Editing Arabidopsis thaliana (section)

===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.