Editing Arabidopsis thaliana

{{short description|Model plant species in the family Brassicaceae}}
{{Use dmy dates|date=January 2015}}
{{Speciesbox
|image=Arabidopsis thaliana.jpg
|genus=Arabidopsis
|species=thaliana
 |authority=([[Carl Linnaeus|L.]]) [[Heynh.]]
|range_map=Arabidopsis thaliana distribution.svg
|range_map_caption=The range of ''Arabidopsis thaliana''.
{{unbulleted list|style=text-align:left;
 |{{Legend2|#007000|Countries where ''A. thaliana'' is native}}
 |{{Legend2|#0000FF|Countries where ''A. thaliana'' is naturalized}}
 |{{Legend2|#E0E0E0|Countries where ''A. thaliana'' is not found}}
}}
|synonyms=''Arabis thaliana''
|synonyms_ref=<ref name=Warwick>{{cite journal |url=http://www.catalogueoflife.org/col/details/species/id/15f369ef1876a27d77ed279da54f96d2 |vauthors=Warwick SI, Francis A, Al-Shehbaz IA |year=2016 |title=Brassicaceae species checklist and database |journal=Species 2000 & ITIS Catalogue of Life |edition=26 |issn=2405-8858 |access-date=1 June 2016 |archive-date=9 December 2018 |archive-url=https://web.archive.org/web/20181209124239/http://www.catalogueoflife.org/col/details/species/id/15f369ef1876a27d77ed279da54f96d2 |url-status=live}}</ref> 
}}

'''''Arabidopsis thaliana''''', the '''thale cress''', '''mouse-ear cress''' or '''arabidopsis''', is a small plant from the mustard family ([[Brassicaceae]]), native to Eurasia and Africa.<ref name=grin>{{GRIN |access-date=11 December 2017}}</ref><ref>{{cite journal |title=Biogeography of ''Arabidopsis thaliana'' (L.) Heynh. (Brassicaceae) |first1=Matthias H. |last1=Hoffmann |name-list-style=vanc |journal=Journal of Biogeography |volume=29 |pages=125–134 |year=2002 |issue=1 |doi=10.1046/j.1365-2699.2002.00647.x |bibcode=2002JBiog..29..125H |s2cid=84959150}}</ref><ref>{{cite journal |title=''Arabidopsis thaliana'' and its wild relatives: a model system for ecology and evolution |first1=Thomas |last1=Mitchell-Olds |name-list-style=vanc |journal=Trends in Ecology & Evolution |volume=16 |issue=12 |pages=693–700 |date=December 2001 |doi=10.1016/s0169-5347(01)02291-1}}</ref><ref>{{cite journal |journal=Molecular Ecology |year=2000 |volume=9 |issue=12 |pages=2109–2118 |doi=10.1046/j.1365-294x.2000.01122.x |pmid=11123622 |title=Genetic isolation by distance in ''Arabidopsis thaliana'': biogeography and postglacial colonization of Europe |first1=Timothy F. |last1=Sharbel |first2=Bernhard |last2=Haubold |first3=Thomas |last3=Mitchell-Olds |bibcode=2000MolEc...9.2109S |s2cid=1788832 |name-list-style=vanc}}</ref><ref name="kramer-natural-history">{{cite journal |vauthors=Krämer U |title=Planting molecular functions in an ecological context with ''Arabidopsis thaliana'' |journal=eLife |volume=4 |pages=–06100 |date=March 2015 |pmid=25807084 |pmc=4373673 |doi=10.7554/eLife.06100 |doi-access=free }}</ref><ref name="pmid28473417">{{cite journal |vauthors=Durvasula A, Fulgione A, Gutaker RM, Alacakaptan SI, Flood PJ, Neto C, Tsuchimatsu T, Burbano HA, Picó FX, Alonso-Blanco C, Hancock AM |title=''Arabidopsis thaliana'' |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=114 |issue=20 |pages=5213–5218 |date=May 2017 |pmid=28473417 |pmc=5441814 |doi=10.1073/pnas.1616736114 |doi-access=free}}</ref> 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 [[Base pair#Length measurements|megabase pairs]].<ref name="Genome Assembly">{{cite web |title=Genome Assembly |url=http://www.arabidopsis.org/portals/genAnnotation/gene_structural_annotation/agicomplete.jsp |publisher=The Arabidopsis Information Resource |access-date=29 March 2016 |archive-date=7 March 2021 |archive-url=https://web.archive.org/web/20210307232045/https://www.arabidopsis.org/portals/genAnnotation/gene_structural_annotation/agicomplete.jsp |url-status=live}}</ref> 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 [[phototropism|light sensing]].<ref>{{Cite web |title=Nifty 50: ARABIDOPSIS -- A PLANT GENOME PROJECT |url=https://www.nsf.gov/od/lpa/nsf50/nsfoutreach/htm/n50_z2/pages_z3/05_pg.htm |access-date=2023-02-10 |website=www.nsf.gov |archive-date=3 January 2024 |archive-url=https://web.archive.org/web/20240103021232/https://www.nsf.gov/od/lpa/nsf50/nsfoutreach/htm/n50_z2/pages_z3/05_pg.htm |url-status=dead }}</ref>

