{{short description|Species of plant}} {{Use mdy dates|date=August 2014}} {{speciesbox |image=Mature Rice (India) by Augustus Binu.jpg |image_caption=Mature seed heads |image2=Oryza sativa at Kadavoor.jpg |image2_caption=Inflorescence |genus=Oryza |species=sativa |authority=L. |synonyms_ref=<ref name="316812-2" >{{cite web |url=https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:316812-2 |title=''Oryza sativa'' L. |author=<!--Not stated--> |date=2017 |website= Plants of the World Online |publisher=Board of Trustees of the Royal Botanic Gardens, Kew |access-date=21 December 2020 }}</ref> |synonyms={{collapsible list| * ''Oryza aristata'' <small>Blanco</small> * ''Oryza communissima'' <small>Lour.</small> * ''Oryza denudata'' <small>(Desv.) Steud.</small> * ''Oryza elongata'' <small>(Desv.) Steud.</small> * ''Oryza formosana'' <small>Masam. & Suzuki</small> * ''Oryza glutinosa'' <small>Lour.</small> * ''Oryza marginata'' <small>(Desv.) Steud.</small> * ''Oryza montana'' <small>Lour.</small> * ''Oryza mutica'' <small>Steud.</small> * ''Oryza palustris'' <small>Salisb.</small> * ''Oryza parviflora'' <small>P.Beauv.</small> * ''Oryza perennis'' <small>Moench</small> * ''Oryza plena'' <small>(Prain) N.P.Chowdhury</small> * ''Oryza praecox'' <small>Lour.</small> * ''Oryza pubescens'' <small>(Desv.) Steud.</small> * ''Oryza pumila'' <small>Steud.</small> * ''Oryza repens'' <small>Buch.-Ham. ex Steud.</small> * ''Oryza rubribarbis'' <small>(Desv.) Steud.</small> * ''Oryza sativa'' subsp. ''indica'' <small>Shig.Kato</small> * ''Oryza sativa'' subsp. ''japonica'' <small>Shig.Kato</small> * ''Oryza segetalis'' <small>Russell ex Steud.</small> }}}}
'''''Oryza sativa''''', having the common name '''Asian cultivated rice''',<ref>{{cite web|author= |title=Oryza sativa (Asian cultivated rice) |publisher=National Library of Medicine |url= https://pubchem.ncbi.nlm.nih.gov/taxonomy/Oryza-sativa |date= |access-date=24 July 2024 }}</ref> is the much more common of the two rice species cultivated as a cereal, the other species being ''O. glaberrima'', African rice. It was first domesticated in the Yangtze River basin in China 13,500 to 8,200 years ago.<ref name="Normile">{{cite journal |last=Normile |first=Dennis |year=1997 |title=Yangtze seen as earliest rice site |journal=Science |volume=275 |issue=5298 |pages=309–310 |doi=10.1126/science.275.5298.309 |s2cid=140691699}}</ref><ref name="Vaughanetal2008">{{cite journal |last1=Vaughan |first1=D.A. |last2=Lu |first2=B. |last3=Tomooka |first3=N. |year=2008 |title=The evolving story of rice evolution |url=https://www.researchgate.net/publication/222526251 |journal=Plant Science |volume=174 |issue=4 |pages=394–408 |doi=10.1016/j.plantsci.2008.01.016|bibcode=2008PlnSc.174..394V }}</ref><ref name="harris">{{cite book |last=Harris |first=David R. |title=The Origins and Spread of Agriculture and Pastoralism in Eurasia |publisher=Psychology Press |year=1996 |isbn=978-1-85728-538-3 |page=565}}</ref><ref name="Zhang2012">{{cite journal |last1=Zhang |first1=Jianping |last2=Lu |first2=Houyuan |last3=Gu |first3=Wanfa |last4=Wu |first4=Naiqin |last5=Zhou |first5=Kunshu |last6=Hu |first6=Yayi |last7=Xin |first7=Yingjun |last8=Wang |first8=Can |last9=Kashkush |first9=Khalil |date=December 17, 2012 |title=Early Mixed Farming of Millet and Rice 7800 Years Ago in the Middle Yellow River Region, China |journal=PLOS ONE |volume=7 |issue=12 |article-number=e52146 |bibcode=2012PLoSO...752146Z |doi=10.1371/journal.pone.0052146 |pmc=3524165 |pmid=23284907 |doi-access=free}}</ref>
''Oryza sativa'' belongs to the genus ''Oryza'' and the BOP clade in the grass family Poaceae. With a genome consisting of 430{{nbsp}}Mbp across 12 chromosomes, it is renowned for being easy to genetically modify and is a model organism for the study of the biology of cereals and monocots.<ref>{{Cite journal |last1=Haberer |first1=Georg |last2=Mayer |first2=Klaus F.X. |last3=Spannagl |first3=Manuel |date=2016-04-01 |title=The big five of the monocot genomes |url=https://www.sciencedirect.com/science/article/pii/S1369526616300048 |journal=Current Opinion in Plant Biology |series=SI: 30: Genome studies and molecular genetics |volume=30 |pages=33–40 |doi=10.1016/j.pbi.2016.01.004 |pmid=26866569 |bibcode=2016COPB...30...33H |issn=1369-5266|url-access=subscription }}</ref>
