Skip to main content
SpringerLink
Log in

Phenotyping of Arabidopsis Mutants for Developmental Effects of Gene Deletions

  • Protocol
Plant Signal Transduction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 479))

Abstract

With the completion of the Arabidopsis thaliana genome sequencing project the next major challenge is the assignment of biological functions to the more than 25,000 genes. Reverse genetics is a powerful tool to elucidate gene function in Arabidopsis. Increasingly sophisticated genetic approaches are being developed for reverse genetics with the long-term goal of understanding how the coordinated activity of all proteins rises to a complex organism. Identification of a biological function for each gene is often doomed to fail as many loss- or gain-of-function lines exhibit no obvious phenotypes under normal propagation conditions. Here we provide an overview on how to phenotype plants during their development. This phenotypic streamlined analysis is based on a series of defined growth stages (germination, seedling, vegetative, and reproductive stages), which can be used for the profiling of mutants.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. The Arabidopsis Genome Initiative (AGI) (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.

    Google Scholar 

  2. Alonso, J.M., and Ecker, J.R (2006) Moving forward in reverse: Genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nature Rev. Genet. 7, 524–536.

    Article  PubMed  CAS  Google Scholar 

  3. Østergaard, L., and Yanofsky, M.F. (2004) Establishing gene function by mutagenesis in Arabidopsis thaliana. Plant J. 39, 682–696.

    Article  PubMed  Google Scholar 

  4. Henikoff, S., Bradley, J.T., and Comai, L. (2004) TILLING. Traditional Mutagenesis Meets Functional Genomics. Plant Physiol. 135, 630–636.

    CAS  Google Scholar 

  5. Murashige, T., and Skoog, F. (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol. Plant. 15, 473–497.

    Article  CAS  Google Scholar 

  6. Gubler, F., Millar, A.A., and Jacobsen, J.V. (2005) Dormancy release, ABA and preharvest sprouting. Curr. Opin. Plant Biol. 8, 183–187.

    Article  PubMed  CAS  Google Scholar 

  7. Koornneef, M., Bentsink, L., and Hilhorst, H. (2002) Seed dormancy and germination. Curr. Opin. Plant Biol. 5, 33–36.

    Article  PubMed  CAS  Google Scholar 

  8. Razem, F.A., Baron, K., and Hill, R.D. (2006) Turning on gibberellin and abscisic acid signaling. Curr. Opin. Plant Biol. 9, 454–459.

    Article  PubMed  CAS  Google Scholar 

  9. Penfield, S., Graham, S., Graham, I.A. (2005) Storage reserve mobilization in germinating oilseeds: Arabidopsis as a model system. Biochem. Soc. Trans. 33, 380–383.

    Article  PubMed  CAS  Google Scholar 

  10. Footitt, S., Slocombe, S.P., Larner, V., Kurup, S., Wu, Y., Larson, T., Graham, I. , Baker, A., and Holdsworth, M. (2002) Control of germination and lipid mobilization by COMATOSE, the Arabidopsis homologue of human ALDP. EMBO J. 21, 2912–2922.

    Article  PubMed  CAS  Google Scholar 

  11. Vicente-Carbajosa, J., and Carbonero, P. (2005) Seed maturation: developing an intrusive phase to accomplish a quiescent state. Int.J. Dev. Biol. 49, 645–651.

    Article  PubMed  CAS  Google Scholar 

  12. Fankhauser, C., and Casal, J.J. (2004) Phenotypic characterization of a photomorphogenic mutant. Plant J. 39, 747–760.

    Article  PubMed  CAS  Google Scholar 

  13. Casimiro, I., Beeckman, T., Graham, N., Bhalerao, R, Zhang, H., Casero, P., Sandberg, G. and Bennett, M.J. (2003) Dissecting Arabidopsis lateral root development. Trends Plant Sci. 8,165–171.

    Article  PubMed  CAS  Google Scholar 

  14. Benfey, P.N., and Scheres, B. (2000) Root development. Curr. Biol. 10, R813–815.

    Article  PubMed  CAS  Google Scholar 

  15. Fukaki, H., Okushima, Y., and Tasaka, M. (2007) Auxin-mediated lateral root formation in higher plants. Int. Rev. Cytol. 256,111–137.

    Article  PubMed  CAS  Google Scholar 

  16. Schellmann, S., Hulskamp, M., and Uhrig, J. (2007) Epidermal pattern formation in the root and shoot of Arabidopsis. Biochem. Soc. Trans. 35,146–148.

