Oryza rufipogon

Oryza rufipogon
Scientific classification Edit this classification
Kingdom: Plantae
Clade: Tracheophytes
Clade: Angiosperms
Clade: Monocots
Clade: Commelinids
Order: Poales
Family: Poaceae
Genus: Oryza
Species:
O. rufipogon
Binomial name
Oryza rufipogon
The range of Oryza rufipogon.
Synonyms[2]
  • Oryza sativa var. rufipogon (Griff.) Watt
  • Oryza sativa subsp. rufipogon (Griff.) De Wet
  • Oryza cubensis Ekman ex K.Gotoh & Okura
  • Oryza fatua J.Koenig ex Ridl.
  • Oryza fatua (Prain) Zhuk.
  • Oryza fatua f. aquatica (Roshev.) Roshev.
  • Oryza fatua var. longe-aristata Ridl.
  • Oryza glumipatula Steud.
  • Oryza jeyporensis Govindasw. & K.H.Krishnam.
  • Oryza meridionalis N.Q.Ng
  • Oryza nivara S.D.Sharma & Shastry
  • Oryza paraguayensis Franch.
  • Oryza perennis var. glumipatula (Steud.) C.Chev.
  • Oryza perennis var. paragayensis A.Chev.
  • Oryza sativa var. abuensis Watt
  • Oryza sativa var. aquatica Roshev.
  • Oryza sativa var. bengalensis Watt
  • Oryza sativa var. coarctata Watt
  • Oryza sativa subsp. fatua (Prain) De Wet
  • Oryza sativa var. fatua Prain
  • Oryza sativa var. paraguayensis Körn.
  • Oryza sativa var. paraguayensis Parodi
  • Oryza sativa var. paraguayensis Franch.
  • Oryza sativa var. sundensis Körn.

Oryza rufipogon is a species of flowering plant in the family Poaceae.[2][3] It is known as brownbeard rice,[4] wild rice,[5] and red rice.[5] In 1965, Oryza nivara was separated off from O. rufipogon. The separation has been questioned,[6] and now many sources consider O. nivara to be a synonym of O. rufipogon.[7] O. nivara may be treated as the annual form of O. rufipogon.[8]

It is native to East-, Southeast- and South- Asia. It has a close evolutionary relation to Oryza sativa, the plant grown as a major rice food crop throughout the world. Oryza nivara is a possible wild progenitor of cultivated rice.[8][9][10][11][12] Both have an AA genome.[13]

Description

For those who accept Oryza nivara as a separate species, it is an annual, short to intermediate height (usually <2 metres (6 ft 7 in)) grass; panicles usually compact, rarely open; spikelets large, 6–10.4 millimetres (0.24–0.41 in) long and 1.9–3.4 millimetres (0.075–0.134 in) wide, with strong awn (4–10 centimetres (1.6–3.9 in) long); anthers 1.5–3 millimetres (0.059–0.118 in) long. It grows in shallow water up to 0.3 metres (1 ft 0 in), in seasonally dry and open habitats. It is found growing in swampy areas, at edge of pond and tanks, beside streams, in ditches, in or around rice fields.[11]

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.[14]

Precious germplasm

In India, the Pallikaranai marshland contains the wild rice O. rufipogon, described by the Sálim Ali Centre for Ornithology and Natural History (SACON) as a "precious germplasm."[15]

Domestication

Dai et al., 2012 discover LHD1, an allele of DTH8/Ghd8.[16] Dai also finds LHD1 produces the late heading O. rufipogon phenotype.[16] This is one of the traits bred out during O. sativa domestication.[16]

Genome

The genome of O. nivara was first sequenced in 2015.[17]

Stein et al., 2018 sequenced the genomes of O. nivara and other domesticated and wild relatives.[18] They produced reference assemblies and analyses for divergence time and genetic distance.[18] (The O. nivara assembly is 338 Mb.) They demonstrated that this species and Oryza sativa subsp. indica are most closely related and that the same is true for Oryza sativa subsp. japonica and Oryza rufipogon.[18]

Invasive species

Oryza rufipogon is an invasive species and listed as a 'noxious weed' by the United States,[19] and 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.[20]

