Arabidopsis thaliana as an Experimental Organism


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. , Copyright American Society of Plant Biologists.


Alonso JM, Stepanova AN, Leisse TJ, et al. (2003) Genome‐wide insertional mutagenesis of Arabidopsis thaliana. Science (New York, N.Y.) 301 (5633): 653–657.

Alonso JM and Ecker JR (2006) Moving forward in reverse: genetic technologies to enable genome‐wide phenomic screens in Arabidopsis. Nature Reviews Genetics 7 (7): 524–536.

Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 (6814): 796–815.

Baev V, Milev I, Naydenov M, et al. (2014) Insight into small RNA abundance and expression in high‐ and low‐temperature stress response using deep sequencing in Arabidopsis. Plant Physiology and Biochemistry 84: 105–114.

Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 (2): 281–297.

Bino RJ, Hall RD, Fiehn O, et al. (2004) Potential of metabolomics as a functional genomics tool. Trends in Plant Science 9 (9): 418–425.

Bowers JL, Chapman BA, Rong J and Paterson AH (2003) Unraveling angiosperms genome evolution by phylogenetic analysis of chromosomal duplications events. Nature 422: 433–438.

Coen ES and Meyerowitz EM (1991) The war of the whorls: genetic interactions controlling flower development. Nature 353 (6339): 31–37.

Feng Z, Mao Y, Xu N, et al. (2014) Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas‐induced gene modifications in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 111 (12): 4632–4637.

Gardiner J and Marc J (2011) Arabidopsis thaliana, a plant model organism for the neuronal microtubule cytoskeleton? Journal of Experimental Botany 62 (1): 89–97.

Gusmaroli G, Figueroa P, Serino G and Deng XW (2007) Role of the MPN subunits in COP9 signalosome assembly and activity, and their regulatory interaction with Arabidopsis Cullin3‐Based E3 Ligases. The Plant Cell 19 (2): 564–581.

Harter K and Weber AP (2013) Arabidopsis 2010 and beyond‐big science with a small weed. Frontiers in Plant Science 4: 18.

Jakob K, Goss EM, Araki H, et al. (2002) Pseudomonas viridiflava and P. syringae – natural pathogens of Arabidopsis thaliana. Molecular Plant‐Microbe Interactions: MPMI 15 (12): 1195–1203.

Jones JDG and Dangl JL (2006) The plant immune system. Nature 444 (7117): 323–329.

Jones AM, Chory J, Dangl JL, et al. (2008) The impact of Arabidopsis on human health: diversifying our portfolio. Cell 133 (6): 939–943.

Joshi R, Wani SH, Singh B, et al. (2016) Transcription factors and plants response to drought stress: current understanding and future directions. Frontiers in Plant Science 7: 1029.

Liu X, Hao L, Li D, Zhu L and Hu S (2015) Long non‐coding RNAs and their biological roles in plants. Genomics, Proteomics & Bioinformatics 13 (3): 137–147.

Lowder LG, Zhang D, Baltes NJ, et al. (2015) A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiology 169 (2): 971–985.

McGary KL, Park TJ, Woods JO, et al. (2010) Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proceedings of the National Academy of Sciences 107 (14): 6544–6549.

McGinnis KM (2010) RNAi for functional genomics in plants. Briefings in Functional Genomics 9 (2): 111–117.

Oh E, Zhu JY, Bai MY, et al. (2014) Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl. eLife 3: 1–19.

Page DR and Grossniklaus U (2002) The art and design of genetic screens: Arabidopsis thaliana. Nature Reviews Genetics 3 (2): 124–136.

Parinov S and Sundaresan V (2000) Functional genomics in Arabidopsis: large‐scale insertional mutagenesis complements the genome sequencing project. Current Opinion in Biotechnology 11 (2): 157–161.

Schwab R, Ossowski S, Riester M, et al. (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18 (5): 1121–1133.

Sessions A, Burke E, Presting G, et al. (2002) A high‐throughput Arabidopsis reverse genetics system. Plant Cell 14: 2985–2994.

Sham A, Moustafa K, Al‐Ameri S, et al. (2015) Identification of Arabidopsis candidate genes in response to biotic and abiotic stresses using comparative microarrays. PLoS One 10 (5): e0125666.

Song YH, Ito S and Imaizumi T (2010) Similarities in the circadian clock and photoperiodism in plants. Current Opinion in Plant Biology 13 (5): 594–603.

Stepanova AN and Ecker JR (2000) Ethylene signaling: from mutants to molecules. Current Opinion in Plant Biology 3 (5): 353–360.

Surovtseva YV, Churikov D, Boltz KA, et al. (2009) Conserved telomere maintenance component 1 interacts with STN1 and maintains chromosome ends in higher eukaryotes. Molecular Cell 36 (2): 207–218.

Ting JPY, Kastner DL and Hoffman HM (2006) CATERPILLERs, pyrin and hereditary immunological disorders. Nature Reviews. Immunology 6 (3): 183–195.

Van Norman JM and Benfey PN (2009) Arabidopsis thaliana as a model organism in systems biology. Wiley Interdisciplinary Reviews: Systems Biology and Medicine 1 (3): 372–379.

Voss U, Larrieu A and Wells DM (2013) From jellyfish to biosensors: the use of fluorescent proteins in plants. International Journal of Developmental Biology 57 (6–8): 525–533.

Waterhouse PM and Helliwell CA (2003) Exploring plant genomes by RNA‐induced gene silencing. Nature Reviews Genetics 4 (1): 29–38.

Wei N and Deng XW (1996) The role of the COP/DET/FUS genes in light control of Arabidopsis seedling development. Plant Physiology 1122: 871–878.

Wei N, Serino G and Deng XW (2008) The COP9 signalosome: more than a protease. Trends in Biochemical Sciences 33 (12): 592–600.

Weigel D and Nordborg M (2005) Natural variation in Arabidopsis. How do we find the causal genes? Plant Physiology 138 (2): 567–568.

Weigel D (2012) Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiology 158 (1): 2–22.

Zhang S, Raina S, Li H, et al. (2003) Resources for targeted insertional and deletional mutagenesis in Arabidopsis. Plant Molecular Biology 53 (1–2): 133–150.

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. [doi: 10.1002/9780470015902.a0002031.pub3]