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Multi-functional T-DNA/Ds tomato lines designed for gene cloning and molecular and physical dissection of the tomato genome

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Abstract

In order to make the tomato genome more accessible for molecular analysis and gene cloning, we have produced 405 individual tomato (Lycopersicon esculentum) lines containing a characterized copy of pJasm13, a multifunctional T-DNA/modifiedDs transposon element construct. Both the T-DNA and the Ds element in pJasm13 harbor a set of selectable marker genes to monitor excision and reintegration of Ds and additionally, target sequences for rare cutting restriction enzymes (I-PpoI, SfiI, NotI) and for site-specific recombinases (Cre, FLP, R). Blast analysis of flanking genomic sequences of 174 T-DNA inserts revealed homology to transcribed genes in 69 (40%), of which about half are known or putatively identified as genes and ESTs. The map position of 140 individual inserts was determined on the molecular genetic map of tomato. These inserts are distributed over the 12 chromosomes of tomato, allowing targeted and non-targeted transposon tagging, marking of closely linked genes of interest and induction of chromosomal rearrangements including translocations or creation of saturation-deletions or inversions within defined regions linked to the T-DNA insertion site. The different features of pJasm13 were successfully tested in tomato and Arabidopsis thaliana, thus providing a new tool for molecular/genetic dissection studies, including molecular and physical mapping, mutation analysis and cloning strategies in tomato and potentially, in other plants as well.

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References

  • Albert, H., Dale, E.C. and Ow. D.W. 1995. Site-specific integration of DNA into wild type and mutant lox sites placed in the plant genome. Plant J. 7: 649–659.

    Google Scholar 

  • Carroll, B.J., Klimyuk, V.I., Thomas, C.M., Bishop, G.J., Harrison, K., Scofield, S.R. and Jones, J.D.G. 1995. Germinal transpositions of the maize element Dissociation from T-DNA loci in tomato. Genetics 139: 407–420.

    Google Scholar 

  • Chang, A.C.Y. and Cohen, S.N. 1978. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the p15A cryptic miniplasmid. J. Bacteriol. 134: 1141–1156.

    Google Scholar 

  • Chuck, G., Robbins, T., Nijjar, C., Ralston, E., Courtney-Gutterson, N and Dooner H.K. 1993. Tagging and cloning of a petunia flower color gene with the maize transposable element Activator. Plant Cell 5: 371–378.

    Google Scholar 

  • Cooley, MB., Goldsbrough, A.P., Still, D.W. and Yoder J.I. 1996. Site-selected insertional mutagenesis of tomato with maize Ac and Ds elements. Mol. Gen. Genet. 252: 184–194.

    Google Scholar 

  • Danielsen, S., Kilstrup, M., Barilla, K., Jochimsen, B. and Neuhard, J. 1992. Characterization of the Escherichia coli CodBA operon encoding cytosine permease and cytosine deaminase. Mol. Microbiol. 6: 1335–1344.

    Google Scholar 

  • De Block, M., Botterman, J., Vandeweile, M., Dockx, J., Thoen, C., Gossele, V., Thompson, C., Van Montagu, M. and Leemans, J. 1987. Engineering herbicide resistant plants by expression of a detoxifying enzyme. EMBO J. 6: 2513–2518.

    Google Scholar 

  • Dellaporta, S.L., Wood, J. and Hicks, J.B. 1983. A plant DNA minipreparation: version II. Plant Mol. Biol. Rep. 1: 19–21.

    Google Scholar 

  • DeRisi, J. and Iyer, V. 1999. Genomics and array technology. Curr. Opin. Oncol. 11: 76–79.

    Google Scholar 

  • Emmanuel, E. and Levy, A.A. 2002. Tomato mutants as tools for functional genomics. Curr. Opin. Plant Biol. 5: 112–117.

    Google Scholar 

  • Eshed, Y. and Zamir, D. 1994. A genomic library of Lycopersicon pennellii in L. esculentum: a tool for fine mapping of genes. Euphytica 79: 175–179.

    Google Scholar 

  • Izawa, T., Ohnishi, T., Nakano, T., Ishida, N., Enoki, H., Hashimoto, H., Itoh, K., Terada, R., Wu, C., Miyazaki, C., Endo, T., Iida, S. and Shimamoto, K. 1997. Transposon tagging in rice. Plant Mol. Biol. 35: 219–229.