==Description==
[[File:194 Arabidopsis thaliana, Turritis glabra.jpg|thumb|left|upright|Botanical illustration]]

''Arabidopsis thaliana'' is an [[annual plant|annual]] (rarely [[biennial plant|biennial]]) plant, usually growing to 20–25&nbsp;cm tall.<ref name="kramer-natural-history" /> The [[leaf|leaves]] form a rosette at the base of the plant, with a few leaves also on the flowering [[Plant stem|stem]]. The basal leaves are green to slightly purplish in color, 1.5–5&nbsp;cm long, and 2–10&nbsp;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 [[trichome]]s. The [[flower]]s are 3&nbsp;mm in diameter, arranged in a [[Inflorescence#Simple inflorescences|corymb]]; their structure is that of the typical [[Brassicaceae]]. The fruit is a [[silique]] 5–20&nbsp;mm long, containing 20–30 [[seed]]s.<ref name=fnwe>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 }}</ref><ref name=blamey>Blamey, M. & Grey-Wilson, C. (1989). ''Flora of Britain and Northern Europe''. {{ISBN|0-340-40170-2}}</ref><ref name=fop>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 }}</ref><ref name=foc>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 }}</ref> 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 (ecology)|rhizosphere]] bacteria such as ''[[Bacillus megaterium]]''.<ref>{{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}}</ref>

[[File:Müürlooga (Arabidopsis thaliana) lehekarv (trihhoom) 311 0804.JPG|thumb|upright|[[Scanning electron microscope|Scanning electron micrograph]] 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.<ref>{{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}}</ref>

==Taxonomy==
The plant was first described in 1577 in the [[Harz Mountains]] by {{interlanguage link|Johannes Thal|de}} (1542–1583), a physician from [[Nordhausen, Thuringia|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 [[genus|generic]] name, ''[[wikt:Arabidopsis|Arabidopsis]]'', comes from [[Greek (language)|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.<ref name="GenomesConsortium2016">{{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}}</ref> These accessions exhibit considerable genetic and phenotypic variation, which can be used to study the adaptation of this species to different environments.<ref name="GenomesConsortium2016" />

==Distribution and habitat==

''A. thaliana'' is native to Europe, Asia, and Africa, and its geographic distribution is rather continuous from the [[Mediterranean Sea|Mediterranean]] to [[Scandinavia]] and Spain to [[Greece]].<ref>{{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}}</ref> It also appears to be native in tropical alpine ecosystems in Africa and perhaps South Africa.<ref>{{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}}</ref><ref>{{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 |hdl=21.11116/0000-0002-C3C7-1 |hdl-access=free }}</ref> It has been introduced and naturalized worldwide,<ref name=eol>{{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}}</ref> including in North America around the 17th century.<ref>{{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 }}</ref>

''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,<ref name=eol/><ref>{{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}}</ref> but due to its limited competitive ability and small size, it is not categorized as a noxious weed.<ref>{{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}}</ref> 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.<ref name="EOL">{{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}}</ref>