    Article  PubMed  CAS  Google Scholar 

  17. Hermans, C., Hammond, J.P., White, P.J., and Verbruggen, N. (2006) How do plants respond to nutrient shortage by biomass allocation? Trends Plant Sci. 11,610–617.

    Article  PubMed  CAS  Google Scholar 

  18. Morita, M.T., and Tasaka, M. (2004) Gravity sensing and signaling. Curr. Opin. Plant Biol. 7, 712–718.

    Article  PubMed  CAS  Google Scholar 

  19. Stone, B.B., Esmon, C.A., and Liscum, E. (2005) Phototropins, other photoreceptors, and associated signaling: The lead and supporting cast in the control of plant movement responses. Curr. Top. Dev. Biol. 66,215–238.

    Article  PubMed  CAS  Google Scholar 

  20. Tsukaya, H. (2005) Leaf shape: genetic controls and environmental factors. Int. J. Dev. Biol. 49, 547–555.

    Article  PubMed  Google Scholar 

  21. Tsukaya, H. (2006) Mechanism of leaf shape determination. Annu. Rev. Plant Biol. 57, 477–496.

    Article  PubMed  CAS  Google Scholar 

  22. Tsukaya, H., Kozuka, T., and Kim, G.T. (2002) Genetic control of petiole length in Arabidopsis thaliana. Plant Cell Physiol. 43, 1221–1228.

    Article  PubMed  CAS  Google Scholar 

  23. Kim, G.T., Yano, S., Kozuka, T., and Tsukaya, H. (2005) Photomorphogenesis of leaves: shade-avoidance and differentiation of sun and shade leaves. Photochem. Photobiol. Sci. 4, 770–774.

    Article  PubMed  CAS  Google Scholar 

  24. Candela, H., Martinez-Laborda, A., and Micol, J.L. (1999) Venation pattern formation in Arabidopsis thaliana vegetative leaves. Dev. Biol. 205, 205–216.

    Article  PubMed  CAS  Google Scholar 

  25. Nadeau, J.A., and Sack, F.D. (2002) Control of stomatal distribution on the Arabidopsis leaf surface. Science 296, 1697–1700.

    Article  PubMed  CAS  Google Scholar 

  26. Horiguchi, G., Fujikura, U., Ferjani, A., Ishikawa, N., and Tsukaya, H. (2006) Large- scale histological analysis of leaf mutants using two simple leaf observation methods: Identification of novel genetic pathways governing the size and shape of leaves. Plant J. 48, 638–644.

    Article  PubMed  CAS  Google Scholar 

  27. Schellmann, S., and Hulskamp, M. (2005) Epidermal differentiation: trichomes in Arabidopsis as a model system. Int. J. Dev. Biol. 49, 579–584.

    Article  PubMed  Google Scholar 

  28. Chien, J.C., and Sussex, I.M. (1996) Differential regulation of trichome formation on the adaxial and abaxial leaf surfaces by gibberellins and photoperiod in Arabidopsis thaliana (L.) Heynh. Plant Physiol. 111, 1321–1328.

    Article  PubMed  CAS  Google Scholar 

  29. Arnon, D.I. (1949) Copper enzymes in isolated chloroplasts. Polyphenoloxidase in Beta vulgaris. Plant Physiol. 24,1–15.

    Article  CAS  Google Scholar 

  30. Miles, D. (1982) The use of mutations to probe photosynthesis in higher plants. In: Edelman, M., Hallick, R.B., and Chua, N.H., (eds.) Methods in Chloroplast Molecular Biology. Elsevier Biomedical Press, New York, pp. 75–107.

    Google Scholar 

  31. Lempe, J., Balasubramanian, S., Sureshkumar, S., Singh, A., Schmid, M., and Weigel, D. (2005) Diversity of flowering responses in wild Arabidopsis thaliana strains. PLoS Genet. 1, 109–118.

    Article  PubMed  CAS  Google Scholar 

  32. Baurle, I. and Dean, C. (2006) The timing of developmental transitions in plants. Cell 125, 655–664.

    Article  PubMed  CAS  Google Scholar 

  33. Ausin, I., Alonso-Bianco, C., and Martinez- Zapater, J.M. (2005) Environmental regulation of flowering. Int. J. Dev. Biol. 49, 689–705.

