arabidopsis - metabolism
A hierarchical scheme for the central role of the plant hormones auxin and gibberellins in fruit set and development has been established for the model plants Arabidopsis and tomato. In the fruit crop Capsicum annuum, the importance of auxin as an early signal in fruit set has also been recognized; however, the effect of gibberellins and their interaction with auxin has not yet been studied. The aim of this study was to determine the role of gibberellin and the hierarchy between auxin and gibberellin. We applied gibberellin alone or in combination with auxin or with the gibberellin biosynthesis inhibitor paclobutrazol on stigmas of emasculated flowers. Gibberellin application enhanced fruit set, whereas application of paclobutrazol reduced fruit set. The effect of paclobutrazol treatment could be counteracted by coapplication of gibberellin but not by auxin. These results indicate that in C. annuum, like in Arabidopsis and tomato, auxin is the major inducer of fruit set that acts in part by inducing gibberellin biosynthesis. Interestingly, gibberellin does not significantly contribute to the final fruit size but seems to play an important role in preventing flower and fruit abscission, a major determinant of production loss in C. annuum. At the same time, gibberellin together with auxin seems to balance cell division and cell expansion during fruit growth.
Structural homology in the Solanaceae: analysis of genomic regions in support of synteny studies in tomato, potato and pepper
Peters, S.A. ; Bargsten, J.W. ; Szinay, D. ; Belt, J. van de; Visser, R.G.F. ; Bai, Y. ; Jong, H. de - \ 2012
The Plant Journal 71 (2012)4. - ISSN 0960-7412 - p. 602 - 614.
genetic-linkage map - chromosomal rearrangements - lycopersicon-esculentum - solanum-lycopersicoides - repetitive sequences - mammalian evolution - resistance - fish - recombination - organization
We have analysed the structural homology in euchromatin regions of tomato, potato and pepper with special attention for the long arm of chromosome 2 (2L). Molecular organization and colinear junctions were delineated using multi-color BAC FISH analysis and comparative sequence alignment. We found large-scale rearrangements including inversions and segmental translocations that were not reported in previous comparative studies. Some of the structural rearrangements are specific for the tomato clade, and differentiate tomato from potato, pepper and other Solanaceous species. Although local gene vicinity is largely preserved, there are many small-scale synteny perturbations. Gene adjacency in the aligned segments was frequently disrupted for 47% of the ortholog pairs as a result of gene and LTR retrotransposon insertions, and occasionally by single gene inversions and translocations. Our data also suggests that long distance intra-chromosomal rearrangements and local gene rearrangements have evolved frequently during speciation in the Solanum genus, and that small changes are more prevalent than large-scale differences. The occurrence of sonata and harbinger transposable elements and other repeats near or at junction breaks is considered in the light of repeat-mediated rearrangements and a reconstruction scenario for an ancestral 2L topology is discussed.
The tomato genome sequence provides insights into fleshy fruit evolution
Sato, S. ; Tabata, S. ; Hirakawa, H. ; Klein Lankhorst, R.M. ; Jong, H. de; Ham, R.C.H.J. van; Datema, E. ; Smit, S. ; Schijlen, E.G.W.M. ; Haarst, J.C. van; Peters, S.A. ; Henkens, M.H.C. ; Staveren, M.J. van; Mooijman, P.J.W. ; Hesselink, T. ; Belt, J. van de; Szinay, D. ; Bai, Y. ; Visser, R.G.F. - \ 2012
Nature 485 (2012). - ISSN 0028-0836 - p. 635 - 641.
lycopersicon-esculentum - gene - diversification - arabidopsis - patterns - ortholog - history - sorghum - potato
Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.
Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations
Uwimana, B. ; Smulders, M.J.M. ; Hooftman, D.A.P. ; Hartman, Y. ; Tienderen, P.H. van; Jansen, J. ; McHale, L.K. ; Michelmore, R. ; Visser, R.G.F. ; Wiel, C.C.M. van de - \ 2012
BMC Plant Biology 12 (2012). - ISSN 1471-2229
quantitative trait loci - genetically-engineered organisms - gene flow - qtl analysis - lycopersicon-esculentum - domestication traits - helianthus-paradoxus - sunflower hybrids - field conditions - mixed models
After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F1 hybrid was backcrossed to L. serriola to generate BC1 and BC2 populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC1S1 and BC2S1). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). Results Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC1S1 and BC2S1 hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC1 and BC2 hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. Conclusion As it was shown that the crop contributed QTLs with either a positive or a negative effect on plant vigour, we hypothesize that genomic regions exist where transgenes could preferentially be located in order to mitigate their persistence in natural populations through genetic hitchhiking.
