Oryza rufipogon: Difference between revisions
Content deleted Content added
m Correct name and wikilink North American Plant Protection Organization. |
New ==Genetics==, put ==Precious germplasm== into it (by the way I hate that name). New ===Selection===, effective population size<-correlation->magnitude of selection, from Hough et al 2013. |
||
| Line 14: | Line 14: | ||
'''''Oryza rufipogon''''', known as '''brownbeard rice''',<ref>{{PLANTS|id=ORRU|taxon=Oryza rufipogon|accessdate=25 July 2015}}</ref> '''wild rice,'''<ref name=GRIN>{{GRIN | accessdate = 12 January 2018}}</ref> and '''red rice''',<ref name=GRIN/> is a member of the genus ''[[Oryza]]''. |
'''''Oryza rufipogon''''', known as '''brownbeard rice''',<ref>{{PLANTS|id=ORRU|taxon=Oryza rufipogon|accessdate=25 July 2015}}</ref> '''wild rice,'''<ref name=GRIN>{{GRIN | accessdate = 12 January 2018}}</ref> and '''red rice''',<ref name=GRIN/> is a member of the genus ''[[Oryza]]''. |
||
It is native to [[East Asia|East]], [[South Asia|South]] and [[Southeast Asia]]. It has a close [[evolution]]ary relation to ''[[Oryza sativa]]'', the plant grown as a major [[rice]] [[food crop]] throughout the world. Both have an AA genome.<ref name="phylo">{{cite journal |doi-access=free |last1=Stein |first1=Joshua C. |last2=Yu |first2=Yeisoo |last3=Copetti |first3=Dario |last4=Zwickl |first4=Derrick J. |last5=Zhang |first5=Li |last6=Zhang |first6=Chengjun |last7=Chougule |first7=Kapeel |last8=Gao |first8=Dongying |last9=Iwata |first9=Aiko |last10=Goicoechea |first10=Jose Luis |last11=Wei |first11=Sharon |last12=Wang |first12=Jun |last13=Liao |first13=Yi |last14=Wang |first14=Muhua |last15=Jacquemin |first15=Julie |last16=Becker |first16=Claude |last17=Kudrna |first17=Dave |last18=Zhang |first18=Jianwei |last19=Londono |first19=Carlos E. M. |last20=Song |first20=Xiang |last21=Lee |first21=Seunghee |last22=Sanchez |first22=Paul |last23=Zuccolo |first23=Andrea |last24=Ammiraju |first24=Jetty S. S. |last25=Talag |first25=Jayson |last26=Danowitz |first26=Ann |last27=Rivera |first27=Luis F. |last28=Gschwend |first28=Andrea R. |last29=Noutsos |first29=Christos |last30=Wu |first30=Cheng-chieh |last31=Kao |first31=Shu-min |last32=Zeng |first32=Jhih-wun |last33=Wei |first33=Fu-jin |last34=Zhao |first34=Qiang |last35=Feng |first35=Qi |last36=El Baidouri |first36=Moaine |last37=Carpentier |first37=Marie-Christine |last38=Lasserre |first38=Eric |last39=Cooke |first39=Richard |last40=Rosa Farias |first40=Daniel da |last41=da Maia |first41=Luciano Carlos |last42=dos Santos |first42=Railson S. |last43=Nyberg |first43=Kevin G. |last44=McNally |first44=Kenneth L. |last45=Mauleon |first45=Ramil |last46=Alexandrov |first46=Nickolai |last47=Schmutz |first47=Jeremy |last48=Flowers |first48=Dave |last49=Fan |first49=Chuanzhu |last50=Weigel |first50=Detlef |last51=Jena |first51=Kshirod K. |last52=Wicker |first52=Thomas |last53=Chen |first53=Mingsheng |last54=Han |first54=Bin |last55=Henry |first55=Robert |last56=Hsing |first56=Yue-ie C. |last57=Kurata |first57=Nori |last58=de Oliveira |first58=Antonio Costa |last59=Panaud |first59=Olivier |last60=Jackson |first60=Scott A. |last61=Machado |first61=Carlos A. |last62=Sanderson |first62=Michael J. |last63=Long |first63=Manyuan |last64=Ware |first64=Doreen |last65=Wing |first65=Rod A. |title=Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza |journal=Nature Genetics |date=22 January 2018 |volume=50 |issue=2 |pages=285–296 |doi=10.1038/s41588-018-0040-0|pmid=29358651 }}</ref> |
