Editing Arabidopsis thaliana (section)

===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>