Model plant species in the family Brassicaceae
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Arabidopsis thaliana, the thale cress, mouse-ear cress or arabidopsis, is a small plant from the mustard family (Brassicaceae), native to Eurasia and Africa. Commonly found along the shoulders of roads and in disturbed land, it is generally considered a weed.
A winter annual with a relatively short lifecycle, "A. thaliana" is a popular model organism in plant biology and genetics. For a complex multicellular eukaryote, "A. thaliana" has a relatively small genome of around 135 megabase pairs. It was the first plant to have its genome sequenced, and is an important tool for understanding the molecular biology of many plant traits, including flower development and light sensing.
Description.
"Arabidopsis thaliana" is an annual (rarely biennial) plant, usually growing to 20–25 cm tall. The leaves form a rosette at the base of the plant, with a few leaves also on the flowering stem. The basal leaves are green to slightly purplish in color, 1.5–5 cm long, and 2–10 mm broad, with an entire to coarsely serrated margin; the stem leaves are smaller and unstalked, usually with an entire margin. Leaves are covered with small, unicellular hairs called trichomes. The flowers are 3 mm in diameter, arranged in a corymb; their structure is that of the typical Brassicaceae. The fruit is a silique 5–20 mm long, containing 20–30 seeds. Roots are simple in structure, with a single primary root that grows vertically downward, later producing smaller lateral roots. These roots form interactions with rhizosphere bacteria such as "Bacillus megaterium".
"A. thaliana" can complete its entire lifecycle in six weeks. The central stem that produces flowers grows after about 3 weeks, and the flowers naturally self-pollinate. In the lab, "A. thaliana" may be grown in Petri plates, pots, or hydroponics, under fluorescent lights or in a greenhouse.
Taxonomy.
The plant was first described in 1577 in the Harz Mountains by Johannes Thal (1542–1583), a physician from Nordhausen, Thüringen, Germany, who called it "Pilosella siliquosa". In 1753, Carl Linnaeus renamed the plant "Arabis thaliana" in honor of Thal. In 1842, German botanist Gustav Heynhold erected the new genus "Arabidopsis" and placed the plant in that genus. The generic name, "Arabidopsis", comes from Greek, meaning "resembling "Arabis"" (the genus in which Linnaeus had initially placed it).
Thousands of natural inbred accessions of "A. thaliana" have been collected from throughout its natural and introduced range. These accessions exhibit considerable genetic and phenotypic variation, which can be used to study the adaptation of this species to different environments.
Distribution and habitat.
"A. thaliana" is native to Europe, Asia, and Africa, and its geographic distribution is rather continuous from the Mediterranean to Scandinavia and Spain to Greece. It also appears to be native in tropical alpine ecosystems in Africa and perhaps South Africa. It has been introduced and naturalized worldwide, including in North America around the 17th century.
"A. thaliana" readily grows and often pioneers rocky, sandy, and calcareous soils. It is generally considered a weed, due to its widespread distribution in agricultural fields, roadsides, railway lines, waste ground, and other disturbed habitats, but due to its limited competitive ability and small size, it is not categorized as a noxious weed. Like most Brassicaceae species, "A. thaliana" is edible by humans in a salad or cooked, but it does not enjoy widespread use as a spring vegetable.
Use as a model organism.
Botanists and biologists began to research "A. thaliana" in the early 1900s, and the first systematic description of mutants was done around 1945. "A. thaliana" is now widely used for studying plant sciences, including genetics, evolution, population genetics, and plant development. Although "A. thaliana" the plant has little direct significance for agriculture, "A. thaliana" the model organism has revolutionized our understanding of the genetic, cellular, and molecular biology of flowering plants.
The first mutant in "A. thaliana" was documented in 1873 by Alexander Braun, describing a double flower phenotype (the mutated gene was likely "Agamous", cloned and characterized in 1990). Friedrich Laibach (who had published the chromosome number in 1907) did not propose "A. thaliana" as a model organism, though, until 1943. His student, Erna Reinholz, published her thesis on "A. thaliana" in 1945, describing the first collection of "A. thaliana" mutants that they generated using X-ray mutagenesis. Laibach continued his important contributions to "A. thaliana" research by collecting a large number of accessions (often questionably referred to as "ecotypes"). With the help of Albert Kranz, these were organised into a large collection of 750 natural accessions of "A. thaliana" from around the world.
