Advertisement

Physical Mapping of the Arabidopsis thaliana Genome

  • Melanie Stammers
  • Renate Schmidt
  • Caroline Dean
Part of the Stadler Genetics Symposia Series book series (SGSS)

Abstract

Arabidopsis thaliana has been adopted by the plant community as a model system for studying plants using a molecular approach. Arabidopsis is well suited to conventional genetics because it has a short life cycle, is small and has a prolific seed set (Meyerowitz, 1987). It has one of the smallest known genomes with a remarkably low content of interspersed repetitive DNA (Meyerowitz, 1987; Pruitt and Meyerowitz, 1986) making it eminently suitable for molecular studies.

Keywords

Arabidopsis Genome Centromeric Heterochromatin Chromosome Walking Arabidopsis Chromosome Columbia Ecotype 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Albini, S.M., 1994, A karyotype of the Arabidopsis thaliana genome derived from synaptonemal complex analysis at prophase I of meiosis, Plant J. 5: 665.CrossRefGoogle Scholar
  2. Arumuganathan, K., and Earle, ED., 1991, Nuclear DNA content of some important plant species, Plant. Mol. Biol. Rep. 9: 208.CrossRefGoogle Scholar
  3. Bennett, M.D., and Smith, J.B., 1976, Nuclear DNA amounts in angiosperms, Phil. Trans. R. Soc. Lond. 274: 227.CrossRefGoogle Scholar
  4. Chang, C., Bowman, J.L, DeJohn, A.W., Lander, ES., and Meyerowitz, E.M., 1988, Restriction fragment length polymorphism linkage map for Arabidopsis thaliana, Proc. Natl. Acad. Sci. USA 85: 6856.PubMedCrossRefGoogle Scholar
  5. Chowdhury, V., Olds, R.J., Lane, D.A., Conard, J., Pabinger, I., Ryan, K., Bauer, K.A., Bhavnani, M., Abildgaard, U., Finazzi, G., Castaman, G., Mannucci, P.M., and Thein, S.L, 1993, Identification of nine novel mutations in type I antithrombin deficiency by heteroduplex screening, British J. Haem. 84: 656.CrossRefGoogle Scholar
  6. Civardi, L, Xia, Y., Edwards, K.J., Schnable, P.S., and Nikolau, B.J., 1994, The relationship between the genetic and physical distances in the cloned alsh2 interval of the Zea mays L genome, Proc. Natl. Acad. Sci. USA 91: 8268.PubMedCrossRefGoogle Scholar
  7. Copenhaver, G.P., and Pikaard, C.S., 1995, Genetic and physical mapping of the nucleolus variant rRNA genes at NOR2 and NOR4 using 1- and 2dimensional pulsed-field gel analysis, Mol. Cell. Biol. (In Press)Google Scholar
  8. Creusot, F., Billault, A., Bouchez, D., Caboche, M., Camilleri, C., Chaboute, M.E, Cohen, D., Dron, M., Durr, A., Feltrin, P., Fleck, J., Fovilloux, E, Gigot, C., Lafleuriel, J., Ougen, P., Perrot, V., Picard, G., and Saumier, M., 1994, Construction of a large insert YAC library of Arabidopsis thaliana, Fourth International Congress of Plant Molecular Biology no.88.(Abstract)Google Scholar
  9. Dolezal, O., and Cobbett, C.S., 1991, Arabinose kinase-deficient mutant of Arabidopsis thaliana, Plant Physiol. 96: 1255.PubMedCrossRefGoogle Scholar
  10. Ecker, J.R, 1990, PFGE and YAC analysis of the Arabidopsis genome, Methods 1: 186.CrossRefGoogle Scholar
  11. Francis, D.M., Hulbert, S.H., and Michelmore, R.W., 1990, Genome size and complexity of the obligate fungal pathogen Bremia lactucae, Exp. Mycol. 14: 299.CrossRefGoogle Scholar
  12. Galbraith, D.W„ Harkins, K.R., and Knapp, S., 1991, Systemic Endopolyploidy in Arabidopsis thaliana, Plant Physiol. 96: 985.CrossRefGoogle Scholar
