How Arabidopsis became the world's most studied plant

Arabidopsis plants before harvest inside Plant Habitat-01 in the International Space Station’s Columbus laboratory module. The study compared plant genetics, metabolism, photosynthesis and gravity sensing in space and on Earth. Image: NASA, 2018.

Few plants have attracted as much scientific attention as Arabidopsis thaliana. Since 2020, an average of approximately eight studies involving the species have been published each day, covering almost every aspect of plant genetics, growth, development and survival. Outside the lab, Arabidopsis is a small annual plant with a low rosette of leaves, slender flowering stems and tiny white flowers — most gardeners would consider it a weed. The simple appearance, combined with the fact that it was neither a valued ornamental nor an important crop, meant that much of its early scientific history centred on describing and naming the plant.

The first known description of Arabidopsis dates to 1577, when the German physician and botanist Johannes Thal recorded the plant in the Harz Mountains and named it Pilosella siliquata. This can be translated as “the little hairy, pod-bearing plant.” His account was published posthumously in 1588, together with the earliest known illustration of the species. Carl Linnaeus later renamed it Arabis thaliana in Thal’s honour. In 1842, the botanist Gustav Heynhold placed it in the genus Arabidopsis, giving the plant its present name.

The first hint of its experimental future came in 1873, when the botanist Alexander Braun described an unusual plant bearing distorted, double flowers. It is now thought to have carried a mutation in AGAMOUS, a gene that helps determine the arrangement of organs within a flower. But genetics was still a young science, and the significance of the plant didn’t become clear for another few decades.

In 1907, the German botanist Friedrich Laibach examined its chromosomes and discovered that Arabidopsis possessed only five pairs, which is very few for a flowering plant. He saw its potential then but it was 30 years later, in 1943 he formally argued that Arabidopsis could become an ideal organism for genetics. It was small, quick to reproduce, self-pollinating and capable of producing thousands of seeds. Soon afterwards, his student Erna Reinholz exposed plants to X-rays and produced a collection of inherited mutations, demonstrating how Arabidopsis could be used to connect visible characteristics with changes in its genes. 

Progress from there remained gradual. During the 1950s and 1960s, a small international community began collecting natural varieties, exchanging seeds and developing methods for studying them. The Arabidopsis Information Service newsletter appeared in 1964, followed by the first international Arabidopsis symposium in 1965. Molecular genetics accelerated research during the 1980s and 1990s, and in 2000 Arabidopsis became the first plant to have its genome sequenced. Its five chromosomes contain approximately 135 million base pairs, giving it a comparatively compact genome for a flowering plant. By then, it had become the leading model organism in plant biology.

Built for the laboratory

A. thaliana’s compact genome made individual genes comparatively easy to locate, sequence and study, but this was only part of its experimental value. Genetic changes could also be followed through the plant’s entire life cycle and into the next generation within a matter of weeks.

For the first weeks of its life, Arabidopsis remains close to the ground, its leaves arranged in a compact circular rosette. Then a dramatic change occurs, the plant “bolts,” sending a slender flowering stem upwards from its centre. The small white flowers appear along the stem and pollinate themselves, before developing into long, narrow seed pods known as siliques. Each plant can produce thousands of seeds, providing researchers with the next experimental generation. 

Arabidopsis is equally revealing below ground. Its roots are small and almost transparent, allowing living cells to be observed through a microscope as they divide, elongate and respond to light, gravity and chemical signals. Seedlings can even be grown against clear agar plates, turning processes normally hidden beneath the soil into a process scientists can watch unfold in real time.

Arabidopsis gave researchers a practical way to investigate the biological processes it may share with other plants. Researchers could alter a single gene, grow the resulting plants and observe the consequences within weeks. In this way, the plant helped turn questions that had puzzled botanists for centuries into identifiable molecular pathways. However, Arabidopsis did not become the world’s most studied plant just because it was convenient. Its practical advantages made it an ideal  experimental organism; the knowledge and resources generated through its use made it increasingly valuable. Each discovery produced new mutants, genetic maps and experimental tools, making the next question easier to answer. More scientists joined the field, resources accumulated and the plant became increasingly difficult to replace. Arabidopsis had entered a self-reinforcing cycle: the more researchers learned from it, the more useful it became.

