A single Arabidopsis plant in a pot.

Arabidopsis thaliana – the botanist’s lab rat

What is Arabidopsis thaliana and why do botanists like it so much?

Model Organisms: Definition, Characteristics and Examples

The term model organism defines a species that is used in the lab to study biological processes with the assumption that novel findings in a simple system can provide insights into similar mechanisms in other complex organisms. This expectation is based on the evolutionary principle that all living organisms originated from a common ancestor and share conserved features that make life possible.

The famous naturalist Charles Darwin sketched an imaginary Tree of Life to graphically represent his theory of evolution all existing species derived from few primordial organisms and evolved over time thanks to random variation and natural selection. A century after the release of the revolutionary book “On the Origin of Species by Means of Natural Selection”, modern genetics studies found evidence of crossbreeding and gene transfer between species over evolutionary time and space, thus supporting a web of life rather than a tree. Though, the concept of the Last Universal Common Ancestor (LUCA) – a life form with complex mechanisms to convert information encoded in the DNA to RNAs and proteins (i.e., transcription and translation) – that gave rise to the great diversity of life on earth is still valid.

Nevertheless, different lineages across the Tree of Life have also diversified several developmental patterns and metabolic pathways over million years of evolution.

Good experimental models share the following characteristics:

  • ease of manipulation in the lab (to perform experiments efficiently)
  • small size (to grow more individuals in a reduced space)
  • short life cycle (to study more generations in short periods of time)
  • high fertility rates (to produce a large number of offspring for further analyses)

In Life Sciences, the bacterium Escherichia coli (naturally found in the human digestive tract) and the budding yeast Saccharomyces cerevisiae (used in the preparation of bread, beer and wine since ancient times) are among the most commonly used model systems for research, together with the animal model species Drosophila melanogaster (fruit fly), Cavia porcellus (Guinea pig) and Mus musculus (mouse).

Arabidopsis thaliana: The Top Model for Research in Plant Biology

Gloved hands handle Arabidopsis in tubs.
Image: Canva.

At the beginning of the 20th century, botanists started to use the flowering plant Arabidopsis thaliana (commonly known as thale cress or mouse-ear cress) in their laboratory experiments. Its reduced dimension makes it a great tool in plant research: Arabidopsis reaches an average height of 20-25 cm at maturity, allowing scientists to grow several individuals in a reduced space (hundreds of plants in growth chambers and thousands in greenhouses). In addition, Arabidopsis is an annual plant with a short life cycle: it takes only 6 weeks from seed germination to seed maturation under inductive conditions (Long Days, 20-24 C). Therefore, several generations can be grown in less than one year.

Another advantage relies on its mode of sexual reproduction: flowers naturally self-pollinate, and each fruit (called silique) can contain up to 60 seeds. Given that each plant harbours several siliques, individuals produce large number of siblings – useful to study the segregation of plant characteristics. Seeds are super tiny (250 -500 μm diameter): although they are difficult to handle, their small size facilitates the storage of big populations, making Arabidopsis a great system to study genetic and phenotypic variation.

Since the 1980s, Arabidopsis has been adopted as a popular model worldwide for different fields of plant research (e.g., developmental and population genetics studies, cellular and molecular biology, evolutionary genomics etc.) also because it is amenable to genetic transformation and became the first plant genome to be sequenced (2000). Furthermore, huge collections of biological materials (mutants, accessions) and the increasing number of OMICS datasets are publicly available for the scientific community.  

Crucial Discoveries in Arabidopsis

Many Arabidopsis plants in tubs seen from above in a 9 x 8 grid.
Image: Canva.

In the last decades, the use of Arabidopsis has increased our understanding of important biological and physiological processes such as plant-pathogen interactions, light sensing, and the circadian clock. Furthermore, Arabidopsis was instrumental to dissect the genetic pathways underlying the formation of plant organs such as roots, leaves and flowers. For example, molecular studies of mutant plants promoted the conceptualization of the famous ABC model of flower formation that explains the interaction among regulatory factors involved in the development of reproductive structures (4 sepals, 4 petals, 6 stamens, 2 fused carpels).

A Valuable Member of the Brassicaceae Family

Arabidopsis is a weed with a wide geographic distribution that also grows along roadsides. Although it’s not a relevant species for agriculture, it belongs to the mustard family that includes agronomically important plants of the Brassica genus such as Brassica napus (oilseed rape), Brassica rapa (turnip), and various cole crops (cabbage, broccoli, cauliflower, brussel sprouts). As an example of applied research, discoveries in Arabidopsis have supported the comprehension of inflorescence development in more complex edible crops such as Romanesco broccoli.


Suggested links

TAIR – Home Page (arabidopsis.org)

The ABC model of floral development (cell.com)

Cauliflower fractal forms arise from perturbations of floral gene networks | Science


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Michela Osnato

Plant Molecular Biologist passionate about Science Communication and Education.
Science Editor @ Botany One

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  • […] by a cheat sheet with brief annotations and visuals for quick reference. We have started with “Arabidopsis thaliana – the botanist’s lab rat” [PDF]to introduce the most used model organism in plant research and continued with “Plants […]

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