  13. Ganal, M.W., Young, N.D., and Tanksley, S.D., 1989, Pulsed field electrophoresis andphysical mapping of large DNA fragments in the Tm-2a region of chromosome 9 in tomato, Mol. Gen. Genet. 215: 395.CrossRefGoogle Scholar
  14. Greenwald, I., Coulson, A., Sulston, J., and Priess, J., 1987, Correlation of the physical and genetic maps in the lin-12 region of Caenorhabditis elegans, Nucl. Acids Res. 15: 2295.PubMedCrossRefGoogle Scholar
  15. Grill, E, and Somerville, C., 1991, Construction and characterization of a yeast artificial chromosome library of Arabidopsis which is suitable for chromosome walking, Mol. Gen. Genet. 226: 484.PubMedCrossRefGoogle Scholar
  16. Gustafson, J.P., and Dille, J.E, 1992, Chromosome location of Oryza sativa recombination linkage groups, Proc. Natl. Acad. Sci. USA 89: 8646.PubMedCrossRefGoogle Scholar
  17. Hauge, B.M., Giraudat, J., Hanley, S., Hwang, I., Kochi, T., and Goodman, H.M., 1991, Physical Mapping of the Arabidopsis genome and its applications, in: Plant Molecular Biology, edited by Herman, R.G., ed., Plenum, New York.Google Scholar
  18. Heslop-Harrison, J.S., and Schwarzacher, T., 1990, The ultrastructure of Arabidopsis thaliana chromosomes, Fourth International Conference on Arabidopsis Research (Abstract)Google Scholar
  19. Hofte, H., Desprez, T., Amselem, J., Chiapello, H., and Caboche, M., 1993, An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana, Plant J. 4: 1051.PubMedCrossRefGoogle Scholar
  20. Koncz, C., Mayerhofer, R., KonczKalman, Z., Nawrath, C., Reiss, B., Redei, G.P., and Schell,J., 1990, Isolation of a gene encoding a novel chloroplast protein by T-DNA tagging in Arabidopsis thaliana, EMBO J. 9: 1337PubMedGoogle Scholar
  21. Konieczny, A., and Ausubel, F.M., 1993, A procedure for mapping Arabidopsis thaliana mutations using co-dominant ecotype-specific PCR-based markers, Plant J. 4 (2): 403.PubMedCrossRefGoogle Scholar
  22. Laibach, F., 1907, Zur fragr nach der individualitat der chromosomen im pflanzenreich, Beih. Bot. Cbl. (1 abt.) 22: 19.Google Scholar
  23. Leutwiler, LS., Hough-Evans, B.R., and Meyerowitz, EM., 1984, The DNA of Arabidopsis thaliana, Mol. Gen. Genet. 194: 15.CrossRefGoogle Scholar
  24. Lister, C., and Dean, C., 1993, Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana, Plant J. 4: 745.CrossRefGoogle Scholar
  25. Little, R.D., Pilia, G., Johnson, S., D’Urso, M., and Schlessinger, D., 1992, Yeast artificial artificial chromosomes spanning 8 megabases and 10–15 centimorgans of human cytogenetic band Xq26, Proc. Natl. Acad. Sci. USA 89: 177.PubMedCrossRefGoogle Scholar
  26. Maluszynska, J., and Heslop-Harrison, J.S., 1991, Localization of tandemly repeated DNA sequences in Arabidopsis thaliana, Plant J. 1: 159.CrossRefGoogle Scholar
  27. Martinez-Zapater, J.M., Estelle, M.A., and Somerville, C.R., 1986, A highly repeated DNA sequence un Arabidopsis thaliana, Mol. Gen. Genet. 204: 417.CrossRefGoogle Scholar
  28. Meyerowitz, EM., 1987, Arabidopsis thaliana, Ann.Rev.Gen. 21: 93.CrossRefGoogle Scholar
  29. Meyerowitz, EM., 1992, Introduction to the Arabidopsis genome, in: Methods in Arabidopsis Research, C. Koncz, N-H. Chua, and J. Schell (ed), World Scientific, Singapore.p. 100.Google Scholar