It is native to [[East Asia|East]], [[South Asia|South]] and [[Southeast Asia]]. It has a close [[evolution]]ary relation to ''[[Oryza sativa]]'', the plant grown as a major [[rice]] [[food crop]] throughout the world. Both have an AA genome.<ref name="phylo">{{cite journal |doi-access=free |last1=Stein |first1=Joshua C. |last2=Yu |first2=Yeisoo |last3=Copetti |first3=Dario |last4=Zwickl |first4=Derrick J. |last5=Zhang |first5=Li |last6=Zhang |first6=Chengjun |last7=Chougule |first7=Kapeel |last8=Gao |first8=Dongying |last9=Iwata |first9=Aiko |last10=Goicoechea |first10=Jose Luis |last11=Wei |first11=Sharon |last12=Wang |first12=Jun |last13=Liao |first13=Yi |last14=Wang |first14=Muhua |last15=Jacquemin |first15=Julie |last16=Becker |first16=Claude |last17=Kudrna |first17=Dave |last18=Zhang |first18=Jianwei |last19=Londono |first19=Carlos E. M. |last20=Song |first20=Xiang |last21=Lee |first21=Seunghee |last22=Sanchez |first22=Paul |last23=Zuccolo |first23=Andrea |last24=Ammiraju |first24=Jetty S. S. |last25=Talag |first25=Jayson |last26=Danowitz |first26=Ann |last27=Rivera |first27=Luis F. |last28=Gschwend |first28=Andrea R. |last29=Noutsos |first29=Christos |last30=Wu |first30=Cheng-chieh |last31=Kao |first31=Shu-min |last32=Zeng |first32=Jhih-wun |last33=Wei |first33=Fu-jin |last34=Zhao |first34=Qiang |last35=Feng |first35=Qi |last36=El Baidouri |first36=Moaine |last37=Carpentier |first37=Marie-Christine |last38=Lasserre |first38=Eric |last39=Cooke |first39=Richard |last40=Rosa Farias |first40=Daniel da |last41=da Maia |first41=Luciano Carlos |last42=dos Santos |first42=Railson S. |last43=Nyberg |first43=Kevin G. |last44=McNally |first44=Kenneth L. |last45=Mauleon |first45=Ramil |last46=Alexandrov |first46=Nickolai |last47=Schmutz |first47=Jeremy |last48=Flowers |first48=Dave |last49=Fan |first49=Chuanzhu |last50=Weigel |first50=Detlef |last51=Jena |first51=Kshirod K. |last52=Wicker |first52=Thomas |last53=Chen |first53=Mingsheng |last54=Han |first54=Bin |last55=Henry |first55=Robert |last56=Hsing |first56=Yue-ie C. |last57=Kurata |first57=Nori |last58=de Oliveira |first58=Antonio Costa |last59=Panaud |first59=Olivier |last60=Jackson |first60=Scott A. |last61=Machado |first61=Carlos A. |last62=Sanderson |first62=Michael J. |last63=Long |first63=Manyuan |last64=Ware |first64=Doreen |last65=Wing |first65=Rod A. |title=Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus ''Oryza'' |journal=Nature Genetics |date=22 January 2018 |volume=50 |issue=2 |pages=285–296 |doi=10.1038/s41588-018-0040-0|pmid=29358651 }}</ref> |
||
'''''Oryza glumaepatula''''' is a related species according to molecular biology approaches. It used to be considered a synonym referring to the South American race of ''O. rufipogon''.<ref name="phylo"/> |
'''''Oryza glumaepatula''''' is a related species according to molecular biology approaches. It used to be considered a synonym referring to the South American race of ''O. rufipogon''.<ref name="phylo"/> |
||
| Line 21: | Line 21: | ||
''Oryza rufipogon'' is an [[invasive species]] and listed as a '[[noxious weed]]' by the United States,<ref>Plant Protection and Quarantine. 2006. Federal noxious weed list (24 May 2006). USDA Animal and Plant Health Inspection Service. Washington, DC. 2pp. http://plants.usda.gov/java/profile?symbol=ORRU</ref> and also listed as a noxious weed in [[Alabama]], [[California]], [[Florida]], [[Massachusetts]], [[Minnesota]], [[North Carolina]], [[Oregon]], [[South Carolina]], and [[Vermont]]. According to the NAPPO ([[North American Plant Protection Organization]]), ''O. rufipogon'' blends in with cultivated ''O. sativa'' so well that it cannot be detected. In this position it [[competition (biology)|competes]] with the cultivated rice and uses valuable [[fertilizer]] and space. ''O. rufipogon'' sheds most of its [[seeds]] before the harvest, therefore contributing little to the overall yield. In addition, the rice grains produced by the plant are not eaten by consumers, who see it as a strange foreign particle in otherwise white rice.<ref>NAPPO - PRA / Grains Panel Pest Fact Sheet - Oryza rufipogon Griff. June / 2003, http://www.nappo.org/PRA-sheets/Oryzarufipogon.pdf {{Webarchive|url=https://web.archive.org/web/20070730103504/http://www.nappo.org/PRA-sheets/Oryzarufipogon.pdf |date=2007-07-30 }}</ref> |