Deciding when to flower

For an annual plant, the timing of flowering determines how long it can continue growth before reproducing and whether its seeds will mature before conditions become unfavourable. Research in Arabidopsis found that this transition is controlled by a network of genes that integrates information about day length, the internal clock and prolonged winter cold.

The circadian clock controls the daily rhythm of a gene called CONSTANS (CO). Under long day conditions, CO activity peaks while it is still light, allowing the CO protein to accumulate in the leaves. CO then activates FLOWERING LOCUS T (FT). The resulting FT protein travels through the plant’s vascular system to the tip of the shoot, where it helps switch the growing point from producing leaves to producing flowers. Winter cold provides another layer of control. In winter-growing varieties of Arabidopsis, FLOWERING LOCUS C (FLC) represses FT and delays flowering. Prolonged exposure to cold causes stable changes to the chromatin surrounding FLC, silencing the gene even after temperatures rise again. This provides the plant with a cellular memory of winter. Once FLC has been silenced, lengthening days can activate FT and flowering can begin.

Researchers reconstructed much of this network by studying plants that flowered unusually early or late. Each mutant helped identify another gene, while crosses with existing lines revealed where it acted within the pathway. The resulting mutants, genetic maps and experimental methods could then be reused to investigate the next component, illustrating how knowledge accumulated around Arabidopsis and made increasingly detailed questions possible.

Growing plants without gravity 

The usefulness of Arabidopsis is not confined to laboratories on Earth. In 2018, NASA grew the plant aboard the International Space Station as part of its Plant Habitat-01 study, alongside matching plants kept on Earth. Researchers at Washington State University then compared the two groups to see how spaceflight affected their gene activity, metabolism, photosynthesis and growth.

On Earth, gravity gives plants a reliable sense of direction: roots generally grow downwards and shoots upwards. In orbit, that familiar guide is dramatically reduced, allowing scientists to investigate how plants direct the growth of their roots and shoots without a strong gravitational cue. Because the normal development of Arabidopsis has been documented in such detail, changes caused by spaceflight are easier to recognise. Its small size, rapid life cycle and abundant seeds also make it well suited to the limited growing space aboard the station.

The research soon raised a longer-term question: could the effects of spaceflight persist in the next generation? NASA’s Plant Habitat-03 experiment, conducted in 2022 and 2023, investigated whether epigenetic changes (changes in how genes are switched on or off without altering the DNA sequence itself) could be passed on to offspring. Seeds produced aboard the station were returned to Earth and later sent into orbit again to grow a second generation. The experiment has been completed, but at the time of writing its findings had not yet been published, so whether these changes persisted across generations remains unknown.

The experiment also shows why Arabidopsis remains valuable as a model plant. Identifying changes that persist into the next generation requires a reliable baseline for comparison: how the plant normally develops, how its genes behave and how much variation occurs under ordinary conditions. Decades of research have provided that baseline, helping scientists distinguish the effects of spaceflight from natural variation.

Arabidopsis cannot represent every aspect of plant biology, and discoveries made using it must still be tested in crops and other species. Its value lies in giving researchers a well-understood plant that can serve as a shared point of comparison. Because many genes and biological pathways are shared across flowering plants, discoveries made in Arabidopsis can guide experiments addressing disease resistance, responses to drought, heat and a changing climate. More than four centuries after Johannes Thal first recorded it, the species remains central to plant science.

Recommended reading

• Chamovitz, D. (2017). What a Plant Knows: A Field Guide to the Senses. An accessible introduction to how plants perceive light, gravity and other environmental signals, drawing substantially on research in Arabidopsis.
• Bowman, J. L., ed. (1994). Arabidopsis: An Atlas of Morphology and Development. A detailed visual guide to the plant’s anatomy, development and mutant forms.
• Weigel, D. and Glazebrook, J. (2002). Arabidopsis: A Laboratory Manual. A practical and more technical guide to growing, crossing and genetically analysing Arabidopsis.
• American Society of Plant Biologists. The Arabidopsis Book. A free, peer-reviewed collection of detailed chapters covering Arabidopsis genetics, development, physiology and cell biology.