==Use as a model organism==
{{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.<ref>[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]]''</ref> ''A. thaliana'' is now widely used for studying [[plant sciences]], including [[genetics]], [[evolution]], population genetics, and plant development.<ref>{{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}}</ref><ref>{{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}}</ref><ref>{{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 }}</ref> 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|thumb|right|A double-flower mutant, first documented in 1873]]

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).<ref>{{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}}</ref> [[Friedrich Laibach]] (who had published the chromosome number in 1907) did not propose ''A. thaliana'' as a model organism, though, until 1943.<ref name="meyerowitz2001">{{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}}</ref> 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 "[[ecotype]]s"). 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,<ref name="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}}</ref> 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.<ref name="meyerowitz2001" /> 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 [[Transfer DNA|T-DNA]]-mediated [[Transformation (genetics)#Plants|transformation]] and the first [[clone (genetics)|clone]]d ''A. thaliana'' gene were described.<ref>{{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}}</ref><ref>{{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}}</ref>

===Genomics===

[[File:Plastomap of Arabidopsis thaliana.svg|thumb|Chloroplast genome map of ''A. thaliana'':<ref name="NCBI_NC_000932"/><ref name="Sato1999"/> Introns are in grey. Some genes consist of 5′ and 3′ portions. Strand 1 and 2 genes are transcribed clockwise and counterclockwise, respectively. The innermost circle provides the boundaries of the large and small single-copy regions (LSC and SSC, violet) separated by a pair of inverted repeats (IRa and IRB, black).]]

====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<ref>{{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}}</ref> and five [[chromosome]]s, ''A. thaliana'' has one of the smallest genomes among plants.<ref name="Genome Assembly"/> It was long thought to have the smallest genome of all flowering plants,<ref>(Leutwileret al., 1984). In our survey Arabidopsis ...</ref> 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&nbsp;Mbp.<ref name="Fleischmann 2014">{{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}}</ref> It was the first plant genome to be sequenced, completed in 2000 by the ''Arabidopsis'' Genome Initiative.<ref>{{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}}</ref> The most up-to-date version of the ''A. thaliana'' genome is maintained by the Arabidopsis Information Resource.<ref>{{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}}</ref>

The genome encodes ~27,600 [[protein]]-coding [[gene]]s and about 6,500 non-coding genes.<ref>{{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}}</ref> However, the Uniprot database lists 39,342 proteins in their ''Arabidopsis'' reference proteome.<ref>{{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}}</ref> Among the 27,600 protein-coding genes 25,402 (91.8%) are now annotated with "meaningful" product names,<ref>{{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 }}</ref> 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,<ref name="NCBI_NC_000932">{{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}}</ref> a size typically encountered in most flowering plants (see the [[List of sequenced plastomes#Flowering plants|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).<ref name="Sato1999">{{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}}</ref>

====Mitochondrial genome====

The mitochondrial genome of ''A. thaliana'' is 367,808 base pairs long and contains 57 genes.<ref name="NCBI_BK010421">{{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}}</ref> There are many repeated regions in the ''Arabidopsis'' mitochondrial genome. The largest repeats [[Genetic recombination|recombine]] regularly and isomerize the genome.<ref>{{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}}</ref> Like most plant mitochondrial genomes, the ''Arabidopsis'' mitochondrial genome exists as a complex arrangement of overlapping branched and linear molecules ''in vivo''.<ref>{{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}}</ref>

===Genetics===

[[Transformation (genetics)|Genetic transformation]] of ''A. thaliana'' is routine, using ''[[Agrobacterium tumefaciens]]'' to transfer [[deoxyribonucleic acid|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.<ref>{{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}}</ref><ref>{{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}}</ref> 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.<ref>{{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}}</ref> 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.<ref name="arabidopsis.info">{{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}}</ref> 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.<ref>{{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}}</ref>) 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<ref name="arabidopsis.info" /> and the Arabidopsis Biological Resource Center-ABRC in Ohio, USA.<ref>{{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}}</ref>
The Col-0 accession was selected by Rédei from within a (nonirradiated) population of seeds designated 'Landsberg' which he received from Laibach.<ref>{{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}}</ref> Columbia (named for the location of Rédei's former institution, [[University of Missouri]]-[[Columbia, 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. [[Gene knockout|Knockouts]] of the corresponding gene lead to [[Glossary of botanical terms#glabrous|glabrous]] plants. This [[phenotype]] has already been used in [[genome editing|gene editing]] experiments and might be of interest as visual marker for plant research to improve gene editing methods such as [[CRISPR#Genome engineering|CRISPR/Cas9.]]<ref>{{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}}</ref><ref>{{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}}</ref>

