Arabidopsis thaliana as an Experimental Organism

Abstract

In the past decades, plant research has experienced an incredibly fast growth, thanks both to the increasing number of scientists joining the field and the great number of publicly available tools. In this context, Arabidopsis thaliana still retains a central role in Plant Science, being the prominent plant model adopted worldwide. Indeed, its main features such as easy and fast growth, high seed production, easy genetic manipulation and a completely sequenced genome still place Arabidopsis as the best model for studying plants. Arabidopsis has proven to be an ideal organism for studying plant development at the molecular, cellular, organismal and ecological levels. By concentrating their efforts on a single model system, Arabidopsis scientists have made outstanding advances in almost any field of plant research. Further, discoveries made in Arabidopsis have been translated to other plant species such as economically important crops, as well as to animal systems, including complex human disease processes.

Key Concepts

  • Arabidopsis is a small flowering plant, which has emerged as the primary experimental organism for the study of all aspects of plant biology.
  • Arabidopsis genome has been fully sequenced in 2000 and contains approximately 28 000 genes.
  • Several molecular tools have been established to identify Arabidopsis transcription profiles, epigenetic landscape, protein and metabolite composition.
  • Systems biology is currently being used in Arabidopsis to investigate the transcriptional networks regulating root development, the metabolic response to stress and the genetic regulation of metabolic variability.
  • Gain of function and loss of function transgenic lines for specific Arabidopsis genes can be easily produced or obtained from public collections.
  • Most of the information on Arabidopsis research is available from dedicated websites.
  • Discoveries made in Arabidopsis can be easily translated to other plant species, as well as to animal systems.

Keywords: Arabidopsis thaliana; plant development; forward genetics; reverse genetics; mutagenesis; transgenic; transcriptome analysis

Figure 1. An approximately 5‐week‐old plant of the frequently used laboratory accession Columbia 0. Total plant height is at this stage 25 cm.
Figure 2. Establishment of the Arabidopsis body plan in the embryo and the structure of a primary root. A, apical region; C, central region; B, basal region; HY, hypophyseal cell; SAM, shoot apical meristem; COT, cotyledon; H, hypocotyl; ER, embryonic root; RM, root meristem; RMI, root meristem initials.
Figure 3. Gene functional analysis using reverse genetics tools. (a) Outline of the ‘reverse genetics’ strategy used for the functional analysis of genes of interest. (b) Examples of the application of reverse genetics tools to the functional study of small gene families regulating crucial developmental pathways in Arabidopsis. In Arabidopsis, two COP9 signalosome complex (CSN) subunits, CSN5 and CSN6, are both encoded by two highly conserved genes, named CSN5A and CSN5B, and CSN6A and CSN6B, respectively. The availability of T‐DNA insertion lines in each member of these small gene families has allowed the generation of the csn5a csn5b and csn6a cns6b double null mutants. In both cases, as shown in (b), complete loss of function of CSN5 or CSN6 results in severe developmental defects causing postembryonic arrest at the seedling stage. Reproduced from Gusmaroli et al. 2007, http://www.plantcell.org. Copyright American Society of Plant Biologists.
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Further Reading

Hansen BO, Vaid N, Musialak‐Lange M, et al. (2014) Elucidating gene function and function evolution through comparison of coexpression networks of plants. Frontiers in Plant Science 5: 394.

Koornneef M and Meinke D (2010) The development of Arabidopsis as a model plant. Plant Journal 61: 909–921.

O'Malley RC, Barragan CC and Ecker JR (2015) A user's guide to the Arabidopsis T‐DNA insertional mutant collections. Methods in Molecular Biology (Clifton, N.J.) 1284: 323–342.

Raikhel N (2010) 2020 vision for biology: the role of plants in addressing grand challenges in biology. Molecular Plant 1: 561–563.

Salinas J and Sanchez‐Serrano JJ (eds) (2006) Arabidopsis Protocols, 2nd edn. Totowa, NJ: Humana Press.

Weigel D and Glazebrook J (2002) Arabidopsis: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

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Serino, Giovanna, and Marzi, Davide(Mar 2018) Arabidopsis thaliana as an Experimental Organism. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0002031.pub3]