Plant Cuttings

This image, entitled “A. Rockentrav, Turritis glabra L., B. Backtrav, Arabidopsis thaliana (L.) Schur.” (from Bilder ur Nordens Flora) is in the public domain.

This blog shares news and information about plants, the way they work and the ways in which they interact with people. But, how do we get that understanding about plants in the first place? Scientists undertake studies on actual plants. After all, and unarguably, the only way one to understand plant biology is to work with plants themselves. But, with approx. 369,400 species of flowering plants (Nigel Chaffey, Rebecca Morelle, Vasudevan Sridharan) on the planet to study that’s a bit of a problem: Do we have to study – and in-depth – each and every one of those species before we can reasonably claim to know how plants ‘work’? Or, is there some sort of ‘work-around’ that means we don’t have to do that? Well, and you surely won’t be too surprised to hear this, but such a time-saving ‘dodge’ does exist, it’s called ‘model plants’.

What is a model plant?

By way of a definition, “Model plants* are extensively studied plant species chosen for the ease of investigating particular biological phenomena or for their value in biotechnology or agronomy. Research on model plants provides biological insights relevant to other organisms in areas such as biochemistry, genetics, physiology, ecology, evolution and development” [quoted from here]. [Ed. – for a good – if a little technical – consideration of what a model species is, and should achieve, see the articles by Richard Flavell (2009) and Soham Ray et al. (2022).]

What is the model plant?

The model organism selected for this singular honour in plant biology is thale cress, Arabidopsis thaliana (DW Meinke et al., 1998; Anthony W Woodward & Bonnie Bartel, 2018; Marc Somssich, 2019; Madhabendra Mohon Kar & Ayan Raichaudhuri, 2022; Abel Cerdà; Gülce Tekin)**.

Although the plant has been known for many hundreds of years, and Linnaeus had a hand in naming it in the 18^th century [Ed. – that’s what the L. stands for in its full scientific name of Arabidopsis thaliana (L.) Heynh. (Marc Somssich, 2019)], its promotion as a model organism for plant studies didn’t really take place until the 1950s. However, interest in use of this plant soon increased and in 1965 the first International Arabidopsis Symposium took place. Since that time – and particularly since the 1980s (Richard Flavell, 2009) –  the amount of work undertaken with this rather unlikely star of the botanical firmament has ‘exploded’, and the number of scientific papers published that report the various plant biological findings and discoveries made with this small botanic has ‘mushroomed’ in the intervening decades (Gülce Tekin; Ibrokhim Y Abdurakhmonov, 2022).

Why? What is it about Arabidopsis that makes it so attractive as a model organism? Some of the advantages of using this plant as the model for all of plant biology are…

Why is Arabidopsis the model plant?

One of the most valuable traits of Arabidopsis is its rapid growth. The entire life cycle – from seed-germination to production of seed for the next generation – can take place within 6 to 8 weeks, which allows scientists to study multiple generations in a short amount of time (Beta Life Science). This trait is extremely valuable in trying to get results when grant-funded research has to be carried out within short time periods from a few months to three years or so (e.g., here, here, here, here).

Not only can Arabidopsis grow quickly, but its growth requirements are reasonably simple and it can be grown under relatively basic conditions, in the laboratory in pots or Petri dishes with minimal space (Beta Life Science). This greatly reduces costs and logistical challenges of research with this plant compared to other species with more exacting growth requirements, especially if they need to be grown outside [Ed. – for a useful comparison of the challenges of laboratory-based investigations compared to field work, see Chris Goforth’s highly readable blog post “Science Sunday: Field Research vs. Lab Research”]. Importantly, Its small size means researchers can cultivate hundreds of samples in a single growth chamber, maximizing data collection and experimental variation (Beta Life Science). Furthermore, each plant can produce thousands of seeds, providing abundant opportunities for the sample sizes required for statistically-robust evidence to support research findings (Jorge Faber & Lilian Martins Fonseca, 2014; Chittaranjan Andrade, 2020).

So much for the practicalities of working with Arabidopsis. Some of the most compelling arguments for its favoured status as a model plant relate to its DNA, in particular its genome [“The complete set of DNA (genetic material) in an organism”]. The Arabidopsis genome is comparatively small – about 135 mega base pairs (Justin Corfield) – which is compact and easier to work with compared to other plant genomes. That small size greatly facilitated publication of its complete sequence in 2000 (The Arabidopsis Genome Initiative, 2000). Knowing the genome sequence allows scientists to identify the genes that ultimately – largely – dictate how the plant ‘works’ and interacts with its environment (Sarah Lee). With that insight one can slowly put together the information of what gene does what and how it contributes to the overall biology of the plant.

Additionally, Arabidopsis is highly amenable to genetic transformation, particularly through the Agrobacterium tumefaciens-mediated method. This enables scientists to introduce or silence genes with high efficiency, allowing for the creation of transgenic lines to study gene expression, protein function, and genetic pathways. Combined with the availability of such genetic manipulation as the gene-editing CRISPR technology (McKenzie Prillaman), “Arabidopsis offers an unmatched toolkit for plant genetic engineering”. These techniques of molecular biology and therefore the modern-day emphasis on studying the genes that underpin plant growth and development*** – particularly the ability to add or remove or change a gene to see what effect that has on plant biology – has led to an almost unprecedented increase in our knowledge and understanding of the biology of plants. So much so that it has produced “a trove of genetic information that has facilitated numerous studies in plant biology”.