In the 1950s and 1960s, John Langridge and George Rédei played an important role in establishing "A. thaliana" as a useful organism for biological laboratory experiments. Rédei wrote several scholarly reviews instrumental in introducing the model to the scientific community. The start of the "A. thaliana" research community dates to a newsletter called "Arabidopsis" Information Service, established in 1964. The first International "Arabidopsis" Conference was held in 1965, in Göttingen, Germany.
In the 1980s, "A. thaliana" started to become widely used in plant research laboratories around the world. It was one of several candidates that included maize, petunia, and tobacco. The latter two were attractive, since they were easily transformable with the then-current technologies, while maize was a well-established genetic model for plant biology. The breakthrough year for "A. thaliana" as a model plant was 1986, in which T-DNA-mediated transformation and the first cloned "A. thaliana" gene were described.
Genomics.
Nuclear genome.
Due to the small size of its genome, and because it is diploid, "Arabidopsis thaliana" is useful for genetic mapping and sequencing — with about 157 megabase pairs and five chromosomes, "A. thaliana" has one of the smallest genomes among plants. It was long thought to have the smallest genome of all flowering plants, but that title is now considered to belong to plants in the genus "Genlisea", order Lamiales, with "Genlisea tuberosa", a carnivorous plant, showing a genome size of approximately 61 Mbp. It was the first plant genome to be sequenced, completed in 2000 by the "Arabidopsis" Genome Initiative. The most up-to-date version of the "A. thaliana" genome is maintained by the Arabidopsis Information Resource.
The genome encodes ~27,600 protein-coding genes and about 6,500 non-coding genes. However, the Uniprot database lists 39,342 proteins in their "Arabidopsis" reference proteome. Among the 27,600 protein-coding genes 25,402 (91.8%) are now annotated with "meaningful" product names, although a large fraction of these proteins is likely only poorly understood and only known in general terms (e.g. as "DNA-binding protein without known specificity"). Uniprot lists more than 3,000 proteins as "uncharacterized" as part of the reference proteome.
Chloroplast genome.
The plastome of "A. thaliana" is a 154,478 base-pair-long DNA molecule, a size typically encountered in most flowering plants (see the list of sequenced plastomes). It comprises 136 genes coding for small subunit ribosomal proteins ("rps", in yellow: see figure), large subunit ribosomal proteins ("rpl", orange), hypothetical chloroplast open reading frame proteins ("ycf", lemon), proteins involved in photosynthetic reactions (green) or in other functions (red), ribosomal RNAs ("rrn", blue), and transfer RNAs ("trn", black).
Mitochondrial genome.
The mitochondrial genome of "A. thaliana" is 367,808 base pairs long and contains 57 genes. There are many repeated regions in the "Arabidopsis" mitochondrial genome. The largest repeats recombine regularly and isomerize the genome. Like most plant mitochondrial genomes, the "Arabidopsis" mitochondrial genome exists as a complex arrangement of overlapping branched and linear molecules "in vivo".
Genetics.
Genetic transformation of "A. thaliana" is routine, using "Agrobacterium tumefaciens" to transfer DNA into the plant genome. The current protocol, termed "floral dip", involves simply dipping flowers into a solution containing "Agrobacterium" carrying a plasmid of interest and a detergent. This method avoids the need for tissue culture or plant regeneration.
The "A. thaliana" gene knockout collections are a unique resource for plant biology made possible by the availability of high-throughput transformation and funding for genomics resources. The site of T-DNA insertions has been determined for over 300,000 independent transgenic lines, with the information and seeds accessible through online T-DNA databases. Through these collections, insertional mutants are available for most genes in "A. thaliana".
Characterized accessions and mutant lines of "A. thaliana" serve as experimental material in laboratory studies. The most commonly used background lines are L"er" (Landsberg "erecta"), and Col, or Columbia. Other background lines less-often cited in the scientific literature are Ws, or Wassilewskija, C24, Cvi, or Cape Verde Islands, Nossen, etc. (see for ex.) Sets of closely related accessions named Col-0, Col-1, etc., have been obtained and characterized; in general, mutant lines are available through stock centers, of which best-known are the Nottingham Arabidopsis Stock Center-NASC and the Arabidopsis Biological Resource Center-ABRC in Ohio, USA.
The Col-0 accession was selected by Rédei from within a (nonirradiated) population of seeds designated 'Landsberg' which he received from Laibach. Columbia (named for the location of Rédei's former institution, University of Missouri-Columbia) was the reference accession sequenced in the "Arabidopsis" Genome Initiative. The Later (Landsberg erecta) line was selected by Rédei (because of its short stature) from a Landsberg population he had mutagenized with X-rays. As the L"er" collection of mutants is derived from this initial line, L"er"-0 does not correspond to the Landsberg accessions, which designated La-0, La-1, etc.
Trichome formation is initiated by the GLABROUS1 protein. Knockouts of the corresponding gene lead to glabrous plants. This phenotype has already been used in gene editing experiments and might be of interest as visual marker for plant research to improve gene editing methods such as CRISPR/Cas9.
Non-Mendelian inheritance controversy.
In 2005, scientists at Purdue University proposed that "A. thaliana" possessed an alternative to previously known mechanisms of DNA repair, producing an unusual pattern of inheritance, but the phenomenon observed (reversion of mutant copies of the "HOTHEAD" gene to a wild-type state) was later suggested to be an artifact because the mutants show increased outcrossing due to organ fusion.
Lifecycle.
The plant's small size and rapid lifecycle are also advantageous for research. Having specialized as a spring ephemeral, it has been used to found several laboratory strains that take about 6 weeks from germination to mature seed. The small size of the plant is convenient for cultivation in a small space, and it produces many seeds. Further, the selfing nature of this plant assists genetic experiments. Also, as an individual plant can produce several thousand seeds, each of the above criteria leads to "A. thaliana" being valued as a genetic model organism.
Cellular biology.
"Arabidopsis" is often the model for study of SNAREs in plants. This has shown SNAREs to be heavily involved in vesicle trafficking. Zheng et al. 1999 found an "Arabidopsis" SNARE called ;templatestyles src="Template:Visible anchor/styles.css" / ;AtVTI1a is probably essential to Golgi-vacuole trafficking. This is still a wide open field and plant SNAREs' role in trafficking remains understudied.
DNA repair.
The DNA of plants is vulnerable to ultraviolet light, and DNA repair mechanisms have evolved to avoid or repair genome damage caused by UV. Kaiser et al. showed that in "A. thaliana" cyclobutane pyrimidine dimers (CPDs) induced by UV light can be repaired by expression of CPD photolyase.
Germination in lunar regolith.
On May 12, 2022, NASA announced that specimens of "Arabidopsis thaliana" had been successfully germinated and grown in samples of lunar regolith. While the plants successfully germinated and grew into seedlings, they were not as robust as specimens that had been grown in volcanic ash as a control group, although the experiments also found some variation in the plants grown in regolith based on the location the samples were taken from, as "A. thaliana" grown in regolith gathered during Apollo 12 &amp; Apollo 17 were more robust than those grown in samples taken during Apollo 11.
Development.
Flower development.
"A. thaliana" has been extensively studied as a model for flower development. The developing flower has four basic organs - sepals, petals, stamens, and carpels (which go on to form pistils). These organs are arranged in a series of whorls, four sepals on the outer whorl, followed by four petals inside this, six stamens, and a central carpel region. Homeotic mutations in "A. thaliana" result in the change of one organ to another—in the case of the "agamous" mutation, for example, stamens become petals and carpels are replaced with a new flower, resulting in a recursively repeated sepal-petal-petal pattern.
Observations of homeotic mutations led to the formulation of the ABC model of flower development by E. Coen and E. Meyerowitz. According to this model, floral organ identity genes are divided into three classes - class A genes (which affect sepals and petals), class B genes (which