    Google Scholar 

  • James, D.J., Lim, E., Keller, J., Plooy, I., Ralston, E. and Dooner, H.K. 1995. Directed tagging of the Arabidopsis Fatty Acid Elongation (FAE1) gene with the maize transposon Activator. Plant Cell 7: 309–319.

    Google Scholar 

  • Jones, D.A., Thomas, CMD., Hammond-Kosack, K.E., Balint-Kurti, P.J. and Jones J.D.G. 1994. Isolation of the tomato Cf-9 gene for resistance to Cladosporium fulvum by transposon tagging. Science 266: 789–792.

  • Kilby, N.J., Snaith, M.R. and Murray, J.A.H. 1993. Site-specific recombinases: tools for genome engineering. Trends Genet. 9: 413–421.

    Google Scholar 

  • Knapp, S., Larondelle, Y., Robert, M., Furtek, D. and Theres. K. 1994. Transgenic tomato lines containing Ds elements at defined genomic positions as tools for targeted transposon tagging. Mol. Gen. Genet. 243: 666–673.

    Google Scholar 

  • Koncz, C., Martini, N., Mayerhofer, R., Koncz-Kalman, Z., Korber, H., Redei, G.P. and Schell, J. 1989. High-frequency T-DNAmediated gene tagging in plants. Proc. Natl. Acad. Sci. USA 86: 8467–8471.

    Google Scholar 

  • Konieczny, A. and Ausubel, FM. 1993. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCRbased markers. Plant J. 4: 403–410.

    Google Scholar 

  • Koornneef, M., van Diepen, J.A.M., Hanhart, C.J., Kieboom-de Waart, A.C., Martinelli, L., Schoenmakers, H.C.H. and Wijbrandi, J. 1989. Chromosomal instability in cell-and tissue cultures of tomato haploids and diploids. Euphytica 43: 179–186.

    Google Scholar 

  • Koshinsky, H.A., Lee, E. and Ow, D.W. 2000. Cre-lox site-specific recombination between Arabidopsis and tobacco chromosomes. Plant J. 23: 715–722.

    Google Scholar 

  • Kunze, R. 1996. The maize transposable element Activator (Ac). Curr. Top. Micr. Imm. 204: 162–194.

    Google Scholar 

  • Levin, I., Gilboa, N., Yeselson, E., Shen, S. and Schaffer, A.A. 2000. Frg, a major locus that modulates fructose to glucose ratio in mature tomato fruits. Theor. Appl. Genet. 100: 256–262.

    Google Scholar 

  • Maes, T., De Keukeleire, P. and Gerats, T. 1999. Plant tagnology. Trends Plant Sci. 4: 90–96.

    Google Scholar 

  • Machida, C., Onouchi, H., Koizumi, J., Hamada, S., Semiarti, E., Torikai, S. and Machida, Y. 1997. Characterization of the transposition pattern of the Ac element in Arabidopsis thaliana using endonuclease I-SceI. Proc. Natl. Acad. Sci. USA 94: 8675–8680.

    Google Scholar 

  • Mandal, A., Lang, V., Orczyk, W. and Palva, E.T. 1993. Improved efficiency for T-DNA-mediated transformation and plasmid rescue in Arabidopsis thaliana. Theor. Appl. Genet. 86: 621–628.

    Google Scholar 

  • Marshall, S.W., Boocock, M.R. and Sherrat, D.J. 1992. Catalysis by site-specific recombinases. Trends Genet. 8: 432–439.

    Google Scholar 

  • McBride, K.E. and Summerfelt, K.R. 1990. Improved binary vectors for Agrobacterium-mediated plant transformation. Plant Mol. Biol. 14: 269–276.

    Google Scholar 

  • Medberry, S.L., Dale, E.C., Qin, M.M. and Ow, D.W. 1995. Intra-chromosomal rearrangement generated by site-specific recombination. Nucl. Acids Res. 23: 485–490.

    Google Scholar 

  • Meinke, D.W., Cherry, J.M., Dean, C., Rounsley, S.D. and Koornneef, M. 1998. Arabidopsis thaliana: a model plant for genome analysis. Science 282: 662–682.

    Google Scholar 

  • Meissner, R., Chague, V., Zhu, Q., Emmanuel, E., Elkind, Y. and Levy, A.A. 2000. A high throughput system for transposon tagging and promoter trapping in tomato. Plant J. 22: 265–274.