Since the first International Arabidopsis Symposium in 1965, the Arabidopsis research community is now well-established – and global – providing expertise, resources, and protocols, which further strengthen the species’ position as a model organism. [Ed. – although this argument is a little ‘circular’ (Richard Nordquist, Kassiani Nikolopoulou) in that widerspread use of Arabidopsis encouraged development of this community of researchers, whose work further encouraged use of Arabidopsis as a model plant, which in turn inspired more people to work with the plant. But, whichever way you look at it, there’s a lot of Arabidopsis scientists out there.]

And, although not of general plant biological relevance, “As a member of the Brassicaceae family (Melissa Petruzzello) it is linked to more important cultivated species such as cabbage, mustard and radish” (Alan Mullan & Aleksandra Marsh. [Ed. – Which, at least, should make Arabidopsis an appropriate model for those crops…]

Altogether – and there are other more-technical reasons (e.g., here; here; Abel Cerdà; Anthony W Woodward & Bonnie Bartel, 2018) – that’s a pretty impressive list of reasons in favour of Arabidopsis as the model plant. [Ed. – and, since “A. thaliana is easy to look after compared with animal model organisms” (Alan Mullan & Aleksandra Marsh) – and poses fewer ethical considerations than research on primates (Marci Regambal; Constança Carvalho et al., 2018) – it has even been used to provide insights into the biology of animals, including humans (Gülce Tekin; Alan M Jones et al., 2008)].

Some Arabidopsis achievements…

And quite what has been achieved by studying Arabidopsis is celebrated in an extremely useful timeline that highlights “some of the exceptional discoveries, innovations, and community milestones in Arabidopsis research over the past 150+ years” in the Open Access scientific article by Catherine Freed et al. (2025). Beginning in 1873, with the report of the first Arabidopsis mutant (Vladimir Tarakanov), it concludes in 2024 with the commercial release of anthocyanin-rich purple tomatoes (Cathie Martin & Eugenio Butelli, 2024), development of which crop was directly aided by “Arabidopsis-based gene discovery” because “AtMYB12 protein from Arabidopsis revealed that AtMYB12 increases flavonoid accumulation and phenylpropanoid biosynthesis in tomato” (Freed et al., 2025). Altogether, “This timeline showcases multinational Arabidopsis efforts from as early as 1873 to the present, divided into five categories: technology, community, landmark paper, resource, and application”. [Ed. – readers might – correctly – surmise that lack of details regarding the innovations, etc. in Arabidopsis research in this post is down to the limits of Mr P Cuttings’ understanding of the significance of such matters – and their quite detailed technical nature…].

For more on breakthrough discoveries using Arabidopsis, see Nicholas J Provart et al., 2015; Anthony W Woodward & Bonnie Bartel, 2018; Siobhan Brady et al., 2025; here; and here.

That’s quite a catalogue of achievements [i.e., when you look at the specifics within the articles cited above re breakthroughs, etc. with Arabidopsis] – which have been hard-won by thousands of researchers in institutions across the globe over decades of intensive work, often on government-funded projects. And that’s great. It is something that’s well worth celebrating. But, Arabidopsis is very particular type of plant.

But, what is Arabidopsis not?

Arabidopsis is not a crop plant (Diane Boudreau et al.), but is a small, weedy, terrestrial, herbaceous (Jeffer Bartel), dicotyledonous, flowering plant (an angiosperm (Martin Huldrych Zimmermann & Peter Stevens)) in the cabbage family, the Brassicaceae (which is also known as the Cruciferae).

As such, it’s not a monocot – such as an orchid, a grass, or a palm – nor a tree, nor an epiphyte, nor a seagrass (Pamela L Reynolds). Neither is it a gymnosperm (Christopher J Earle), or a fern, or a moss, or a liverwort, nor any of the other types of plant within the plant kingdom (Becki Brunelli, Samantha Fowler et al.). Neither is it a green alga****, nor any of the other important photosynthetic algae such as brown seaweeds, or cyanobacteria. In other words, because Arabidopsis is a very specific type of flowering plant, its in-depth study doesn’t – necessarily – advance our understanding of the biology of any other type of photosynthetic organism.

Some of those objections are dealt with in more detail in the comprehensive article here. In particular the following constraints: the limited ecological relevance of Arabidopsis [which may not accurately represent the diversity of plant species with different growth habits or environmental adaptations]; its small size and simple morphology [which can be inadequate for studying traits like wood formation or complex root systems*****]; and its limited complexity [Arabidopsis is a relatively simple plant compared to more complex crops, which may decrease its applicability for studying intricate plant traits or interactions] [Ed. – and even where Arabidopsis insights may have relevance to a crop plant, there can be major problems in applying that knowledge to crops (Cristóbal Uauy et al., 2025)].