====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 [[Mendelian inheritance|inheritance]], but the phenomenon observed (reversion of mutant copies of the ''[[HOTHEAD (gene)|HOTHEAD]]'' gene to a wild-type state) was later suggested to be an artifact because the mutants show increased outcrossing due to organ fusion.<ref>{{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 }}</ref><ref>{{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}}</ref><ref>{{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 }}</ref>

===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 [[SNARE (protein)#In plants|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 apparatus|Golgi]]-[[vacuole]] trafficking. This is still a wide open field and plant SNAREs' role in trafficking remains understudied.<ref name="Raikhel-2017">{{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 (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 }}</ref>

===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.<ref>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</ref> 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]] & [[Apollo 17]] were more robust than those grown in samples taken during [[Apollo 11]].<ref>{{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 }}</ref>

==Development==

===Flower development===
{{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 - [[sepal]]s, [[petal]]s, [[stamen]]s, and [[Gynoecium|carpel]]s (which go on to form [[Gynoecium|pistil]]s). 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|thumb|150px|The ABC model of flower development was developed through studying ''A. thaliana''.]]

Observations of homeotic mutations led to the formulation of the [[ABC model|ABC model of flower development]] by [[Enrico Coen|E. Coen]] and [[Elliot Meyerowitz|E. Meyerowitz]].<ref>{{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}}</ref> 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 factor]]s 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.

===Leaf development===
Studies of ''A. thaliana'' have provided considerable insights with regards to the genetics of leaf morphogenesis, particularly in [[Dicotyledon|dicotyledon-type]] plants.<ref>{{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}}</ref><ref>{{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}}</ref> 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 ''[[Evolutionary history of plants|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 [[Anatomical terms of location|dorsal]] (adaxial) surface of the leaf is different from the ventral (abaxial) surface.<ref>{{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}}</ref>

===Microscopy===
''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 microscopy|fluorescence]] and [[confocal laser scanning microscopy]].<ref>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</ref> By wet-mounting seedlings in water or in culture media, plants may be imaged uninvasively, obviating the need for [[Fixation (histology)|fixation]] and [[dissection|sectioning]] and allowing [[time-lapse]] measurements.<ref>{{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}}</ref> Fluorescent protein constructs can be introduced through [[Transformation (genetics)|transformation]]. The [[plant morphology|developmental]] stage of each cell can be inferred from its location in the plant or by using [[green fluorescent protein|fluorescent protein]] [[biomarker|markers]], allowing detailed [[developmental biology|developmental analysis]].

==Physiology==

===Light sensing, light emission, and circadian biology===
The photoreceptors [[phytochrome]]s A, B, C, D, and E mediate red light-based [[phototropism|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 (plant gene)|FCA]]'',<ref name="Simpson-Dean-2002">{{cite journal |last1=Simpson |first1=Gordon G. |last2=Dean |first2=Caroline |title=''Arabidopsis'', the Rosetta Stone of Flowering Time? |journal=[[Science (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}}</ref> ''[[fy (plant gene)|fy]]'',<ref name="Simpson-Dean-2002" /> ''[[fpa (plant gene)|fpa]]'',<ref name="Simpson-Dean-2002" /> ''[[LUMINIDEPENDENS]]'' (''ld''),<ref name="Simpson-Dean-2002" /> ''[[fly (plant gene)|fly]]'',<ref name="Simpson-Dean-2002" /> ''[[fve (plant gene)|fve]]''<ref name="Simpson-Dean-2002" /> and ''[[FLOWERING LOCUS C]]'' (''FLC'')<ref name="Friedman-2020">{{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 (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}}</ref><ref name="Whittaker-Dean-2017">{{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 (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 }}</ref> 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]].<ref name="Simpson-Dean-2002" />