''Oryza rufipogon'' is an [[invasive species]] and listed as a '[[noxious weed]]' by the United States,<ref>Plant Protection and Quarantine. 2006. Federal noxious weed list (24 May 2006). USDA Animal and Plant Health Inspection Service. Washington, DC. 2pp. http://plants.usda.gov/java/profile?symbol=ORRU</ref> and also listed as a noxious weed in [[Alabama]], [[California]], [[Florida]], [[Massachusetts]], [[Minnesota]], [[North Carolina]], [[Oregon]], [[South Carolina]], and [[Vermont]]. According to the NAPPO ([[North American Plant Protection Organization]]), ''O. rufipogon'' blends in with cultivated ''O. sativa'' so well that it cannot be detected. In this position it [[competition (biology)|competes]] with the cultivated rice and uses valuable [[fertilizer]] and space. ''O. rufipogon'' sheds most of its [[seeds]] before the harvest, therefore contributing little to the overall yield. In addition, the rice grains produced by the plant are not eaten by consumers, who see it as a strange foreign particle in otherwise white rice.<ref>NAPPO - PRA / Grains Panel Pest Fact Sheet - Oryza rufipogon Griff. June / 2003, http://www.nappo.org/PRA-sheets/Oryzarufipogon.pdf {{Webarchive|url=https://web.archive.org/web/20070730103504/http://www.nappo.org/PRA-sheets/Oryzarufipogon.pdf |date=2007-07-30 }}</ref> |
||
==Genetics== |
|||
| ⚫ | |||
===Selection=== |
|||
As with a great many plants and animals, ''O. rufipogon'' has a positive correlation between [[effective population size]] and magnitude of [[selection pressure]]. ''O. r.'' having an EPS of ~140,000, it clusters with others of about the same EPS, and has 78% of its [[amino acid]] sites under selection.<ref name="Hough-et-al-2013">{{cite journal | last=Hough | first=Josh | last2=Williamson | first2=Robert J. | last3=Wright | first3=Stephen I. | title=Patterns of Selection in Plant Genomes | journal=[[Annual Review of Ecology, Evolution, and Systematics]] | publisher=[[Annual Reviews (publisher)|Annual Reviews]] | volume=44 | issue=1 | date=2013-11-23 | issn=1543-592X | doi=10.1146/annurev-ecolsys-110512-135851 | pages=31–49}}</ref> |
|||
| ⚫ | |||
A paper on [[conservation genetics]] of wild rice in the [[scientific journal|journal]] ''Molecular Ecology'' has this to say about ''O. rufipogon'': "This is the most agriculturally important but seriously [[endangered]] wild rice species." |
A paper on [[conservation genetics]] of wild rice in the [[scientific journal|journal]] ''Molecular Ecology'' has this to say about ''O. rufipogon'': "This is the most agriculturally important but seriously [[endangered]] wild rice species." |
||
Revision as of 21:03, 10 July 2021
| Oryza rufipogon | |
|---|---|
| |
Scientific classification 
| |
| Kingdom: | Plantae |
| Clade: | Tracheophytes |
| Clade: | Angiosperms |
| Clade: | Monocots |
| Clade: | Commelinids |
| Order: | Poales |
| Family: | Poaceae |
| Genus: | Oryza |
| Species: | O. rufipogon
|
| Binomial name | |
| Oryza rufipogon Griff.
| |
| |
| The range of Oryza rufipogon. | |
Oryza rufipogon, known as brownbeard rice,[2] wild rice,[3] and red rice,[3] is a member of the genus Oryza.