    Google Scholar 

  • Osborne, B.I., Wirtz, U. and Baker, B. 1995. A system for insertional mutagenesis and chromosomal rearrangement using the Ds transposon and Cre-lox. Plant J. 7: 687–701.

    Google Scholar 

  • Ow, D.W. 1996. Recombinase-directed chromosome engineering in plants. Curr. Opin. Biotechnol. 7: 181–186.

    Google Scholar 

  • Ow, D.W. and Medberry, S.L. 1995. Genome manipulation through site-specific recombination. Crit. Rev. in Plant Sciences 14: 239–261.

    Google Scholar 

  • Parinov, S., Sevugan, M., Ye, D., Yang, W-C., Kumaran, M. and Sundaresan, V. 1999. Analysis of flanking sequences from Dissociation insertion lines: a database for reverse genetics in Arabidopsis. Plant Cell 11: 2263–2270.

    Google Scholar 

  • Paterson, A.H., Lan, T.H., Reischmann, K.P., Chang, C., Lin, Y.R., Liu, S.C., Burow, M.D., Kowalski, S.P., Katsar, C.S., DelMonte, T.A., Feldmann, K.A., Schertz, K.F. and Wende, J.F. 1996. Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence. Nature Genet. 14: 380–382.

    Google Scholar 

  • Pillen, K., Alpert, K.B., Giovannoni, J.J., Ganal, M.W. and Tanksley, S.D. 1996. Rapid and reliable screening of a tomato YAC library exclusively based on PCR. Plant Mol. Biol. Rep. 14: 58–67.

    Google Scholar 

  • Qin, M., Lee, E., Zanke, T. and Ow, D.W. 1995. Site-specific cleavage of chromosomes in vitro through Cre-lox recombination. Nucl. Acids Res. 23: 1923–1927.

    Google Scholar 

  • Ramirez-Solis, R., Liu, P. and Bradley, A. 1995. Chromosome engineering in mice. Nature 378: 720–724.

    Google Scholar 

  • Rommens, C.M.T., Van der Biezen, E.A., Ouwerkerk, P.B.F., Nijkamp, H.J.J. and Hille, J. 1991. Ac-induced disruption of the double Ds structure in tomato. Mol. Gen. Genet. 228: 453–458.

    Google Scholar 

  • Rommens, C.M.T., van Haaren, M.J.J., Buchel, A.S., Mol, J.N.M., van Tunen, A.J., Nijkamp, H.J.J. and Hille, J. 1992. Trans activation of Ds by Ac-transposase gene fusions in tobacco. Mol. Gen. Genet. 231: 433–41.

    Google Scholar 

  • Sambrook, J., Fritsch, E.F. and Maniatis, T. 1989. Molecular cloning, a laboratory manual. Cold Spring Harbor, New York.

    Google Scholar 

  • Scofield, S.R., Harrison, K., Nurrish, S.J. and Jones, J.D.G. 1992. Promoter fusions to the Activator transposase gene cause distinct patterns of Dissociation excision in tobacco cotyledons. Plant Cell 4: 573–582.

    Google Scholar 

  • Somerville, C. and Somerville, S. 1999. Plant functional genomics. Science 285: 380–383.

    Google Scholar 

  • Stuurman, J., de Vroomen, M.J., Nijkamp, H.J.J. and van Haaren, M.J.J. 1996. Single-site manipulation of tomato chromosomes in vitro and in vivo using Cre-lox site-specific recombination. Plant Mol. Biol. 32: 901–913.

    Google Scholar 

  • Stuurman, J., Nijkamp, H.J.J. and van Haaren, M.J.J. 1998. Molecular insertion-site selectivity of Ds in tomato. Plant J. 14: 215–223.

    Google Scholar 

  • Tanksley, S.D., Ganal, M.W., Prince, J.P., DeVicente, M.C., Bonierbale, M.W., Broun, P., Fulton, T.M., Giovannoni, J.J., Grandillo, S., Martin, G.B., Messeguer, R., Miller, J.C., Miller, L., Paterson, A.H., Pineda, O., Roder, M.S., Wing, R.A., Wu, W. and Young, N.D. 1992. High density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141–1160.

    Google Scholar 

  • Tanksley, S.D., Ganal, M.W. and Martin, G.B. 1995. Chromosome landing: a paradigm for map-base gene cloning in plants with large genomes. Trends Genet. 11: 63–68.