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 [[stoma]]l aperture and other blue light-influenced processes.<ref>{{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}}</ref> 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 rhythm]]s.<ref>{{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}}</ref> When the onset of darkness is unusually early, ''A. thaliana'' reduces its metabolism of starch by an amount that effectively requires [[Plant arithmetic|division]].<ref>{{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 }}</ref>

Light responses were even found in roots, previously thought to be largely insensitive to light. While the [[gravitropism|gravitropic]] response of ''A. thaliana'' root organs is their predominant tropic response, specimens treated with [[mutagen]]s 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.<ref>{{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}}</ref>

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.<ref>[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</ref>{{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.

=== Thigmomorphogenesis (Touch response) ===
In 1990, Janet Braam and [[Ronald W. Davis]] determined that ''A. thaliana'' exhibits [[thigmomorphogenesis]] in response to wind, rain and touch.<ref name="Braam-1990">{{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 }}</ref> Four or more touch induced genes in ''A. thaliana'' were found to be regulated by such stimuli.<ref name="Braam-1990" /> 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]].<ref>{{Cite journal |last=Pigliucci |first=Massimo |date=May 2002 |title=Touchy and Bushy: Phenotypic Plasticity and Integration in Response to Wind Stimulation in''Arabidopsis 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 |s2cid=84173889 |issn=1058-5893}}</ref>

===On the Moon===
On January 2, 2019, China's [[Chang'e-4]] lander brought ''A. thaliana'' to the moon.<ref name="Letzter2019">{{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}}</ref> A small [[Microcosm (experimental ecosystem)|microcosm]] 'tin' in the lander contained ''A. thaliana'', seeds of potatoes, and [[Bombyx mori|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,<ref>{{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}}</ref> researchers will evaluate whether plants successfully perform [[photosynthesis]], and grow and bloom in the lunar environment.<ref name="Letzter2019" />

===Secondary metabolites===
{{visible anchor|Thalianin}} is an ''Arabidopsis'' root [[triterpene]].<ref name="combinatorial"/> Potter ''et al.'', 2018 finds [[biosynthesis|synthesis]] is induced by a combination of at least 2 facts, cell-specific [[transcription factor]]s (TFs) and the accessibility of the [[chromatin]].<ref name="combinatorial">{{cite journal |year=2020 |issue=1 |volume=36 |publisher=[[Annual Reviews (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}}</ref>

==Plant–pathogen interactions==

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]], [[fungi|fungal]], [[oomycete]], [[virus|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]].
{| class="wikitable"
|-
! Pathogen type !! Example in ''A. thaliana''
|-
| '''Bacteria''' || ''[[Pseudomonas syringae]]'', [[Xanthomonas campestris pv. campestris|''Xanthomonas campestris'']]
|-
| '''Fungi''' || ''[[Colletotrichum destructivum]]'', ''[[Botrytis cinerea]]'', ''[[Golovinomyces]] [[Golovinomyces orontii|orontii]]''
|-
| '''Oomycete''' || ''[[Hyaloperonospora arabidopsidis]]''
|-
| '''Viral''' || [[Cauliflower mosaic virus|Cauliflower mosaic virus (CaMV)]], [[Tobacco mosaic virus|tobacco mosaic virus (TMV)]]
|-
| '''Nematode''' || [[Meloidogyne|''Meloidogyne incognita'']], [[Heterodera|''Heterodera schachtii'']]
|}