  30. Nam, 11.-G., Giraudat, J., den Boer, B., Moonan, F., Loos, W.D.B., Hauge, B.M., and Goodman, H.M., 1989, Restriction fragment length polmorphism linkage map of Arabidopsis thaliana, Plant Cell 1: 699.Google Scholar
  31. Newman, T., de Bruijn, F., Green, P., Keegstra, K., Kende, H., McIntosh, L, and Ohlrogge, J., 1994, Genes Galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous cDNA clones, Plant Physiol. 106: 1241.PubMedCrossRefGoogle Scholar
  32. Oliver, S.G., van der Aart, QJ.M., Agostoni-Carbone, M.L, Aigle, M., Alberghina, L, et al., 1992, The complete DNA sequence of yeast chromosome 111, Nature 357: 38.PubMedCrossRefGoogle Scholar
  33. Orita, M., Iwahana, H., Kanazawa, H., Hayashi, K., and Sekiya, T., 1989, Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms, Proc. Natl. Acad. Sci. USA 86: 2766.PubMedCrossRefGoogle Scholar
  34. Pruitt, R.E., and Meyerowitz, E.M., 1986, Characterisation of the genome of Arabidopsis thaliana, J.Mol.Biol 187: 169.PubMedCrossRefGoogle Scholar
  35. Richards, E.J., and Ausubel, F.M., 1988, Isolation of a higher eukaryotic telomere from Arabidopsis thaliana, Cell 53: 127.PubMedCrossRefGoogle Scholar
  36. Schmidt, R., Putterill, J., West, J., Cnops, G., Robson, F., Coupland, G., and Dean, C., 1994, Analysis of clones carrying repeated DNA sequences in two YAC libraries of Arabidopsis thaliana, Plant J. 5: 735.PubMedCrossRefGoogle Scholar
  37. Schweizer, D., Ambros, P., Gründler, P., and Varga, F., 1987, Attempts to relate cytological and molecular chromosome data of Arabidopsis thaliana to its genetic linkage map, Arabidopsis Information Service 25: 27.Google Scholar
  38. Segal, G., Sarfatti, M., Schaffer, M.A., Ori, N., Zamir, D., and Fluhr, R., 1992, Correlation of genetic and physical structure in the region surrounding the I2 Fusarium oxyspoprum resistance locus in tomato, Mol. Gen. Genet. 231: 179.PubMedGoogle Scholar
  39. Simchen, G., and Starnberg, J., 1969, Fine and course controls of genetic recombination, Nature 222: 329.PubMedCrossRefGoogle Scholar
  40. Simoens, C.R., Gielen, J., Van Montagu, M., and Inze, D., 1988, Characterization of highly repetitive sequences of Arabidopsis thaliana, Nucl.Acids Res. 16: 6753.PubMedCrossRefGoogle Scholar
  41. Steinmetz, M., Stephan, D., and Fischer Lindahl, K., 1986, Gene organisation and recombination hotspots in the murine major histocompatibility complex, Cell 44: 895.PubMedCrossRefGoogle Scholar
  42. Symington, LS., and Petes, T.D., 1988, Expansions and contractions of the genetic map relative to the physical map of yeast chromosome III, MoL Cell BioL 8: 595.PubMedGoogle Scholar
  43. Tanksley, S.D., Ganal, M.W., Prince, J.P., de Vincente, 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, RA., Wu, W., and Young, N.D., 1992, High density molecular linkage maps of the tomato and potato genomes, Genetics 132: 1141.PubMedGoogle Scholar
  44. Ward, ER, and Jen, G.C., 1990, Isolation of single-copy-sequence clones from a yeast artificial chromosome library of randomly-sheared Arabidopsis thaliana DNA, Plant Mol. Biol. 14: 561.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1996

Authors and Affiliations

  • Melanie Stammers
    • 1
  • Renate Schmidt
    • 1
  • Caroline Dean
    • 1
  1. 1.Department of Molecular Genetics, BBSRCJohn Innes CentreNorwichUK

Personalised recommendations