[Ed. – For more on the disadvantages and/or limitations of Arabidopsis as a plant model, see Gülce Tekin; Anthony W Woodward & Bonnie Bartel, 2018; Sarah Shailes; and here.]

So, what’s the answer?

New – and additional – model plants.

Although Arabidopsis has reached – and continues to retain – a pre-eminent position amongst those who study plant biology, there are many who have questioned the ability of that plant to be a true model for all types of plants. Not surprisingly therefore, researchers have studied other plants throughout the period in which Arabidopsis attained ascendancy, and have promoted those plants as models for particular plants, e.g. tomato (Solanum lycopersicum (Wei Liu et al., 2022), and maize (Zea mays (Fakhriddin N Kushanov et al., 2022). But, with better appreciation of the shortcomings of Arabidopsis, many more plants are being put forward as candidate reference plants.

Without the space here to list all of those, it’s worth mentioning a few to give a flavour of the diversity of model plants now being studied almost as intensively as Arabidopsis. In attempts to ‘get a handle on’ the early stages of land colonisation by plants, Marchantia polymorpha (common liverwort) is widely promoted (Igor Cesarino et al., 2020). Phragmites australis (common reed), “a common perennial grass, which can tolerate many different environments such as salt marshes and arid areas” (Juniper Kiss), is being investigated as an invasive species (Igor Cesarino et al., 2020). The crop-destroying scourge of plant parasitism (Alex D Twyford, 2018; Pervin Erdogan, 2022; Olga Cannavacciuolo et al., 2024) is being examined with Striga hermonthica (witchweed) (Igor Cesarino et al., 2020), “a widely distributed parasitic plant that feeds on monocotyledonous plants (e.g. rice, maize, millet, sorghum)” (Juniper Kiss). And Eutrema salsugineum (salt cress), “a halophytic (salt-tolerant) Arabidopsis look-alike plant” (Juniper Kiss), is a major contender for studies of salt tolerance amongst plants (Igor Cesarino et al., 2020).

For more information on model plant alternatives to Arabidopsis, see Andrew Wood et al., 2000; Paul Gepts et al., 2005; Xianmin Diao et al., 2014; Caren Chang et al., 2016; here; Charles F Delwiche et al., 2017; Juniper Kiss; Igor Cesarino et al., 2020; here; Soham Ray et al., 2022; Sandhya Yadav et al., 2023.

Overall conclusion?

Yes, we need to continue to work with Arabidopsis as a ‘model’ plant – the global infrastructure of connections/collaborations, laboratories, and expertise is already in place for that. But, we also need to continue to work on other – and develop more – such ‘reference’ plants, and – arguably – each of the hundreds of thousands of species to fully comprehend what plants are and what they are capable of. There’s plenty of work for everyone interested in plant biology.

* Instead of ‘model’ plant, the best alternative term I’ve come across to date is ‘reference plant‘ (Caren Chang et al., 2016). That seems to be a much more honest acknowledgment of the sort of information [or aspiration thereof] that such a plant can actually provide.

** Because we Botanists are always keen to give a ‘shout-out’ to those who study organisms of somewhat lesser merit, we are happy to state that those other biological disciplines have their own model species, e.g. fruit fly (Drosophila melanogaster) (Alan Mullan & Aleksandra Marsh), and the nematode Caenorhabditis elegans (Mark Edgley et al.) (Alan Mullan & Aleksandra Marsh) for the Zoologists; Escherichia coli (Alan Mullan & Aleksandra Marsh) for the Bacteriologists; and Escherichia virus T4, a bacteriophage, for the Virologists. And it would be very remiss of me not to mention the plant-like Emiliania huxleyi , a “unicellular marine coccolithophore alga, extensively studied as a model phytoplankton species” used by our Phytoplanktonological partners, and the unicellular yeast Saccharomyces cerevisiae (Steve James) for our fungi-favouring friends.

For a more comprehensive listing of non-plant model organisms, see here, and Alan Mullan & Aleksandra Marsh. For a more comprehensive listing of plant models, see here. For more on a variety of ‘popular’ model organisms – but which is in no way comprehensive (although it does cite many sources), see Alyssa Cecchetelli & Lukas Morgan.

*** Which means that modern-day plant biology has largely gone beyond the well-established and previous periods of botanical study during the development of plant science that involved taxonomic considerations, anatomical studies, physiological experiments, and traditional crop-breeding (although all of these disciplines are still carried out…).

**** Which organisms may – or may not – also be included in the plant kingdom when known as the Viridiplantae…

***** For many years the author of this post was a fervent advocate of the view that, since Arabidopsis was not a tree, it was of little use in understanding the cell biology of wood formation in trees (yes, my research specialism for many years! See e.g., here; Nigel Chaffey, 2002). Sadly(!), working with colleagues in the Swedish University of Agricultural Sciences [SLU] it was discovered that, by appropriate manipulation of its growing conditions, Arabidopsis could be encouraged to make wood. Not only that, but the wood it made was rather similar to that produced by a proper tree (Nigel Chaffey et al., 2002). So, another hurdle – to more general relevance of this weedy herb to plant biology – seems to be have been surmounted, and it does appear that Arabidopsis may have some utility in understanding tree-related questions…

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