[[File:ArabidopsisPlantPathology.jpg|thumb|upright=2|'''Components of pathogen recognition in ''A. thaliana'' '''<br/>A schematic of PAMP-triggered immunity: recognition of flagellin by FLS2 (top left); effector-triggered immunity depicted through the recognition of avrRpt2 by RPS2 through RIN4 (top-right); microscopic view of callose deposition in an ''A. thaliana'' leaf (bottom left); an example of no hypersensitive response (HR) above, and HR in ''A. thaliana'' leaves below (bottom right)]]
[[File:Microbial consortia naturally formed on the roots of Arabidopsis thaliana.webp|thumb|upright=2|{{center|'''Microbial consortia naturally formed<br />on the roots of ''Arabidopsis thaliana'''''}} Scanning electron microscopy pictures of root surfaces from natural ''A. thaliana'' populations showing the complex [[Microbial consortium|microbial networks]] formed on roots<br />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 features<ref>Hassani, 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}}. [[File:CC-BY icon.svg|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 }}</ref>]]

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 [[mutagenic|mutagen]] [[ethyl methanesulfonate]] and screened to identify mutants with increased infection by ''B. graminis''.<ref>{{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}}</ref><ref>{{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}}</ref><ref>{{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}}</ref> 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 [[commensalism|nonpathogenic]] microbe, an initial response, known as PAMP-triggered immunity (PTI), occurs because the plant detects conserved motifs known as [[pathogen-associated molecular pattern]]s (PAMPs).<ref>{{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}}</ref> These PAMPs are detected by specialized [[Receptor (biochemistry)|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]],<ref>{{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}}</ref><ref>{{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}}</ref> a specialized organelle used by microorganisms for the purpose of motility, as well as the [[ligand (biochemistry)|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. [[Pamela Ronald#Xa21: Pattern recognition receptor-mediated immunity|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 (biology)|somatic]] effect, they found this to [[epigenetic trait|extend to subsequent generations of the plant]].<ref name="Urban-et-al-2018">{{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}}</ref>

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.<ref>{{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}}</ref> Using [[Agrobacterium#Uses in biotechnology|''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<ref>{{cite journal |vauthors=Lacombe S, Rougon-Cardoso A, Sherwood E, Peeters N, Dahlbeck D, van Esse HP, Smoker M, Rallapalli G, Thomma BP, [[Brian Staskawicz|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}},</ref> 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.<ref>{{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}}</ref>

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 [[R gene|resistance genes (R-genes)]], often described as [[Gene-for-gene relationship|a gene-for-gene relationship]]. This recognition may occur directly or indirectly via a guardee protein in a hypothesis known as [[Gene-for-gene relationship#The guard hypothesis|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.<ref>{{cite journal |vauthors=Kunkel BN, Bent AF, Dahlbeck D, Innes RW, [[Brian Staskawicz|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}}</ref> The bacterial effector avrRpt2 is delivered into ''A. thaliana'' via the [[Type III secretion system]] of [[Pseudomonas syringae#Pseudomonas syringae pv. tomato strain DC3000 and Arabidopsis thaliana|''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.<ref>{{cite journal |vauthors=Axtell MJ, [[Brian Staskawicz|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}}</ref>

[[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'')<ref>{{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}}</ref> due to redox change in the cytosol, resulting in the [[redox|reduction]] of ''NPR1. NPR1'', which usually exists in a multiplex (oligomeric) state, becomes monomeric (a single unit) upon reduction.<ref>{{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}}</ref> When NPR1 becomes monomeric, it [[Protein targeting#Protein translocation|translocates]] to the nucleus, where it interacts with many TGA [[transcription factor]]s, and is able to induce pathogen-related genes such as ''PR1''.<ref>{{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}}</ref> 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<ref name="Delaney, T. 1994">{{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}}</ref>

Although not directly immunological, [[intracellular transport]] affects [[Susceptible individual|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.<ref name="Khaled-et-al-2015">{{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 (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}}</ref>

===Evolutionary aspect of plant-pathogen resistance===
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.<ref name="Bent1994">{{cite journal |vauthors=Bent AF, Kunkel BN, Dahlbeck D, Brown KL, Schmidt R, Giraudat J, Leung J, [[Brian Staskawicz|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}}</ref> ''Arabidopsis thaliana'' is a model organism used to determine specific defense mechanisms of plant-pathogen resistance.<ref name="Zipfel, C. 2004">{{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}}</ref> These plants have special receptors on their cell surfaces that allow for detection of pathogens and initiate mechanisms to inhibit pathogen growth.<ref name="Zipfel, C. 2004"/> 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.<ref name="Zipfel, C. 2004"/> The pathway leads to the recognition of the pathogen causing the infected cells to undergo cell death to stop the spread of the pathogen.<ref name="Zipfel, C. 2004"/> Plants with FLS2 and EF-Tu receptors have shown to have increased fitness in the population.<ref name="Delaney, T. 1994"/> 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.<ref name="Delaney, T. 1994"/>