It is native to East, South and Southeast Asia. It has a close evolutionary relation to Oryza sativa, the plant grown as a major rice food crop throughout the world. Both have an AA genome.[4]
Oryza glumaepatula is a related species according to molecular biology approaches. It used to be considered a synonym referring to the South American race of O. rufipogon.[4]
Invasive species
Oryza rufipogon is an invasive species and listed as a 'noxious weed' by the United States,[5] and also listed as a noxious weed in Alabama, California, Florida, Massachusetts, Minnesota, North Carolina, Oregon, South Carolina, and Vermont. According to the NAPPO (North American Plant Protection Organization), O. rufipogon blends in with cultivated O. sativa so well that it cannot be detected. In this position it competes with the cultivated rice and uses valuable fertilizer and space. O. rufipogon sheds most of its seeds before the harvest, therefore contributing little to the overall yield. In addition, the rice grains produced by the plant are not eaten by consumers, who see it as a strange foreign particle in otherwise white rice.[6]
Genetics
Selection
As with a great many plants and animals, O. rufipogon has a positive correlation between effective population size and magnitude of selection pressure. O. r. having an EPS of ~140,000, it clusters with others of about the same EPS, and has 78% of its amino acid sites under selection.[7]
Precious germplasm
A paper on conservation genetics of wild rice in the journal Molecular Ecology has this to say about O. rufipogon: "This is the most agriculturally important but seriously endangered wild rice species."
In India, the Pallikaranai marshland contains the wild rice Oryza rufipogon, described by the Sálim Ali Centre for Ornithology and Natural History (SACON) as a "precious germplasm."[8]
See also
References
- ^ Watve, A.; Phillips, J.; Yang, L. (2017). "Oryza rufipogon". IUCN Red List of Threatened Species. 2017: e.T176902A61524992. doi:10.2305/IUCN.UK.2017-3.RLTS.T176902A61524992.en.
- ^ USDA, NRCS (n.d.). "Oryza rufipogon". The PLANTS Database (plants.usda.gov). Greensboro, North Carolina: National Plant Data Team. Retrieved 25 July 2015.
- ^ a b "Oryza rufipogon". Germplasm Resources Information Network. Agricultural Research Service, United States Department of Agriculture. Retrieved 12 January 2018.
- ^ a b Stein, Joshua C.; Yu, Yeisoo; Copetti, Dario; Zwickl, Derrick J.; Zhang, Li; Zhang, Chengjun; Chougule, Kapeel; Gao, Dongying; Iwata, Aiko; Goicoechea, Jose Luis; Wei, Sharon; Wang, Jun; Liao, Yi; Wang, Muhua; Jacquemin, Julie; Becker, Claude; Kudrna, Dave; Zhang, Jianwei; Londono, Carlos E. M.; Song, Xiang; Lee, Seunghee; Sanchez, Paul; Zuccolo, Andrea; Ammiraju, Jetty S. S.; Talag, Jayson; Danowitz, Ann; Rivera, Luis F.; Gschwend, Andrea R.; Noutsos, Christos; Wu, Cheng-chieh; Kao, Shu-min; Zeng, Jhih-wun; Wei, Fu-jin; Zhao, Qiang; Feng, Qi; El Baidouri, Moaine; Carpentier, Marie-Christine; Lasserre, Eric; Cooke, Richard; Rosa Farias, Daniel da; da Maia, Luciano Carlos; dos Santos, Railson S.; Nyberg, Kevin G.; McNally, Kenneth L.; Mauleon, Ramil; Alexandrov, Nickolai; Schmutz, Jeremy; Flowers, Dave; Fan, Chuanzhu; Weigel, Detlef; Jena, Kshirod K.; Wicker, Thomas; Chen, Mingsheng; Han, Bin; Henry, Robert; Hsing, Yue-ie C.; Kurata, Nori; de Oliveira, Antonio Costa; Panaud, Olivier; Jackson, Scott A.; Machado, Carlos A.; Sanderson, Michael J.; Long, Manyuan; Ware, Doreen; Wing, Rod A. (22 January 2018). "Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza". Nature Genetics. 50 (2): 285–296. doi:10.1038/s41588-018-0040-0. PMID 29358651.
- ^ Plant Protection and Quarantine. 2006. Federal noxious weed list (24 May 2006). USDA Animal and Plant Health Inspection Service. Washington, DC. 2pp. http://plants.usda.gov/java/profile?symbol=ORRU
- ^ NAPPO - PRA / Grains Panel Pest Fact Sheet - Oryza rufipogon Griff. June / 2003, http://www.nappo.org/PRA-sheets/Oryzarufipogon.pdf Archived 2007-07-30 at the Wayback Machine
- ^ Hough, Josh; Williamson, Robert J.; Wright, Stephen I. (2013-11-23). "Patterns of Selection in Plant Genomes". Annual Review of Ecology, Evolution, and Systematics. 44 (1). Annual Reviews: 31–49. doi:10.1146/annurev-ecolsys-110512-135851. ISSN 1543-592X.
- ^ The Hindu/Vanishing Wetlands- 09 March 2005, http://www.hindu.com/2005/03/09/stories/2005030903421000.htm
Wikimedia Commons has media related to Oryza rufipogon.
 | This Poaceae article is a stub. You can help Wikipedia by expanding it. |