Penalized regression techniques for modeling relationships between metabolites and tomato taste attributes
Menendez, P. ; Eilers, P. ; Tikunov, Y.M. ; Bovy, A.G. ; Eeuwijk, F. van - \ 2012
Euphytica 183 (2012)3. - ISSN 0014-2336 - p. 379 - 387.
lycopersicon-esculentum - nonvolatile components - organoleptic quality - selection - flavor - volatiles - lasso - identification - cultivars - traits
The search for models which link tomato taste attributes to their metabolic profiling, is a main challenge within the breeding programs that aim to enhance tomato flavor. In this paper, we compared such models calculated by the traditional statistical approach, stepwise regression, with models obtained by the new generation of regression techniques, known as penalized regression or regularization methods. In addition, for penalized regression, different scenarios and various model selection criteria were discussed to conclude that classical crossvalidation, selects models with many superfluous variables whereas model selection criteria such as Bayesian information criterion, seem to be more suitable, when the goal is to find parsimonious models, to explain tomato taste attributes based on metabolic information. An exhaustive comparison of the discussed methodology was done for six sensory traits, showing that the most important covariates were identified by the stepwise regression as well as by some of the penalized regression methods, despite the general disagreement on the size of the regression coefficients between them. In particular, for stepwise regression the coefficients are inflated due to their high variance which is not the case with penalized regression, showing that this new methodology, can be an alternative to obtain more accurate models.
GLYCOALKALOID METABOLISM1 Is Required for Steroidal Alkaloid Glycosylation and Prevention of Phytotoxicity
Itkin, M. ; Rogachev, I. ; Alkan, N. ; Rosenberg, T. ; Malitsky, S. ; Masini, L. ; Meir, S. ; Lijima, Y. ; Aoki, K. ; Vos, R.C.H. de; Prusky, D. ; Beekwilder, M.J. ; Aharoni, A. - \ 2011
The Plant Cell 23 (2011)12. - ISSN 1040-4651 - p. 4507 - 4525.
campestris pv. vesicatoria - induced membrane disruption - alpha-tomatine - saponin biosynthesis - lycopersicon-esculentum - solanum-tuberosum - mass-spectrometry - gene-expression - plant - fruit
Steroidal alkaloids (SAs) are triterpene-derived specialized metabolites found in members of the Solanaceae family that provide plants with a chemical barrier against a broad range of pathogens. Their biosynthesis involves the action of glycosyltransferases to form steroidal glycoalkaloids (SGAs). To elucidate the metabolism of SGAs in the Solanaceae family, we examined the tomato (Solanum lycopersicum) GLYCOALKALOID METABOLISM1 (GAME1) gene. Our findings imply that GAME1 is a galactosyltransferase, largely performing glycosylation of the aglycone tomatidine, resulting in SGA production in green tissues. Downregulation of GAME1 resulted in an almost 50% reduction in a-tomatine levels (the major SGA in tomato) and a large increase in its precursors (i.e., tomatidenol and tomatidine). Surprisingly, GAME1-silenced plants displayed growth retardation and severe morphological phenotypes that we suggest occur as a result of altered membrane sterol levels caused by the accumulation of the aglycone tomatidine. Together, these findings highlight the role of GAME1 in the glycosylation of SAs and in reducing the toxicity of SA metabolites to the plant cell.
Identification of Genes in the Phenylalanine Metabolic Pathway by Ectopic Expression of a MYB Transcription Factor in Tomato Fruit
Cin, V. Dal; Tieman, D.M. ; Tohge, T. ; McQuinn, R. ; Vos, C.H.R. de; Osorio, S. ; Schmelz, E.A. ; Taylor, M.G. ; Smits-Kroon, M.T. ; Schuurink, R.C. ; Haring, M.A. ; Giovannoni, J. ; Fernie, A.R. ; Klee, H.J. - \ 2011
The Plant Cell 23 (2011)7. - ISSN 1040-4651 - p. 2738 - 2753.