    Article  PubMed  CAS  Google Scholar 

  34. Boss, P.K., Bastow, R.M., Mylne, J.S., and Dean, C. (2004) Multiple pathways in the decision to flower: enabling, promoting, and resetting. Plant Cell 16(Suppl.), S18–S31.

    PubMed  CAS  Google Scholar 

  35. Corbesier, L., and Coupland, G. (2006) The quest for florigen: A review of recent progress./. Exp. Bot. 57, 3395–3403.

    Article  CAS  Google Scholar 

  36. Fleet, C.M. and Sun, T.P. (2005) A DELLA- cate balance: the role of gibberellin in plant morphogenesis. Curr. Opin. Plant Biol. 8, 77–85.

    Article  PubMed  CAS  Google Scholar 

  37. Schmitz, G. and Theres, K. (2005) Shoot and inflorescence branching. Curr. Opin. Plant Biol. 8, 506–511.

    Article  PubMed  CAS  Google Scholar 

  38. McSteen, P., and Leyser, O. (2005) Shoot branching. Annu. Rev. Plant Biol. 56, 353–374.

    Article  PubMed  CAS  Google Scholar 

  39. Leyser, O. (2005) The fall and rise of apical dominance. Curr. Opin. Genet. Dev. 15, 468–471.

    Article  PubMed  CAS  Google Scholar 

  40. Reinhardt, D. (2005) Phyllotaxis-a new chapter in an old tale about beauty and magic numbers. Curr. Opin. Plant Biol. 8,487–493.

    Article  PubMed  CAS  Google Scholar 

  41. Reinhardt, D. (2005) Regulation of phyllotaxis. Int. J. Dev. Biol. 49, 539–546.

    Article  PubMed  CAS  Google Scholar 

  42. Blazquez, M.A., Ferrandiz, C., Madueno, F., and Parcy, F. (2006) How floral meristems are built. Plant Mol. Biol. 60, 855–870.

    Article  PubMed  CAS  Google Scholar 

  43. Robles, P., and Pelaz, S. (2005) Flower and fruit development in Arabidopsis thaliana. Int. J. Dev. Biol. 49, 633–643.

    Article  PubMed  CAS  Google Scholar 

  44. Riefler, M., Novak, O., Strnad, M., and Schmulling, T. (2006) Arabidopsis cytokinin receptor mutants reveal functions in shoot growth, leaf senescence, seed size, germination, root development, and cytokinin metabolism. Plant Cell 18, 40–54.

    Article  PubMed  CAS  Google Scholar 

  45. Buchanan-Wollaston, V., Earl, S., Harrison, E. , Mathas, E., Navabpour, S., Page, T., and Pink, D. (2003) The molecular analysis of leaf senescence - a genomics approach. Plant Biotechnol. J. 1, 3–22.

    Article  PubMed  CAS  Google Scholar 

  46. Lim, P.O., and Nam, H.G. (2005) The molecular and genetic control of leaf senescence and longevity in Arabidopsis. Curr. Top. Dev. Biol. 67, 49–83.

    Article  PubMed  CAS  Google Scholar 

  47. Bolle, C. (2008) Phenotyping of abioticresponses and hormone treatments in Arabidopsis.

    Google Scholar 

  48. Zimmermann, P., Hirsch-Hoffmann, M., Hennig, L. and Gruissem, W. (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 136,2621–2632.

    Article  CAS  Google Scholar 

  49. Toufighi, K., Brady, S.M., Austin, R, Ly, E. , and Provart, N.J. (2005) The botany array resource: e-Northerns, expression angling, and promoter analyses. Plant J. 43, 153–163.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Ludwig-Maximilians-Universität, Department für Biologie I Lehrstuhl für Botanik, München, Germany

    Cordelia Bolle

Authors
  1. Cordelia Bolle
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Institut für Allgemeine Botanik und Pflanzenphysiologie, Lehrstuhl Pflanzenphysiologie, Friedrich-Schiller-Universität Jena, Jena, Germany

    Thomas Pfannschmidt

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Bolle, C. (2009). Phenotyping of Arabidopsis Mutants for Developmental Effects of Gene Deletions. In: Pfannschmidt, T. (eds) Plant Signal Transduction. Methods in Molecular Biology, vol 479. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59745-289-2_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-289-2_2

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-58829-943-7

  • Online ISBN: 978-1-59745-289-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation