Arabidopsis thaliana

File:194 Arabidopsis thaliana, Turritis glabra.jpg

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.Flora of NW Europe: [http://ip30.eti.uva.nl/BIS/flora.php?selected=beschrijving&menuentry=soorten&id=2273 Arabidopsis thaliana] {{webarchive |url=https://web.archive.org/web/20071208204350/http://ip30.eti.uva.nl/BIS/flora.php?selected=beschrijving&menuentry=soorten&id=2273 |date=8 December 2007 }}Blamey, M. & Grey-Wilson, C. (1989). Flora of Britain and Northern Europe. {{ISBN|0-340-40170-2}}Flora of Pakistan: [http://www.efloras.org/florataxon.aspx?flora_id=5&taxon_id=200009201 Arabidopsis thaliana] {{Webarchive |url=https://web.archive.org/web/20080618174531/http://www.efloras.org/florataxon.aspx?flora_id=5&taxon_id=200009201 |date=18 June 2008 }}Flora of China: [http://www.efloras.org/florataxon.aspx?flora_id=2&taxon_id=200009201 Arabidopsis thaliana] {{Webarchive |url=https://web.archive.org/web/20181005004459/http://www.efloras.org/florataxon.aspx?flora_id=2&taxon_id=200009201 |date=5 October 2018 }} 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.{{cite journal |vauthors=López-Bucio J, Campos-Cuevas JC, Hernández-Calderón E, Velásquez-Becerra C, Farías-Rodríguez R, Macías-Rodríguez LI, Valencia-Cantero E |title=Bacillus megaterium rhizobacteria promote growth and alter root-system architecture through an auxin- and ethylene-independent signaling mechanism in Arabidopsis thaliana |journal=Molecular Plant-Microbe Interactions |volume=20 |issue=2 |pages=207–17 |date=February 2007 |pmid=17313171 |doi=10.1094/MPMI-20-2-0207 |doi-access=free|bibcode=2007MPMI...20..207L }}

File:Müürlooga (Arabidopsis thaliana) lehekarv (trihhoom) 311 0804.JPG of a trichome, a leaf hair of A. thaliana, a unique structure made of a single cell]]

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.{{cite journal |vauthors=Meinke DW, Cherry JM, Dean C, Rounsley SD, Koornneef M |title=Arabidopsis thaliana: a model plant for genome analysis |journal=Science |volume=282 |issue=5389 |pages=662, 679–82 |date=October 1998 |pmid=9784120 |doi=10.1126/science.282.5389.662 |citeseerx=10.1.1.462.4735 |bibcode=1998Sci...282..662M}}

The plant was first described in 1577 in the Harz Mountains by {{interlanguage link|Johannes Thal|de}} (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.{{cite journal |last1=((The 1001 Genomes Consortium)) |title=1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana |journal=Cell |volume=166 |issue=2 |pages=481–491 |date=July 2016 |pmid=27293186 |pmc=4949382 |doi=10.1016/j.cell.2016.05.063}} These accessions exhibit considerable genetic and phenotypic variation, which can be used to study the adaptation of this species to different environments.

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.{{Cite web |url=https://www.gbif.org/species/3052436 |title=Arabidopsis thaliana (L.) Heynh. |website=www.gbif.org |language=en |access-date=2018-12-08 |archive-date=1 June 2019 |archive-url=https://web.archive.org/web/20190601174828/https://www.gbif.org/species/3052436 |url-status=live}} It also appears to be native in tropical alpine ecosystems in Africa and perhaps South Africa.{{cite journal |last=Hedberg |first=Olov |title=Afroalpine Vascular Plants: A Taxonomic Revision |journal=Acta Universitatis Upsaliensis: Symbolae Botanicae Upsalienses |year=1957 |volume=15 |issue=1 |pages=1–144}}{{cite journal |vauthors=Fulgione A, Hancock AM |title=Archaic lineages broaden our view on the history of Arabidopsis thaliana |journal=The New Phytologist |volume=219 |issue=4 |pages=1194–1198 |date=September 2018 |pmid=29862511 |doi=10.1111/nph.15244 |doi-access=free |bibcode=2018NewPh.219.1194F |hdl=21.11116/0000-0002-C3C7-1 |hdl-access=free }} It has been introduced and naturalized worldwide,{{cite web |url=http://eol.org/pages/583954/overview |title=Arabidopsis thaliana – Overview |publisher=Encyclopedia of Life |access-date=31 May 2016 |archive-date=10 June 2016 |archive-url=https://web.archive.org/web/20160610211837/http://eol.org/pages/583954/overview |url-status=live}} including in North America around the 17th century.{{cite journal |vauthors=Exposito-Alonso M, Becker C, Schuenemann VJ, Reiter E, Setzer C, Slovak R, Brachi B, Hagmann J, Grimm DG, Chen J, Busch W, Bergelson J, Ness RW, Krause J, Burbano HA, Weigel D |title=The rate and potential relevance of new mutations in a colonizing plant lineage |journal=PLOS Genetics |volume=14 |issue=2 |pages=e1007155 |date=February 2018 |pmid=29432421 |pmc=5825158 |doi=10.1371/journal.pgen.1007155 |doi-access=free }}

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,{{cite web |url=http://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:277970-1 |title=Arabidopsis thaliana (thale cress) |publisher=Kew Gardens |access-date=27 February 2018 |archive-date=28 February 2018 |archive-url=https://web.archive.org/web/20180228041841/http://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:277970-1 |url-status=live}} but due to its limited competitive ability and small size, it is not categorized as a noxious weed.{{Cite web |url=https://plants.sc.egov.usda.gov/java/noxComposite |title=State and Federal Noxious Weeds List {{!}} USDA PLANTS |website=plants.sc.egov.usda.gov |access-date=2018-12-08 |archive-date=9 December 2018 |archive-url=https://web.archive.org/web/20181209165307/https://plants.sc.egov.usda.gov/java/noxComposite |url-status=dead}} 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.{{cite web |title=IRMNG |url=http://eol.org/collections/100585 |publisher=Encyclopedia of Life |archive-url=https://web.archive.org/web/20180401044655/http://eol.org/collections/100585 |archive-date=1 April 2018}}

{{Main|History of research on Arabidopsis thaliana|l1=History of research on Arabidopsis thaliana}}

Botanists and biologists began to research A. thaliana in the early 1900s, and the first systematic description of mutants was done around 1945.[http://www.arabidopsis.org/portals/education/aboutarabidopsis.jsp] {{Webarchive|url=https://web.archive.org/web/20161022211543/http://www.arabidopsis.org/portals/education/aboutarabidopsis.jsp|date=22 October 2016}} TAIR: About Arabidopsis A. thaliana is now widely used for studying plant sciences, including genetics, evolution, population genetics, and plant development.{{cite journal |vauthors=Rensink WA, Buell CR |title=Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species |journal=Plant Physiology |volume=135 |issue=2 |pages=622–9 |date=June 2004 |pmid=15208410 |pmc=514098 |doi=10.1104/pp.104.040170}}{{cite journal |vauthors=Coelho SM, Peters AF, Charrier B, Roze D, Destombe C, Valero M, Cock JM |title=Complex life cycles of multicellular eukaryotes: new approaches based on the use of model organisms |journal=Gene |volume=406 |issue=1–2 |pages=152–70 |date=December 2007 |pmid=17870254 |doi=10.1016/j.gene.2007.07.025 |s2cid=24427325 |url=https://hal.archives-ouvertes.fr/hal-01926745/file/Life%20cycle%20review%20030807.pdf |access-date=29 June 2021 |archive-date=9 July 2021 |archive-url=https://web.archive.org/web/20210709181559/https://hal.archives-ouvertes.fr/hal-01926745/file/Life%20cycle%20review%20030807.pdf |url-status=live}}{{cite journal |vauthors=Platt A, Horton M, Huang YS, Li Y, Anastasio AE, Mulyati NW, Agren J, Bossdorf O, Byers D, Donohue K, Dunning M, Holub EB, Hudson A, Le Corre V, Loudet O, Roux F, Warthmann N, Weigel D, Rivero L, Scholl R, Nordborg M, Bergelson J, Borevitz JO |title=The scale of population structure in Arabidopsis thaliana |journal=PLOS Genetics |volume=6 |issue=2 |pages=e1000843 |date=February 2010 |pmid=20169178 |pmc=2820523 |doi=10.1371/journal.pgen.1000843 |editor1-last=Novembre |editor1-first=John |doi-access=free }} 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.

File:Arabidopsis mutants.jpg

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).{{cite journal |vauthors=Yanofsky MF, Ma H, Bowman JL, Drews GN, Feldmann KA, Meyerowitz EM |title=The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors |journal=Nature |volume=346 |issue=6279 |pages=35–9 |date=July 1990 |pmid=1973265 |doi=10.1038/346035a0 |bibcode=1990Natur.346...35Y |s2cid=4323431}} Friedrich Laibach (who had published the chromosome number in 1907) did not propose A. thaliana as a model organism, though, until 1943.{{cite journal |vauthors=Meyerowitz EM |title=Prehistory and history of Arabidopsis research |journal=Plant Physiology |volume=125 |issue=1 |pages=15–9 |date=January 2001 |pmid=11154286 |pmc=1539315 |doi=10.1104/pp.125.1.15}} 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,{{cite web |title=About AIS |website=The Arabidopsis Information Resource |date=2018-11-08 |url=http://www.arabidopsis.org/ais/newaishint.jsp |access-date=2021-04-25 |archive-date=27 April 2021 |archive-url=https://web.archive.org/web/20210427093913/https://www.arabidopsis.org/ais/newaishint.jsp |url-status=live}} 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.{{cite journal |vauthors=Lloyd AM, Barnason AR, Rogers SG, Byrne MC, Fraley RT, Horsch RB |title=Transformation of Arabidopsis thaliana with Agrobacterium tumefaciens |journal=Science |volume=234 |issue=4775 |pages=464–6 |date=October 1986 |pmid=17792019 |doi=10.1126/science.234.4775.464 |bibcode=1986Sci...234..464L |s2cid=22125701}}{{cite journal |vauthors=Chang C, Meyerowitz EM |title=Molecular cloning and DNA sequence of the Arabidopsis thaliana alcohol dehydrogenase gene |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=83 |issue=5 |pages=1408–12 |date=March 1986 |pmid=2937058 |pmc=323085 |doi=10.1073/pnas.83.5.1408 |bibcode=1986PNAS...83.1408C |doi-access=free}}

File:Plastomap of Arabidopsis thaliana.svg

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{{cite journal |vauthors=Bennett MD, Leitch IJ, Price HJ, Johnston JS |title=Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb, thus approximately 25% larger than the Arabidopsis genome initiative estimate of approximately 125 Mb |journal=Annals of Botany |volume=91 |issue=5 |pages=547–57 |date=April 2003 |pmid=12646499 |pmc=4242247 |doi=10.1093/aob/mcg057}} 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,(Leutwileret al., 1984). In our survey Arabidopsis ... 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.{{cite journal |vauthors=Fleischmann A, Michael TP, Rivadavia F, Sousa A, Wang W, Temsch EM, Greilhuber J, Müller KF, Heubl G |title=Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms |journal=Annals of Botany |volume=114 |issue=8 |pages=1651–63 |date=December 2014 |pmid=25274549 |pmc=4649684 |doi=10.1093/aob/mcu189}} It was the first plant genome to be sequenced, completed in 2000 by the Arabidopsis Genome Initiative.{{cite journal |author=The Arabidopsis Genome Initiative |title=Analysis of the genome sequence of the flowering plant Arabidopsis thaliana |journal=Nature |volume=408 |issue=6814 |pages=796–815 |date=December 2000 |pmid=11130711 |doi=10.1038/35048692 |bibcode=2000Natur.408..796T |doi-access=free}} The most up-to-date version of the A. thaliana genome is maintained by the Arabidopsis Information Resource.{{Cite web |title=TAIR - Genome Annotation |url=http://www.arabidopsis.org/portals/genAnnotation/gene_structural_annotation/annotation_data.jsp |access-date=29 December 2008 |archive-date=14 October 2008 |archive-url=https://web.archive.org/web/20081014183552/http://www.arabidopsis.org/portals/genAnnotation/gene_structural_annotation/annotation_data.jsp |url-status=live}}

The genome encodes ~27,600 protein-coding genes and about 6,500 non-coding genes.{{Cite web |title=Details - Arabidopsis_thaliana - Ensembl Genomes 63 |url=http://ensembl.gramene.org/Arabidopsis_thaliana/Info/Annotation/#assembly |access-date=2021-06-15 |website=ensembl.gramene.org |language=en-gb |archive-date=24 June 2021 |archive-url=https://web.archive.org/web/20210624195651/http://ensembl.gramene.org/Arabidopsis_thaliana/Info/Annotation/#assembly |url-status=live}} However, the Uniprot database lists 39,342 proteins in their Arabidopsis reference proteome.{{Cite web |title=Arabidopsis thaliana (Mouse-ear cress) |url=https://www.uniprot.org/proteomes/UP000006548 |access-date=2021-06-15 |website=www.uniprot.org |language=en |archive-date=21 May 2021 |archive-url=https://web.archive.org/web/20210521205551/https://www.uniprot.org/proteomes/UP000006548 |url-status=live}} Among the 27,600 protein-coding genes 25,402 (91.8%) are now annotated with "meaningful" product names,{{Cite journal |last1=Cheng |first1=Chia-Yi |last2=Krishnakumar |first2=Vivek |last3=Chan |first3=Agnes P. |last4=Thibaud-Nissen |first4=Françoise |last5=Schobel |first5=Seth |last6=Town |first6=Christopher D. |date=2017 |title=Araport11: a complete reannotation of the Arabidopsis thaliana reference genome |journal=The Plant Journal |language=en |volume=89 |issue=4 |pages=789–804 |doi=10.1111/tpj.13415 |pmid=27862469 |s2cid=12155857 |issn=1365-313X |doi-access=free |bibcode=2017PlJ....89..789C }} 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.

The plastome of A. thaliana is a 154,478 base-pair-long DNA molecule,{{cite web |url=https://www.ncbi.nlm.nih.gov/nuccore/NC_000932 |title=Arabidopsis thaliana chloroplast, complete genome — NCBI accession number NC_000932.1 |publisher=National Center for Biotechnology Information |access-date=November 4, 2018 |archive-date=4 November 2018 |archive-url=https://web.archive.org/web/20181104211116/https://www.ncbi.nlm.nih.gov/nuccore/NC_000932 |url-status=live}} 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).{{Cite journal |vauthors=Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S |year=1999 |title=Complete structure of the chloroplast genome of Arabidopsis thaliana |journal=DNA Research |language=en |volume=6 |issue=5 |pages=283–290 |doi=10.1093/dnares/6.5.283 |pmid=10574454 |issn=1340-2838 |doi-access=free}}

The mitochondrial genome of A. thaliana is 367,808 base pairs long and contains 57 genes.{{cite web |url=https://www.ncbi.nlm.nih.gov/nuccore/bk010421 |title=Arabidopsis thaliana ecotype Col-0 mitochondrion, complete genome — NCBI accession number BK010421 |date=10 October 2018 |publisher=National Center for Biotechnology Information |access-date=April 10, 2019 |archive-date=12 April 2019 |archive-url=https://web.archive.org/web/20190412200017/https://www.ncbi.nlm.nih.gov/nuccore/bk010421 |url-status=live}} There are many repeated regions in the Arabidopsis mitochondrial genome. The largest repeats recombine regularly and isomerize the genome.{{cite journal |vauthors=Klein M, Eckert-Ossenkopp U, Schmiedeberg I, Brandt P, Unseld M, Brennicke A, Schuster W |year=1994 |title=Physical mapping of the mitochondrial genome of Arabidopsis thaliana by cosmid and YAC clones |journal=Plant Journal |volume=6 |issue=3 |pages=447–455 |doi=10.1046/j.1365-313X.1994.06030447.x |pmid=7920724 |doi-access=free}} Like most plant mitochondrial genomes, the Arabidopsis mitochondrial genome exists as a complex arrangement of overlapping branched and linear molecules in vivo.{{cite journal |vauthors=Gualberto JM, Mileshina D, Wallet C, Niazi AK, Weber-Lotfi F, Dietrich A |year=2014 |title=The plant mitochondrial genome: dynamics and maintenance |journal=Biochimie |volume=100 |pages=107–120 |doi=10.1016/j.biochi.2013.09.016 |pmid=24075874}}

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.{{cite journal |vauthors=Clough SJ, Bent AF |title=Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana |journal=The Plant Journal |volume=16 |issue=6 |pages=735–43 |date=December 1998 |pmid=10069079 |doi=10.1046/j.1365-313x.1998.00343.x |s2cid=410286}}{{cite journal |vauthors=Zhang X, Henriques R, Lin SS, Niu QW, Chua NH |title=Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method |journal=Nature Protocols |volume=1 |issue=2 |pages=641–6 |year=2006 |pmid=17406292 |doi=10.1038/nprot.2006.97 |s2cid=6906570}} 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.{{Cite web |url=http://signal.salk.edu/cgi-bin/tdnaexpress |title=T-DNA Express: Arabidopsis Gene Mapping Tool |website=signal.salk.edu |access-date=19 October 2009 |archive-date=25 November 2009 |archive-url=https://web.archive.org/web/20091125151524/http://signal.salk.edu/cgi-bin/tdnaexpress/ |url-status=live}} 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 Ler (Landsberg erecta), and Col, or Columbia.{{Cite web |url=http://arabidopsis.info/ |title=Eurasian Arabidopsis Stock Centre (uNASC) |website=arabidopsis.info |access-date=19 October 2009 |archive-date=12 December 2001 |archive-url=https://web.archive.org/web/20011212001728/http://arabidopsis.info/ |url-status=live}} 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.{{cite journal |vauthors=Magliano TM, Botto JF, Godoy AV, Symonds VV, Lloyd AM, Casal JJ |title=New Arabidopsis recombinant inbred lines (Landsberg erecta x Nossen) reveal natural variation in phytochrome-mediated responses |journal=Plant Physiology |volume=138 |issue=2 |pages=1126–35 |date=June 2005 |pmid=15908601 |pmc=1150426 |doi=10.1104/pp.104.059071}}) 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.{{Cite web |url=https://abrc.osu.edu/ |title=ABRC |website=abrc.osu.edu |access-date=12 December 2020 |archive-date=25 February 2021 |archive-url=https://web.archive.org/web/20210225031213/https://abrc.osu.edu/ |url-status=live}}

The Col-0 accession was selected by Rédei from within a (nonirradiated) population of seeds designated 'Landsberg' which he received from Laibach.{{Cite web |url=http://arabidopsis.info/CollectionInfo?id=94 |title=NASC Collection Info |website=arabidopsis.info |access-date=15 February 2011 |archive-date=19 July 2011 |archive-url=https://web.archive.org/web/20110719022459/http://arabidopsis.info/CollectionInfo?id=94 |url-status=live}} 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 Ler collection of mutants is derived from this initial line, Ler-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.{{cite journal |vauthors=Hahn F, Mantegazza O, Greiner A, Hegemann P, Eisenhut M, Weber AP |title=Arabidopsis thaliana |language=en |journal=Frontiers in Plant Science |volume=8 |pages=39 |date=2017 |pmid=28174584 |pmc=5258748 |doi=10.3389/fpls.2017.00039 |doi-access=free}}{{cite journal |vauthors=Hahn F, Eisenhut M, Mantegazza O, Weber AP |title=Arabidopsis With Cas9-Based Gene Targeting |journal=Frontiers in Plant Science |volume=9 |pages=424 |date=5 April 2018 |pmid=29675030 |pmc=5895730 |doi=10.3389/fpls.2018.00424 |doi-access=free}}

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.{{cite journal |vauthors=Lolle SJ, Victor JL, Young JM, Pruitt RE |title=Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis |journal=Nature |volume=434 |issue=7032 |pages=505–9 |date=March 2005 |pmid=15785770 |doi=10.1038/nature03380 |bibcode=2005Natur.434..505L |s2cid=1352368}}[https://www.washingtonpost.com/wp-dyn/articles/A58349-2005Mar22_2.html Washington Post summary.] {{Webarchive |url=https://web.archive.org/web/20161118043014/http://www.washingtonpost.com/wp-dyn/articles/A58349-2005Mar22_2.html |date=18 November 2016 }}{{cite journal |vauthors=Peng P, Chan SW, Shah GA, Jacobsen SE |title=Plant genetics: increased outcrossing in hothead mutants |journal=Nature |volume=443 |issue=7110 |pages=E8; discussion E8–9 |date=September 2006 |pmid=17006468 |doi=10.1038/nature05251 |bibcode=2006Natur.443E...8P |s2cid=4420979 |doi-access=free}}{{cite journal |vauthors=Pennisi E |author-link=Elizabeth Pennisi |title=Genetics. Pollen contamination may explain controversial inheritance |journal=Science |volume=313 |issue=5795 |pages=1864 |date=September 2006 |pmid=17008492 |doi=10.1126/science.313.5795.1864 |s2cid=82215542|doi-access=free }}

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.

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 {{visible anchor|AtVTI1a}} is probably essential to Golgi-vacuole trafficking. This is still a wide open field and plant SNAREs' role in trafficking remains understudied.{{cite journal |last=Raikhel |first=Natasha V. |author-link=Natasha Raikhel |title=Firmly Planted, Always Moving |journal=Annual Review of Plant Biology |publisher=Annual Reviews |volume=68 |issue=1 |date=2017-04-28 |issn=1543-5008 |doi=10.1146/annurev-arplant-042916-040829 |pages=1–27 |pmid=27860488|doi-access=free |bibcode=2017AnRPB..68....1R }}

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.Kaiser G, Kleiner O, Beisswenger C, Batschauer A. Increased DNA repair in Arabidopsis plants overexpressing CPD photolyase. Planta. 2009 Aug;230(3):505-15. doi: 10.1007/s00425-009-0962-y. Epub 2009 Jun 12. PMID 19521716 showed that in A. thaliana cyclobutane pyrimidine dimers (CPDs) induced by UV light can be repaired by expression of CPD photolyase.

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 & Apollo 17 were more robust than those grown in samples taken during Apollo 11.{{Cite web |last=Keeter |first=Bill |date=2022-05-12 |title=Scientists Grow Plants in Lunar Soil |url=http://www.nasa.gov/feature/biological-physical/scientists-grow-plants-in-soil-from-the-moon |access-date=2022-05-14 |website=NASA |archive-date=14 May 2022 |archive-url=https://web.archive.org/web/20220514200820/https://www.nasa.gov/feature/biological-physical/scientists-grow-plants-in-soil-from-the-moon/ |url-status=live }}

{{Further|ABC model of 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.

File:ABC flower development.svg

Observations of homeotic mutations led to the formulation of the ABC model of flower development by E. Coen and E. Meyerowitz.{{cite journal |vauthors=Coen ES, Meyerowitz EM |title=The war of the whorls: genetic interactions controlling flower development |journal=Nature |volume=353 |issue=6339 |pages=31–7 |date=September 1991 |pmid=1715520 |doi=10.1038/353031a0 |bibcode=1991Natur.353...31C |s2cid=4276098}} 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 affect petals and stamens), and class C genes (which affect stamens and carpels). These genes code for transcription factors that combine to cause tissue specification in their respective regions during development. Although developed through study of A. thaliana flowers, this model is generally applicable to other flowering plants.

Studies of A. thaliana have provided considerable insights with regards to the genetics of leaf morphogenesis, particularly in dicotyledon-type plants.{{cite journal |vauthors=Tsukaya H |title=Leaf development |journal=The Arabidopsis Book |volume=11 |pages=e0163 |date=2013-06-07 |pmid=23864837 |pmc=3711357 |doi=10.1199/tab.0163}}{{cite journal |vauthors=Turner S, Sieburth LE |title=Vascular patterning |journal=The Arabidopsis Book |volume=2 |pages=e0073 |date=2003-03-22 |pmid=22303224 |pmc=3243335 |doi=10.1199/tab.0073}} Much of the understanding has come from analyzing mutants in leaf development, some of which were identified in the 1960s, but were not analysed with genetic and molecular techniques until the mid-1990s. A. thaliana leaves are well suited to studies of leaf development because they are relatively simple and stable.

Using A. thaliana, the genetics behind leaf shape development have become more clear and have been broken down into three stages: The initiation of the leaf primordium, the establishment of dorsiventrality, and the development of a marginal meristem. Leaf primordia are initiated by the suppression of the genes and proteins of class I KNOX family (such as SHOOT APICAL MERISTEMLESS). These class I KNOX proteins directly suppress gibberellin biosynthesis in the leaf primordium. Many genetic factors were found to be involved in the suppression of these class I KNOX genes in leaf primordia (such as ASYMMETRIC LEAVES1, BLADE-ON-PETIOLE1, SAWTOOTH1, etc.). Thus, with this suppression, the levels of gibberellin increase and leaf primordium initiate growth.

The establishment of leaf dorsiventrality is important since the dorsal (adaxial) surface of the leaf is different from the ventral (abaxial) surface.{{cite journal |vauthors=Efroni I, Eshed Y, Lifschitz E |title=Morphogenesis of simple and compound leaves: a critical review |journal=The Plant Cell |volume=22 |issue=4 |pages=1019–32 |date=April 2010 |pmid=20435903 |pmc=2879760 |doi=10.1105/tpc.109.073601|bibcode=2010PlanC..22.1019E }}

A. thaliana is well suited for light microscopy analysis. Young seedlings on the whole, and their roots in particular, are relatively translucent. This, together with their small size, facilitates live cell imaging using both fluorescence and confocal laser scanning microscopy.Moreno N, Bougourd S, Haseloff J and Fiejo JA. 2006. Chapter 44: Imaging Plant Cells. In: Pawley JB (Editor). Handbook of Biological Confocal Microscopy - 3rd edition. SpringerScience+Business Media, New York. p769-787 By wet-mounting seedlings in water or in culture media, plants may be imaged uninvasively, obviating the need for fixation and sectioning and allowing time-lapse measurements.{{cite journal |vauthors=Shaw SL |title=Imaging the live plant cell |journal=The Plant Journal |volume=45 |issue=4 |pages=573–98 |date=February 2006 |pmid=16441350 |doi=10.1111/j.1365-313X.2006.02653.x}} Fluorescent protein constructs can be introduced through transformation. The developmental stage of each cell can be inferred from its location in the plant or by using fluorescent protein markers, allowing detailed developmental analysis.

The photoreceptors phytochromes A, B, C, D, and E mediate red light-based phototropic response. Understanding the function of these receptors has helped plant biologists understand the signaling cascades that regulate photoperiodism, germination, de-etiolation, and shade avoidance in plants. The genes FCA,{{cite journal |last1=Simpson |first1=Gordon G. |last2=Dean |first2=Caroline |title=Arabidopsis, the Rosetta Stone of Flowering Time? |journal=Science |publisher=American Association for the Advancement of Science (AAAS) |volume=296 |issue=5566 |date=2002-04-12 |issn=0036-8075 |doi=10.1126/science.296.5566.285 |pages=285–289 |pmid=11951029 |bibcode=2002Sci...296..285S |citeseerx=10.1.1.991.2232}} fy, fpa, LUMINIDEPENDENS (ld), fly, fve and FLOWERING LOCUS C (FLC){{cite journal |last=Friedman |first=Jannice |title=The Evolution of Annual and Perennial Plant Life Histories: Ecological Correlates and Genetic Mechanisms |journal=Annual Review of Ecology, Evolution, and Systematics |publisher=Annual Reviews |volume=51 |issue=1 |date=2020-11-02 |issn=1543-592X |doi=10.1146/annurev-ecolsys-110218-024638 |pages=461–481 |s2cid=225237602}}{{cite journal |last1=Whittaker |first1=Charles |last2=Dean |first2=Caroline |title=The FLC Locus: A Platform for Discoveries in Epigenetics and Adaptation |journal=Annual Review of Cell and Developmental Biology |publisher=Annual Reviews |volume=33 |issue=1 |date=2017-10-06 |issn=1081-0706 |doi=10.1146/annurev-cellbio-100616-060546 |pages=555–575 |pmid=28693387|doi-access=free }} are involved in photoperiod triggering of flowering and vernalization. Specifically Lee et al 1994 find ld produces a homeodomain and Blazquez et al 2001 that fve produces a WD40 repeat.

The UVR8 protein detects UV-B light and mediates the response to this DNA-damaging wavelength.

A. thaliana was used extensively in the study of the genetic basis of phototropism, chloroplast alignment, and stomal aperture and other blue light-influenced processes.{{cite journal |vauthors=Sullivan JA, Deng XW |title=From seed to seed: the role of photoreceptors in Arabidopsis development |journal=Developmental Biology |volume=260 |issue=2 |pages=289–97 |date=August 2003 |pmid=12921732 |doi=10.1016/S0012-1606(03)00212-4 |doi-access=free}} These traits respond to blue light, which is perceived by the phototropin light receptors. Arabidopsis has also been important in understanding the functions of another blue light receptor, cryptochrome, which is especially important for light entrainment to control the plants' circadian rhythms.{{cite journal |vauthors=Más P |title=Circadian clock signaling in Arabidopsis thaliana: from gene expression to physiology and development |journal=The International Journal of Developmental Biology |volume=49 |issue=5–6 |pages=491–500 |year=2005 |pmid=16096959 |doi=10.1387/ijdb.041968pm |doi-access=free}} When the onset of darkness is unusually early, A. thaliana reduces its metabolism of starch by an amount that effectively requires division.{{cite journal |vauthors=Scialdone A, Mugford ST, Feike D, Skeffington A, Borrill P, Graf A, Smith AM, Howard M |title=Arabidopsis plants perform arithmetic division to prevent starvation at night |journal=eLife |volume=2 |pages=e00669 |date=June 2013 |pmid=23805380 |pmc=3691572 |doi=10.7554/eLife.00669 |arxiv=1306.5148 |doi-access=free }}

Light responses were even found in roots, previously thought to be largely insensitive to light. While the gravitropic response of A. thaliana root organs is their predominant tropic response, specimens treated with mutagens and selected for the absence of gravitropic action showed negative phototropic response to blue or white light, and positive response to red light, indicating that the roots also show positive phototropism.{{cite journal |vauthors=Ruppel NJ, Hangarter RP, Kiss JZ |title=Red-light-induced positive phototropism in Arabidopsis roots |journal=Planta |volume=212 |issue=3 |pages=424–30 |date=February 2001 |pmid=11289607 |doi=10.1007/s004250000410 |bibcode=2001Plant.212..424R |s2cid=28410755}}

In 2000, Dr. Janet Braam of Rice University genetically engineered A. thaliana to glow in the dark when touched. The effect was visible to ultrasensitive cameras.[http://www.bioresearchonline.com/doc/Plants-that-Glow-in-the-Dark-0001 "Plants that Glow in the Dark"] {{Webarchive |url=https://web.archive.org/web/20140203014806/http://www.bioresearchonline.com/doc/plants-that-glow-in-the-dark-0001 |date=3 February 2014 }}, Bioresearch Online, 18 May 2000{{better source needed|date=March 2022}}

Multiple efforts, including the Glowing Plant project, have sought to use A. thaliana to increase plant luminescence intensity towards commercially viable levels.

In 1990, Janet Braam and Ronald W. Davis determined that A. thaliana exhibits thigmomorphogenesis in response to wind, rain and touch.{{Cite journal |last1=Braam |first1=Janet |last2=Davis |first2=Ronald W. |date=1990-02-09 |title=Rain-, wind-, and touch-induced expression of calmodulin and calmodulin-related genes in Arabidopsis |journal=Cell |language=English |volume=60 |issue=3 |pages=357–364 |doi=10.1016/0092-8674(90)90587-5 |pmid=2302732 |s2cid=38574940 |issn=0092-8674|doi-access=free }} Four or more touch induced genes in A. thaliana were found to be regulated by such stimuli. In 2002, Massimo Pigliucci found that A. thaliana developed different patterns of branching in response to sustained exposure to wind, a display of phenotypic plasticity.{{Cite journal |last=Pigliucci |first=Massimo |date=May 2002 |title=Touchy and Bushy: Phenotypic Plasticity and Integration in Response to Wind Stimulation inArabidopsis thaliana |url=http://dx.doi.org/10.1086/339158 |journal=International Journal of Plant Sciences |volume=163 |issue=3 |pages=399–408 |doi=10.1086/339158 |bibcode=2002IJPlS.163..399P |s2cid=84173889 |issn=1058-5893|url-access=subscription }}

On January 2, 2019, China's Chang'e-4 lander brought A. thaliana to the moon.{{Cite web |url=https://www.space.com/42905-china-space-moon-plants-animals.html |title=There Are Plants and Animals on the Moon Now (Because of China) |last=Letzter |first=Rafi |date=2019-01-04 |website=Space.com |access-date=2019-01-15 |archive-date=15 January 2019 |archive-url=https://web.archive.org/web/20190115234256/https://www.space.com/42905-china-space-moon-plants-animals.html |url-status=live}} A small microcosm 'tin' in the lander contained A. thaliana, seeds of potatoes, and silkworm eggs. As plants would support the silkworms with oxygen, and the silkworms would in turn provide the plants with necessary carbon dioxide and nutrients through their waste,{{Cite news |url=https://www.telegraph.co.uk/news/2018/04/13/china-plans-grow-flowers-silkworms-dark-side-moon/ |archive-url=https://ghostarchive.org/archive/20220112/https://www.telegraph.co.uk/news/2018/04/13/china-plans-grow-flowers-silkworms-dark-side-moon/ |archive-date=12 January 2022 |url-access=subscription |url-status=live |title=China plans to grow flowers and silkworms on the dark side of the moon |last=Connor |first=Neil |date=2018-04-13 |work=The Telegraph |access-date=2019-01-15 |language=en-GB |issn=0307-1235}}{{cbignore}} researchers will evaluate whether plants successfully perform photosynthesis, and grow and bloom in the lunar environment.

{{visible anchor|Thalianin}} is an Arabidopsis root triterpene. Potter et al., 2018 finds synthesis is induced by a combination of at least 2 facts, cell-specific transcription factors (TFs) and the accessibility of the chromatin.{{cite journal |year=2020 |issue=1 |volume=36 |publisher=Annual Reviews |journal=Annual Review of Cell and Developmental Biology |issn=1081-0706 |first2=Alain |first1=Elia |last2=Goossens |last1=Lacchini |pages=291–313 |doi=10.1146/annurev-cellbio-011620-031429 |title=Combinatorial Control of Plant Specialized Metabolism: Mechanisms, Functions, and Consequences |pmid=32559387 |s2cid=219947907}}

Understanding how plants achieve resistance is important to protect the world's food production, and the agriculture industry. Many model systems have been developed to better understand interactions between plants and bacterial, fungal, oomycete, viral, and nematode pathogens. A. thaliana has been a powerful tool for the study of the subdiscipline of plant pathology, that is, the interaction between plants and disease-causing pathogens.

File:ArabidopsisPlantPathology.jpg

File:Microbial consortia naturally formed on the roots of Arabidopsis thaliana.webp formed on roots
a) Overview of an A. thaliana root (primary root) with numerous root hairs, b) Biofilm-forming bacteria, c) Fungal or oomycete hyphae surrounding the root surface, d) Primary root densely covered by spores and protists, e, f) Protists, most likely belonging to the Bacillariophyceae class, g) Bacteria and bacterial filaments, h, i) Different bacterial individuals showing great varieties of shapes and morphological featuresHassani, M.A., Durán, P. and Hacquard, S. (2018) "Microbial interactions within the plant holobiont". Microbiome, 6(1): 58. {{doi|10.1186/s40168-018-0445-0|doi-access=free}}. 50px Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License] {{Webarchive |url=https://web.archive.org/web/20171016050101/https://creativecommons.org/licenses/by/4.0/ |date=16 October 2017 }}]]

The use of A. thaliana has led to many breakthroughs in the advancement of knowledge of how plants manifest plant disease resistance. The reason most plants are resistant to most pathogens is through nonhost resistance - not all pathogens will infect all plants. An example where A. thaliana was used to determine the genes responsible for nonhost resistance is Blumeria graminis, the causal agent of powdery mildew of grasses. A. thaliana mutants were developed using the mutagen ethyl methanesulfonate and screened to identify mutants with increased infection by B. graminis.{{cite journal |vauthors=Collins NC, Thordal-Christensen H, Lipka V, Bau S, Kombrink E, Qiu JL, Hückelhoven R, Stein M, Freialdenhoven A, Somerville SC, Schulze-Lefert P |title=SNARE-protein-mediated disease resistance at the plant cell wall |journal=Nature |volume=425 |issue=6961 |pages=973–7 |date=October 2003 |pmid=14586469 |doi=10.1038/nature02076 |bibcode=2003Natur.425..973C |s2cid=4408024}}{{cite journal |vauthors=Lipka V, Dittgen J, Bednarek P, Bhat R, Wiermer M, Stein M, Landtag J, Brandt W, Rosahl S, Scheel D, Llorente F, Molina A, Parker J, Somerville S, Schulze-Lefert P |title=Pre- and postinvasion defenses both contribute to nonhost resistance in Arabidopsis |journal=Science |volume=310 |issue=5751 |pages=1180–3 |date=November 2005 |pmid=16293760 |doi=10.1126/science.1119409 |bibcode=2005Sci...310.1180L |hdl=11858/00-001M-0000-0012-3A32-0 |s2cid=35317665 |url=http://edoc.mpg.de/get.epl?fid=49010&did=249221&ver=0 |hdl-access=free |access-date=5 September 2019 |archive-date=11 March 2022 |archive-url=https://web.archive.org/web/20220311175257/https://pure.mpg.de/?fid=49010&did=249221&ver=0 |url-status=live}}{{cite journal |vauthors=Stein M, Dittgen J, Sánchez-Rodríguez C, Hou BH, Molina A, Schulze-Lefert P, Lipka V, Somerville S |title=Arabidopsis PEN3/PDR8, an ATP binding cassette transporter, contributes to nonhost resistance to inappropriate pathogens that enter by direct penetration |journal=The Plant Cell |volume=18 |issue=3 |pages=731–46 |date=March 2006 |pmid=16473969 |pmc=1383646 |doi=10.1105/tpc.105.038372|bibcode=2006PlanC..18..731S }} The mutants with higher infection rates are referred to as PEN mutants due to the ability of B. graminis to penetrate A. thaliana to begin the disease process. The PEN genes were later mapped to identify the genes responsible for nonhost resistance to B. graminis.

In general, when a plant is exposed to a pathogen, or nonpathogenic microbe, an initial response, known as PAMP-triggered immunity (PTI), occurs because the plant detects conserved motifs known as pathogen-associated molecular patterns (PAMPs).{{cite journal |vauthors=Knepper C, Day B |title=From perception to activation: the molecular-genetic and biochemical landscape of disease resistance signaling in plants |journal=The Arabidopsis Book |volume=8 |pages=e012 |date=March 2010 |pmid=22303251 |pmc=3244959 |doi=10.1199/tab.0124}} These PAMPs are detected by specialized receptors in the host known as pattern recognition receptors (PRRs) on the plant cell surface.

The best-characterized PRR in A. thaliana is FLS2 (Flagellin-Sensing2), which recognizes bacterial flagellin,{{cite journal |vauthors=Gómez-Gómez L, Felix G, Boller T |title=A single locus determines sensitivity to bacterial flagellin in Arabidopsis thaliana |journal=The Plant Journal |volume=18 |issue=3 |pages=277–84 |date=May 1999 |pmid=10377993 |doi=10.1046/j.1365-313X.1999.00451.x |doi-access=free}}{{cite journal |vauthors=Gómez-Gómez L, Boller T |title=FLS2: an LRR receptor-like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis |journal=Molecular Cell |volume=5 |issue=6 |pages=1003–11 |date=June 2000 |pmid=10911994 |doi=10.1016/S1097-2765(00)80265-8 |doi-access=free}} a specialized organelle used by microorganisms for the purpose of motility, as well as the ligand flg22, which comprises the 22 amino acids recognized by FLS2. Discovery of FLS2 was facilitated by the identification of an A. thaliana ecotype, Ws-0, that was unable to detect flg22, leading to the identification of the gene encoding FLS2. FLS2 shows striking similarity to rice XA21, the first PRR isolated in 1995.{{citation needed|date=October 2021}} Both flagellin and UV-C act similarly to increase homologous recombination in A. thaliana, as demonstrated by Molinier et al. 2006. Beyond this somatic effect, they found this to extend to subsequent generations of the plant.{{cite journal |last1=Urban |first1=L. |last2=Chabane Sari |first2=D. |last3=Orsal |first3=B. |last4=Lopes |first4=M. |last5=Miranda |first5=R. |last6=Aarrouf |first6=J. |title=UV-C light and pulsed light as alternatives to chemical and biological elicitors for stimulating plant natural defenses against fungal diseases |journal=Scientia Horticulturae |publisher=Elsevier |volume=235 |year=2018 |issn=0304-4238 |doi=10.1016/j.scienta.2018.02.057 |pages=452–459 |bibcode=2018ScHor.235..452U |s2cid=90436989}}

A second PRR, EF-Tu receptor (EFR), identified in A. thaliana, recognizes the bacterial EF-Tu protein, the prokaryotic elongation factor used in protein synthesis, as well as the laboratory-used ligand elf18.{{cite journal |vauthors=Zipfel C, Kunze G, Chinchilla D, Caniard A, Jones JD, Boller T, Felix G |title=Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated transformation |journal=Cell |volume=125 |issue=4 |pages=749–60 |date=May 2006 |pmid=16713565 |doi=10.1016/j.cell.2006.03.037 |s2cid=6856390 |doi-access=free}} Using Agrobacterium-mediated transformation, a technique that takes advantage of the natural process by which Agrobacterium transfers genes into host plants, the EFR gene was transformed into Nicotiana benthamiana, tobacco plant that does not recognize EF-Tu, thereby permitting recognition of bacterial EF-Tu{{cite journal |vauthors=Lacombe S, Rougon-Cardoso A, Sherwood E, Peeters N, Dahlbeck D, van Esse HP, Smoker M, Rallapalli G, Thomma BP, Staskawicz B, Jones JD, Zipfel C |title=Interfamily transfer of a plant pattern-recognition receptor confers broad-spectrum bacterial resistance |journal=Nature Biotechnology |volume=28 |issue=4 |pages=365–9 |date=April 2010 |pmid=20231819 |doi=10.1038/nbt.1613 |s2cid=7260214}}, thereby confirming EFR as the receptor of EF-Tu.

Both FLS2 and EFR use similar signal transduction pathways to initiate PTI. A. thaliana has been instrumental in dissecting these pathways to better understand the regulation of immune responses, the most notable one being the mitogen-activated protein kinase (MAP kinase) cascade. Downstream responses of PTI include callose deposition, the oxidative burst, and transcription of defense-related genes.{{cite journal |vauthors=Zhang J, Zhou JM |title=Plant immunity triggered by microbial molecular signatures |journal=Molecular Plant |volume=3 |issue=5 |pages=783–93 |date=September 2010 |pmid=20713980 |doi=10.1093/mp/ssq035 |doi-access=free}}

PTI is able to combat pathogens in a nonspecific manner. A stronger and more specific response in plants is that of effector-triggered immunity (ETI), which is dependent upon the recognition of pathogen effectors, proteins secreted by the pathogen that alter functions in the host, by plant resistance genes (R-genes), often described as a gene-for-gene relationship. This recognition may occur directly or indirectly via a guardee protein in a hypothesis known as the guard hypothesis. The first R-gene cloned in A. thaliana was RPS2 (resistance to Pseudomonas syringae 2), which is responsible for recognition of the effector avrRpt2.{{cite journal |vauthors=Kunkel BN, Bent AF, Dahlbeck D, Innes RW, Staskawicz BJ |title=RPS2, an Arabidopsis disease resistance locus specifying recognition of Pseudomonas syringae strains expressing the avirulence gene avrRpt2 |journal=The Plant Cell |volume=5 |issue=8 |pages=865–75 |date=August 1993 |pmid=8400869 |pmc=160322 |doi=10.1105/tpc.5.8.865}} The bacterial effector avrRpt2 is delivered into A. thaliana via the Type III secretion system of P. syringae pv. tomato strain DC3000. Recognition of avrRpt2 by RPS2 occurs via the guardee protein RIN4, which is cleaved.{{clarify|date=October 2021}} Recognition of a pathogen effector leads to a dramatic immune response known as the hypersensitive response, in which the infected plant cells undergo cell death to prevent the spread of the pathogen.{{cite journal |vauthors=Axtell MJ, Staskawicz BJ |title=Initiation of RPS2-specified disease resistance in Arabidopsis is coupled to the AvrRpt2-directed elimination of RIN4 |journal=Cell |volume=112 |issue=3 |pages=369–77 |date=February 2003 |pmid=12581526 |doi=10.1016/S0092-8674(03)00036-9 |s2cid=1497625 |doi-access=free}}

Systemic acquired resistance (SAR) is another example of resistance that is better understood in plants because of research done in A. thaliana. Benzothiadiazol (BTH), a salicylic acid (SA) analog, has been used historically as an antifungal compound in crop plants. BTH, as well as SA, has been shown to induce SAR in plants. {{anchor|NPR1}}The initiation of the SAR pathway was first demonstrated in A. thaliana in which increased SA levels are recognized by nonexpresser of PR genes 1 (NPR1){{cite journal |vauthors=Cao H, Bowling SA, Gordon AS, Dong X |title=Characterization of an Arabidopsis Mutant That Is Nonresponsive to Inducers of Systemic Acquired Resistance |journal=The Plant Cell |volume=6 |issue=11 |pages=1583–1592 |date=November 1994 |pmid=12244227 |pmc=160545 |doi=10.1105/tpc.6.11.1583}} due to redox change in the cytosol, resulting in the reduction of NPR1. NPR1, which usually exists in a multiplex (oligomeric) state, becomes monomeric (a single unit) upon reduction.{{cite journal |vauthors=Mou Z, Fan W, Dong X |title=Inducers of plant systemic acquired resistance regulate NPR1 function through redox changes |journal=Cell |volume=113 |issue=7 |pages=935–44 |date=June 2003 |pmid=12837250 |doi=10.1016/S0092-8674(03)00429-X |s2cid=1562690 |doi-access=free}} When NPR1 becomes monomeric, it translocates to the nucleus, where it interacts with many TGA transcription factors, and is able to induce pathogen-related genes such as PR1.{{cite journal |vauthors=Johnson C, Boden E, Arias J |title=Salicylic acid and NPR1 induce the recruitment of trans-activating TGA factors to a defense gene promoter in Arabidopsis |journal=The Plant Cell |volume=15 |issue=8 |pages=1846–58 |date=August 2003 |pmid=12897257 |pmc=167174 |doi=10.1105/tpc.012211|bibcode=2003PlanC..15.1846J }} Another example of SAR would be the research done with transgenic tobacco plants, which express bacterial salicylate hydroxylase, nahG gene, requires the accumulation of SA for its expression{{cite journal |vauthors=Delaney TP, Uknes S, Vernooij B, Friedrich L, Weymann K, Negrotto D, Gaffney T, Gut-Rella M, Kessmann H, Ward E, Ryals J |title=A central role of salicylic Acid in plant disease resistance |journal=Science |volume=266 |issue=5188 |pages=1247–50 |date=November 1994 |pmid=17810266 |doi=10.1126/science.266.5188.1247 |bibcode=1994Sci...266.1247D |s2cid=15507678}}

Although not directly immunological, intracellular transport affects susceptibility by incorporating - or being tricked into incorporating - pathogen particles. For example, the Dynamin-related protein 2b/drp2b gene helps to move invaginated material into cells, with some mutants increasing PstDC3000 virulence even further.{{cite journal |last1=Ben Khaled |first1=Sara |last2=Postma |first2=Jelle |last3=Robatzek |first3=Silke |title=A Moving View: Subcellular Trafficking Processes in Pattern Recognition Receptor–Triggered Plant Immunity |journal=Annual Review of Phytopathology |publisher=Annual Reviews |volume=53 |issue=1 |date=2015-08-04 |issn=0066-4286 |doi=10.1146/annurev-phyto-080614-120347 |pages=379–402 |pmid=26243727|bibcode=2015AnRvP..53..379B }}

Plants are affected by multiple pathogens throughout their lifetimes. In response to the presence of pathogens, plants have evolved receptors on their cell surfaces to detect and respond to pathogens.{{cite journal |vauthors=Bent AF, Kunkel BN, Dahlbeck D, Brown KL, Schmidt R, Giraudat J, Leung J, Staskawicz BJ |title=RPS2 of Arabidopsis thaliana: a leucine-rich repeat class of plant disease resistance genes |journal=Science |volume=265 |issue=5180 |pages=1856–60 |date=September 1994 |pmid=8091210 |doi=10.1126/science.8091210 |bibcode=1994Sci...265.1856B}} Arabidopsis thaliana is a model organism used to determine specific defense mechanisms of plant-pathogen resistance.{{cite journal |vauthors=Zipfel C, Robatzek S, Navarro L, Oakeley EJ, Jones JD, Felix G, Boller T |title=Bacterial disease resistance in Arabidopsis through flagellin perception |journal=Nature |volume=428 |issue=6984 |pages=764–7 |date=April 2004 |pmid=15085136 |doi=10.1038/nature02485 |bibcode=2004Natur.428..764Z |s2cid=4332562}} These plants have special receptors on their cell surfaces that allow for detection of pathogens and initiate mechanisms to inhibit pathogen growth. They contain two receptors, FLS2 (bacterial flagellin receptor) and EF-Tu (bacterial EF-Tu protein), which use signal transduction pathways to initiate the disease response pathway. The pathway leads to the recognition of the pathogen causing the infected cells to undergo cell death to stop the spread of the pathogen. Plants with FLS2 and EF-Tu receptors have shown to have increased fitness in the population. This has led to the belief that plant-pathogen resistance is an evolutionary mechanism that has built up over generations to respond to dynamic environments, such as increased predation and extreme temperatures.

A. thaliana has also been used to study SAR.{{cite journal |vauthors=Lawton K, Friedrich L, Hunt M |year=1996 |title=Benzothiadizaole induces disease resistance by a citation of the systemic acquired resistance signal transduction pathway |journal=The Plant Journal |volume=10 |issue=1 |pages=71–82 |doi=10.1046/j.1365-313x.1996.10010071.x |pmid=8758979 |doi-access=free}}

This pathway uses benzothiadiazol, a chemical inducer, to induce transcription factors, mRNA, of SAR genes. This accumulation of transcription factors leads to inhibition of pathogen-related genes.

Plant-pathogen interactions are important for an understanding of how plants have evolved to combat different types of pathogens that may affect them. Variation in resistance of plants across populations is due to variation in environmental factors. Plants that have evolved resistance, whether it be the general variation or the SAR variation, have been able to live longer and hold off necrosis of their tissue (premature death of cells), which leads to better adaptation and fitness for populations that are in rapidly changing environments. In the future, comparisons of the pathosystems of wild populations + their coevolved pathogens with wild-wild hybrids of known parentage may reveal new mechanisms of balancing selection. In life history theory we may find that A. thaliana maintains certain alleles due to pleitropy between plant-pathogen effects and other traits, as in livestock.{{cite journal |last=Fridman |first=Eyal |title=Consequences of hybridization and heterozygosity on plant vigor and phenotypic stability |journal=Plant Science |publisher=Elsevier |volume=232 |year=2015 |issn=0168-9452 |doi=10.1016/j.plantsci.2014.11.014 |pages=35–40 |pmid=25617321|bibcode=2015PlnSc.232...35F }}

{{anchor|EDS1 family|CCHELO|EDS1|PAD4}}Research in A. thaliana suggests that the immunity regulator protein family EDS1 in general co-evolved with the CCHELO family of nucleotide-binding{{ndash}}leucine-rich-repeat-receptors (NLRs). Xiao et al. 2005 have shown that the powdery mildew immunity mediated by A. thaliana{{'}}s RPW8 (which has a CC{{sub|HELO}} domain) is dependent on two members of this family: EDS1 itself and PAD4.{{cite journal |last1=Lapin |first1=Dmitry |last2=Bhandari |first2=Deepak D. |last3=Parker |first3=Jane E. |title=Origins and Immunity Networking Functions of EDS1 Family Proteins |journal=Annual Review of Phytopathology |publisher=Annual Reviews |volume=58 |issue=1 |date=2020-08-25 |issn=0066-4286 |doi=10.1146/annurev-phyto-010820-012840 |pages=253–276 |s2cid=218617308 |pmid=32396762 |bibcode=2020AnRvP..58..253L |hdl=1874/413668}}

{{anchor|RPS5|RESISTANCE TO PSEUDOMONAS SYRINGAE 5|PBS1|AvrPphB SUSCEPTIBLE 1}}RESISTANCE TO PSEUDOMONAS SYRINGAE 5/RPS5 is a disease resistance protein which guards AvrPphB SUSCEPTIBLE 1/PBS1. PBS1, as the name would suggest, is the target of AvrPphB, an effector produced by Pseudomonas syringae pv. phaseolicola.{{cite journal |last1=Pottinger |first1=Sarah E. |last2=Innes |first2=Roger W. |title=RPS5-Mediated Disease Resistance: Fundamental Insights and Translational Applications |journal=Annual Review of Phytopathology |publisher=Annual Reviews |volume=58 |issue=1 |date=2020-08-25 |issn=0066-4286 |doi=10.1146/annurev-phyto-010820-012733 |pages=139–160 |pmid=32284014 |s2cid=215757180|doi-access=free |bibcode=2020AnRvP..58..139P }}

Ongoing research on A. thaliana is being performed on the International Space Station by the European Space Agency. The goals are to study the growth and reproduction of plants from seed to seed in microgravity.{{cite journal |vauthors=Link BM, Busse JS, Stankovic B |year=2014 |title=Seed-to-Seed-to-Seed Growth and Development of Arabidopsis in Microgravity |journal=Astrobiology |volume=14 |issue=10 |pages=866–875 |doi=10.1089/ast.2014.1184 |pmid=25317938 |pmc=4201294 |bibcode=2014AsBio..14..866L}}{{cite journal |vauthors=Ferl RJ, Paul AL |title=Lunar plant biology--a review of the Apollo era |journal=Astrobiology |volume=10 |issue=3 |pages=261–74 |date=April 2010 |pmid=20446867 |doi=10.1089/ast.2009.0417 |bibcode=2010AsBio..10..261F}}

Plant-on-a-chip devices in which A. thaliana tissues can be cultured in semi-in vitro conditions have been described.{{cite journal |vauthors=Yetisen AK, Jiang L, Cooper JR, Qin Y, Palanivelu R, Zohar Y |title=A microsystem-based assay for studying pollen tube guidance in plant reproduction |journal=J. Micromech. Microeng. |volume=25 |issue=5 |date=May 2011 |page=054018 |doi=10.1088/0960-1317/21/5/054018 |bibcode=2011JMiMi..21e4018Y |s2cid=12989263 |url=http://iopscience.iop.org/0960-1317/21/5/054018|url-access=subscription }} Use of these devices may aid understanding of pollen-tube guidance and the mechanism of sexual reproduction in A. thaliana.

Researchers at the University of Florida were able to grow the plant in lunar soil originating from the Sea of Tranquillity.{{cite web |url=https://www.nasa.gov/feature/biological-physical/scientists-grow-plants-in-soil-from-the-moon |title=NASA-funded study breaks new ground in plant research |date=12 May 2022 |publisher=NASA |access-date=13 May 2022 |url-status=live |archive-url=https://web.archive.org/web/20220512172110/https://www.nasa.gov/feature/biological-physical/scientists-grow-plants-in-soil-from-the-moon |archive-date=12 May 2022}}

A. thaliana is a predominantly self-pollinating plant with an outcrossing rate estimated at less than 0.3%.{{cite journal |vauthors=Abbott RJ, Gomes MF |year=1989 |title=Population genetic structure and outcrossing rate of Arabidopsis thaliana (L.) Heynh |journal=Heredity |volume=62 |issue=3 |pages=411–418 |doi=10.1038/hdy.1989.56 |doi-access=free|bibcode=1989Hered..62..411A }} An analysis of the genome-wide pattern of linkage disequilibrium suggested that self-pollination evolved roughly a million years ago or more.{{cite journal |vauthors=Tang C, Toomajian C, Sherman-Broyles S, Plagnol V, Guo YL, Hu TT, Clark RM, Nasrallah JB, Weigel D, Nordborg M |title=The evolution of selfing in Arabidopsis thaliana |journal=Science |volume=317 |issue=5841 |pages=1070–2 |date=August 2007 |pmid=17656687 |doi=10.1126/science.1143153 |bibcode=2007Sci...317.1070T |s2cid=45853624}} Meioses that lead to self-pollination are unlikely to produce significant beneficial genetic variability. However, these meioses can provide the adaptive benefit of recombinational repair of DNA damages during formation of germ cells at each generation.Bernstein H; Byerly HC; Hopf FA; Michod RE (1985). "Genetic damage, mutation, and the evolution of sex". Science. 229 (4719): 1277–81. Bibcode:1985Sci...229.1277B. doi:10.1126/science.3898363. PMID 3898363 Such a benefit may have been sufficient to allow the long-term persistence of meioses even when followed by self-fertilization. A physical mechanism for self-pollination in A. thaliana is through pre-anthesis autogamy, such that fertilisation takes place largely before flower opening.

• TAIR and NASC: curated sources for diverse genetic and molecular biology information, links to gene expression databases{{Cite web |url=https://www.arabidopsis.org/portals/expression/microarray/microarrayDatasetsV2.jsp |title=TAIR - Gene Expression - Microarray - Public Datasets |access-date=4 December 2021 |archive-date=4 December 2021 |archive-url=https://web.archive.org/web/20211204171933/https://www.arabidopsis.org/portals/expression/microarray/microarrayDatasetsV2.jsp |url-status=live}} etc.
• Arabidopsis Biological Resource Center (seed and DNA stocks)
• Nottingham Arabidopsis Stock Centre (seed and DNA stocks)
• Artade database
• [https://www.nature.com/articles/s41597-023-02189-w AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana]: see [https://data.indores.fr/dataset.xhtml?persistentId=doi:10.48579/PRO/SW1OQD data repository]

• Sexual selection in Arabidopsis thaliana
• A. thaliana responses to salinity
• BZIP intron plant
• The Thaliana Bridge, installed in 2021 at Harlow Carr was inspired by the work of the botanical scientist Rachel Leech and represents the sequence of an Arabidopsis thaliana chromosome.{{cite journal |title=Genome research inspires new bridge at Harlow Carr |journal=The Garden |date=2021 |issue=September 2021 |page=97}}
• Novosphingobium arabidopsis, isolated from the rhizosphere of the plant

{{Reflist|30em}}

{{Commons category}}

• [https://opendata.pku.edu.cn/dataset.xhtml?persistentId=doi:10.18170/DVN/PNHIYY Arabidopsis transcriptional regulatory map]
• [https://www.arabidopsis.org/ The Arabidopsis Information Resource (TAIR)]
• [http://signal.salk.edu/index.html Salk Institute Genomic Analysis Laboratory] {{Webarchive|url=https://web.archive.org/web/20210308011406/http://signal.salk.edu/index.html |date=8 March 2021 }}
• [http://www.genomenewsnetwork.org/articles/04_00/what_makes_plants.shtml What Makes Plants Grow? The Arabidopsis genome knows] Featured article in Genome News Network
• [https://bioone.org/journals/the-arabidopsis-book/issues The Arabidopsis book] - A comprehensive review published yearly related to research in Arabidopsis
• [https://pax-db.org/species/3702 A. thaliana protein abundance]
• [https://araport.org/ The Arabidopsis Information Portal (Araport)]

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