chromatography-mass spectrometry - prephenate aminotransferase - amino-acids - lycopersicon-esculentum - arabidopsis-thaliana - escherichia-coli - microarray data - cell-cultures - biosynthesis - arogenate
Altering expression of transcription factors can be an effective means to coordinately modulate entire metabolic pathways in plants. It can also provide useful information concerning the identities of genes that constitute metabolic networks. Here, we used ectopic expression of a MYB transcription factor, Petunia hybrida ODORANT1, to alter Phe and phenylpropanoid metabolism in tomato (Solanum lycopersicum) fruits. Despite the importance of Phe and phenylpropanoids to plant and human health, the pathway for Phe synthesis has not been unambiguously determined. Microarray analysis of ripening fruits from transgenic and control plants permitted identification of a suite of coregulated genes involved in synthesis and further metabolism of Phe. The pattern of coregulated gene expression facilitated discovery of the tomato gene encoding prephenate aminotransferase, which converts prephenate to arogenate. The expression and biochemical data establish an arogenate pathway for Phe synthesis in tomato fruits. Metabolic profiling and 13C flux analysis of ripe fruits further revealed large increases in the levels of a specific subset of phenylpropanoid compounds. However, while increased levels of these human nutrition-related phenylpropanoids may be desirable, there were no increases in levels of Phe-derived flavor volatiles.
Diversity between and within farmers’ varieties of tomato from Eritrea
Asgedom, S. ; Vosman, B. ; Esselink, D. ; Struik, P.C. - \ 2011
African journal of biotechnology 10 (2011)12. - ISSN 1684-5315 - p. 2193 - 2200.
simple sequence repeat - ssr-markers - lycopersicon-esculentum - genetic-variation - polymorphic dna - identification - regions - plants - aflp - l.
Tomato yields in Eritrea are low (15 Mg/ha) compared with 19 Mg/ha in Africa and 27 Mg/ha worldwide. This is partly caused by poor quality of varieties used. This study analysed the diversity among and heterogeneity within farmers’ varieties of tomato from Eritrea and compared these varieties with other African and Italian varieties. Fifteen simple sequence repeat (SSR) markers were used for the genetic analysis. Genetic similarities among the varieties were calculated and an Unweighted Pair Group Method with Arithmetic Mean analysis was performed. Furthermore, individual plants of varieties were genotyped to evaluate uniformity within varieties. A high degree of diversity was observed among the Eritrean varieties. Thirteen out of the 15 SSRs were polymorphic, with 2 to 5 alleles per marker. The dendrogram showed two major types of varieties: San-Marzano and Marglob. Eritrean varieties were closely related to old Italian varieties in both types. Analysis of the within-variety variation showed that the Eritrean tomato genotypes were less uniform than the other varieties, probably because of deliberate mixing. A survey among farmers showed that some of them purposely mixed seeds to prolong the harvesting period, for yield stability and stress tolerance. Farmers value ‘new material’ as a source of influx
Seedling salt tolerance in tomato
Junming Li, J. ; Liu, L. ; Bai, Y. ; Zhang, Pujuan ; Finkers, H.J. ; Du, Y. ; Visser, R.G.F. ; Heusden, A.W. van - \ 2011
Euphytica 178 (2011)3. - ISSN 0014-2336 - p. 403 - 414.
quantitative trait loci - introgression line population - lycopersicon-esculentum - vegetative growth - cultivated tomato - bacterial canker - qtl analysis - fruit yield - germination - salinity
Soils with higher concentrations of salt are becoming more and more a constraint for many crops to obtain high yields. Wild tomato species, adapted to adverse environments, are a potential reservoir for genes underlying quantitative trait loci (QTL) related to salt tolerance in tomato. In this study two introgression line (IL) libraries derived from two different wild species, Solanum pennellii LA716 and Solanum lycopersicoides LA2951, were used to identify QTLs for salt tolerance in the seedling stage. In the S. pennellii IL library, four major QTLs were identified on chromosomes 6, 7 and 11. In the S. lycopersicoides IL library, six major QTLs were discovered which are located on chromosomes 4, 6, 9 and 12. Co-localization of QTLs on chromosome 6 in the two IL libraries and previously reports hinted that this locus might be conserved in the tomato crop. Three S. pennellii ILs (IL6-2, IL7-1 and IL7-5) harboring QTLs on chromosome 6 and 7 were crossed. Semi-dominance and dominance were shown for these three QTLs, and non-additive and epistatic interactions between them were observed
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