    Google Scholar 

  • The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815.

    Google Scholar 

  • Van der Biezen, E.A., Cardol, E.F., Chung, H.Y., Nijkamp, H.J.J.and Hille, J. 1996. Frequency and distance of transposition of a modified Dissociation element in transgenic tobacco. Transgen. Res. 5: 343–357.

    Google Scholar 

  • van Haaren, M.J.J. and Ow, D.J. 1993. Prospects of applying a combination of DNA transposition and site-specific recombination in plants: a strategy for gene identification and cloning. Plant Mol. Biol. 23: 525–533.

    Google Scholar 

  • Vergunst, A.C. and Hooykaas, P.J.J. 1998. Cre/lox-mediated sitespecific integration of agrobacterium T-DNA in Arabidopsis thaliana by transient expression of Cre. Plant Mol. Biol. 38: 393–406.

    Google Scholar 

  • Walbot, V. 1992. Strategies for mutagenesis and gene cloning using transposon tagging and T-DNA insertional mutagenesis. Annu. Rev. Plant Physiol. 43: 49–82.

    Google Scholar 

  • Whitman, S., Dinesh-Kumar, S.P., Choi, D., Hehl, R., Corr, C. and Baker, B. 1994. The product of the Tobacco Mosaic Virus resistant gene N: similarity to toll and the interleukin-1 receptor. Cell 78: 1101–1115.

    Google Scholar 

  • Yen, H.C., Shelton, B.A., Howard, L.R., Lee, S., Vrebalov, J. and Jiovannoni, J.J. 1997. The tomato high-pigment (hp) locus maps to chromosome 2 and influences plastome copy number and fruit quality. 95: 1069–1079.

    Google Scholar 

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Authors and Affiliations

  1. Department of Plant Genetics, Institute of Field Crops, The Volcani Center, P.O. Box 6, Bet Dagan, 50250, Israel

    D. Gidoni, A. Mett, J. Feiler & I. Levin

  2. Institute for Genetics, University of Cologne, Cologne, Germany

    E. Fuss & K. Theres

  3. Max Planck Institute for Plant Breeding Research, Cologne

    E. Fuss, E. Fuss, K. Theres & K. Theres

  4. Department of Physiology and Environmental Science, Sutton Bonington Campus, The University of Nottingham, UK

    A. Burbidge & I.B. Taylor

  5. Keygene N.V., Agro Business Park 90, P.O. Box 216, NL-6700 AE, Wageningen, The Netherlands

    G-J. Speckmann, J. Groenendijk, M. de Both & M.J.J van Haaren

  6. Zeneca Plant Science, Jealott's Hill Research Station, Bracknell Berkshire, UK

    S. James, D. Leader & W. Schuch

  7. Department of Genetics, Free University of Amsterdam, The Netherlands

    D. Nijkamp, M.J. de Vroomen, T. Liharska, E. Coppoolse & J.J.M. Smit

  8. Institute for Molecular and Biological Sciences (IMBW), BioCentrum, Amsterdam, The Netherlands

    D. Nijkamp & M. Smoker

  9. Wheat Improvement Centre, Syngenta, Norwich Research Park, Colney, Norwich, NR4 7UH, UK

    D. Leader

  10. CellFor Inc, 355 Burrard Street, Vancouver, British Columbia, V6C 2G8, Canada

    W. Schuch

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  1. D. Gidoni
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  2. E. Fuss
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  3. A. Burbidge
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  4. G-J. Speckmann
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  5. S. James
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  6. D. Nijkamp
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  7. A. Mett
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  8. J. Feiler
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  9. M. Smoker
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  10. M.J. de Vroomen
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  11. D. Leader
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  12. T. Liharska
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  13. J. Groenendijk
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  14. E. Coppoolse
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  15. J.J.M. Smit
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  16. I. Levin
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  17. M. de Both
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  18. W. Schuch
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  19. J.D.G. Jones
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  20. I.B. Taylor
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  21. K. Theres
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  22. M.J.J van Haaren
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Gidoni, D., Fuss, E., Burbidge, A. et al. Multi-functional T-DNA/Ds tomato lines designed for gene cloning and molecular and physical dissection of the tomato genome. Plant Mol Biol 51, 83–98 (2003). https://doi.org/10.1023/A:1020718520618

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