See also

References

  1. ^ 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. Retrieved 19 November 2021.
  2. ^ a b "Oryza rufipogon Griff". Plants of the World Online. The Trustees of the Royal Botanic Gardens, Kew. n.d. Retrieved May 13, 2024.
  3. ^ "Oryza rufipogon Griff". Catalogue of Life. Species 2000. n.d. Archived from the original on July 22, 2023. Retrieved May 13, 2024.
  4. ^ NRCS. "Oryza rufipogon". PLANTS Database. United States Department of Agriculture (USDA). Retrieved 25 July 2015.
  5. ^ a b "Oryza rufipogon". Germplasm Resources Information Network. Agricultural Research Service, United States Department of Agriculture. Retrieved 12 January 2018.
  6. ^ "Oryza nivara S. D. Sharma & Shastry". Germplasm Resources Information Network. Agricultural Research Service, United States Department of Agriculture. Retrieved 2024-07-14.
  7. ^ "Oryza nivara S.D.Sharma & Shastry". Plants of the World Online. Royal Botanic Gardens, Kew. Retrieved 2024-07-20.
  8. ^ a b Choi, Jae Young; Platts, Adrian E.; Fuller, Dorian Q.; Hsing, Yue-Ie; Wing, Rod A.; Purugganan, Michael D. (2017-01-12). "The rice paradox: Multiple origins but single domestication in Asian rice". Molecular Biology and Evolution. 34 (4): 969–979. doi:10.1093/molbev/msx049. ISSN 0737-4038. PMC 5400379. PMID 28087768.
  9. ^ Haritha, Guttikonda; Malathi, Surapaneni; Divya, Balakrishnan; Swamy, B. P. M.; Mangrauthia, S. K.; Sarla, Neelamraju (2018), Mondal, Tapan K.; Henry, Robert J. (eds.), "Oryza nivara Sharma et Shastry", The Wild Oryza Genomes, Compendium of Plant Genomes, Cham: Springer International Publishing, pp. 207–238, doi:10.1007/978-3-319-71997-9_20, ISBN 978-3-319-71997-9
  10. ^ Gressel, Jonathan (2020-03-03). Genetic Glass Ceilings: Transgenics for Crop Biodiversity. JHU Press. ISBN 978-1-4214-2913-7.
  11. ^ a b Rana, M. K. (2014-06-01). Vegetables and their Allied as Protective Food. Scientific Publishers. ISBN 978-93-86237-56-9.
  12. ^ Driem, George Van (2011-01-01). "Lost In The Sands Of Time Somewhere North Of The Bay Of Bengal". Himalayan Languages and Linguistics: 11–38. doi:10.1163/ej.9789004194489.i-322.10. ISBN 9789004216532.
  13. ^ 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.
  14. ^ 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.
  15. ^ The Hindu/Vanishing Wetlands- 09 March 2005, http://www.hindu.com/2005/03/09/stories/2005030903421000.htm Archived 2013-05-30 at the Wayback Machine
  16. ^ a b c Liang, Yameng; Liu, Hai-Jun; Yan, Jianbing; Tian, Feng (2021). "Natural Variation in Crops: Realized Understanding, Continuing Promise". Annual Review of Plant Biology. 72 (1). Annual Reviews: 357–385. doi:10.1146/annurev-arplant-080720-090632. ISSN 1543-5008. PMID 33481630. S2CID 231688091.
  17. ^
    Brozynska, Marta; Furtado, Agnelo; Henry, Robert J. (2015). "Genomics of crop wild relatives: expanding the gene pool for crop improvement". Plant Biotechnology Journal. 14 (4). Association of Applied Biologists (aab) & Society for Experimental Biology (SEB): 1070–1085. doi:10.1111/pbi.12454. PMC 11389173. PMID 26311018. S2CID 3402991.
    This review cites this research.
    Zhang, QJ.; Zhu, T.; Xia, EH.; Shi, C.; Liu, YL.; Zhang, Y.; Liu, Y.; Jiang, WK.; Zhao, YJ.; Mao, Shu-Yan; Zhang, Li-Ping; Huang, Hui; Jiao, Jun-Ying; Xu, Ping-Zhen; Yao, Qiu-Yang; Zeng, Fan-Chun; Yang, Li-Li; Gao, Ju; Tao, Da-Yun; Wang, Yue-Ju; Bennetzen, Jeffrey L.; Gao, Li-Zhi (Nov 2014). "Rapid diversification of five Oryza AA genomes associated with rice adaptation". Proc Natl Acad Sci U S A. 111 (46): E4954–E4962. Bibcode:2014PNAS..111E4954Z. doi:10.1073/pnas.1418307111. PMC 4246335. PMID 25368197.
  18. ^ a b c
    Bailey-Serres, Julia; Parker, Jane E.; Ainsworth, Elizabeth A.; Oldroyd, Giles E. D.; Schroeder, Julian I. (2019). "Genetic strategies for improving crop yields". Nature. 575 (7781): 109–118. Bibcode:2019Natur.575..109B. doi:10.1038/s41586-019-1679-0. hdl:21.11116/0000-0005-3BD7-7. PMC 7024682. PMID 31695205. S2CID 207912531.
    Wing, Rod A.; Purugganan, Michael D.; Zhang, Qifa (2018). "The rice genome revolution: from an ancient grain to Green Super Rice". Nature Reviews Genetics. 19 (8): 505–517. doi:10.1038/s41576-018-0024-z. PMID 29872215. S2CID 216051436.
    These reviews cite this research.
    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. (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. S2CID 4969249.
  19. ^ Animal and Plant Health Inspection Service (2017). Federal Noxious Weed List: Designation of Noxious Weeds (7 C.F.R. § 360.200); U.S. Congress. 2000 (Report). Office of the Federal Register (U.S. National Archives) – via USDA Plants Database.
  20. ^ NAPPO ([[North American Plant Protection Organization ]]) - 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
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