''A. thaliana'' has also been used to study SAR.<ref name="Lawton, K. 1996">{{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}}</ref>
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.<ref name="Lawton, K. 1996"/>

Plant-pathogen interactions are important for an understanding of how plants have evolved to combat different types of pathogens that may affect them.<ref name="Delaney, T. 1994"/> 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.<ref name="Delaney, T. 1994"/> In the future, comparisons of the [[pathosystem]]s of wild populations + their [[coevolution|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.<ref name="Fridman-2015">{{cite journal |last=Fridman |first=Eyal |title=Consequences of hybridization and heterozygosity on plant vigor and phenotypic stability |journal=[[Plant Science (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 }}</ref>

{{anchor|EDS1 family|CCHELO|EDS1|PAD4}}Research in ''A. thaliana'' suggests that the [[EDS1 family|immunity regulator protein family EDS1]] in general co-evolved with the [[CCHELO|CC{{sub|HELO}}]] family of [[NOD-like receptor|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}} [[protein domain|domain]]) is dependent on two members of this family: ''[[EDS1]]'' itself and ''[[PAD4]]''.<ref name="Lapin-et-al-2020">{{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 (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 |hdl=1874/413668}}</ref>

{{anchor|RPS5|RESISTANCE TO PSEUDOMONAS SYRINGAE 5|PBS1|AvrPphB SUSCEPTIBLE 1}}''[[RESISTANCE TO PSEUDOMONAS SYRINGAE 5]]/RPS5'' is a [[plant disease resistance protein|disease resistance protein]] which guards ''[[AvrPphB SUSCEPTIBLE 1]]/PBS1''. ''PBS1'', as the name would suggest, is the target of ''[[AvrPphB]]'', an [[effector (biology)|effector]] produced by [[Pseudomonas syringae pv. phaseolicola|''Pseudomonas syringae'' pv. ''phaseolicola'']].<ref name="Pottinger-Innes-2020">{{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 (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 }}</ref>

==Other research==
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]].<ref>{{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}}</ref><ref>{{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}}</ref>

Plant-on-a-chip devices in which ''A. thaliana'' tissues can be cultured in semi-''in vitro'' conditions have been described.<ref>{{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}}</ref> 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 [[Mare Tranquillitatis|Sea of Tranquillity]].<ref>{{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}}</ref>

===Self-pollination===
''A. thaliana'' is a predominantly self-pollinating plant with an outcrossing rate estimated at less than 0.3%.<ref>{{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}}</ref> An analysis of the genome-wide pattern of linkage disequilibrium suggested that self-pollination evolved roughly a million years ago or more.<ref name="pmid17656687">{{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}}</ref> 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.<ref>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</ref> 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.

==Databases and other resources==
*[[The Arabidopsis Information Resource|TAIR]] and NASC:<ref name="arabidopsis.info"/> curated sources for diverse genetic and molecular biology information, links to gene expression databases<ref>{{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}}</ref> 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]

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

==References==
{{Reflist|30em}}

==External links==
{{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)]

{{Model Organisms}}
{{Bioinformatics}}
{{Taxonbar|from=Q158695}}
{{Authority control}}

[[Category:Arabidopsis thaliana| ]]
[[Category:Flora of Europe]]
[[Category:Flora of Asia]]
[[Category:Flora of Africa]]
[[Category:Flora of Lebanon]]
[[Category:Plant models]]
[[Category:Plants described in 1753]]
[[Category:Taxa named by Carl Linnaeus]]
[[Category:Space-flown life]]
[[Category:Edible plants]]
[[Category:Plant intelligence]]
[[Category:Arabidopsis|thaliana]]