== Description == [[File:Oryza Selective Breeding Diagram.svg|thumb|'''''Oryza rufipogon''''' is the scientific name for brownbeard rice. This wild rice was first domesticated into '''''Oryza sativa''''', and its subsequent divergence into ''japonica'' and ''indica'' subspecies, occurred through a long process of domestication, artificial selection, and hybridization. Domestication led to artificial selection of rice with a mutation that made seeds non-shattering. This forced grains to stay attached and made harvesting easier. The plant was also bred for vertical architecture in its growth to maximize field density, and the awns were selectively bred away to reduce bulk density. ''Oryza sativa'' then led to the creation of two subspecies, ''japonica'' and ''indica''. ''Oryza sativa'' subsp. ''japonica'' was primarily grown in temperate and subtropical regions, the plant was shorter than ''indica'' and had darker leaves. ''Japonica'' grains are short, round, and plump, and have lower amylose content than ''indica''. ''Oryza sativa'' subsp. ''indica'' was primarily grown in tropical and humid regions. ''Indica'' has a taller growth and lighter leaf color. The grains are thinner, longer, and have higher amylose content. '''Diagram Legend''' 1.a - wild rice (''Oryza rufipogon'') 1.b - grains of wild rice (''Oryza rufipogon'') 2.a - Japanese rice (''Oryza sativa'' subsp. ''japonica'') 2.b - grains of Japanese rice (''Oryza sativa'' subsp. ''japonica'') 3.a - Indian rice (''Oryza sativa'' subsp. ''indica'') 3.b - grains of Indian rice (''Oryza sativa'' subsp. ''indica'')]] ''O. sativa'' has an erect stalk stem that grows {{cvt|80|-|120|cm|round=5}} tall, with a smooth surface. The leaf is lanceolate, {{cvt|15|-|30|cm|frac=8}} long, and grows from a ligule {{cvt|10|-|20|mm|frac=8}} long.<ref>{{cite web |last1=Catindig |first1=J.L.A. |last2=Lubigan |first2=R.T. |last3=Johnson |first3=D. |date=n.d. |title=Oryza sativa |url=http://www.knowledgebank.irri.org/training/fact-sheets/item/oryza-sativa |website=Rice Knowledge Bank |publisher=International Rice Research Institute |access-date=29 June 2023 |archive-date=August 9, 2024 |archive-url=https://web.archive.org/web/20240809145447/http://www.knowledgebank.irri.org/training/fact-sheets/item/oryza-sativa }}</ref>
<gallery mode="packed"> Image:Kerbau Jawa.jpg|Water buffalo ploughing a rice paddyfield, Java File:Jumli Marshi Oryza sativa Rice.jpg|Jumli Marshi, brown rice from Nepal File:Niyamgiri rice.jpg|Traditional rice of Niyamgiri Hills, India File:Medicinal Rice.jpg|From Chhattisgarh File:Koeh-232.jpg| File:RiceStemcs400x1.jpg|Stem cross section magnified 400 times </gallery>
== Taxonomy ==
{{see also|History of rice cultivation|List of rice varieties}}
''Oryza sativa'' contains two major subspecies: the sticky, short-grained ''japonica'' or ''sinica'' variety, and the nonsticky, long-grained ''{{visible anchor |indica}}'' rice variety. ''Japonica'' was domesticated in the Yangtze Valley 6,000–9,000 years ago,<ref name="Purugganan-Fuller-2009">{{cite journal |last1=Purugganan |first1=Michael D. |last2=Fuller |first2=Dorian Q. |title=The nature of selection during plant domestication |journal=Nature |publisher=Nature Research |volume=457 |issue=7231 |year=2009 |issn=0028-0836 |doi=10.1038/nature07895 |pages=843–848 |pmid=19212403 |bibcode=2009Natur.457..843P |s2cid=205216444 }}</ref> and its varieties can be cultivated in dry fields (it is cultivated mainly submerged in Japan), in temperate East Asia, upland areas of Southeast Asia, and high elevations in South Asia, while ''indica'' was domesticated around the Ganges 4,500–8,500 years ago,<ref name="Purugganan-Fuller-2009" /> and its varieties are mainly lowland rices, grown mostly submerged, throughout tropical Asia. Rice grain occurs in a variety of colors, including white, brown, black (purple when cooked), and red.<ref>Oka (1988)</ref><ref>{{cite journal |last1=Mohammadi Shad |first1=Z. |last2=Atungulu |first2=G. |title=Post-harvest kernel discoloration and fungi activity in long-grain hybrid, pureline and medium-grain rice cultivars as influenced by storage environment and antifungal treatment |journal=Journal of Stored Products Research |date=March 2019 |volume=81 |pages=91–99 |doi=10.1016/j.jspr.2019.02.002 |s2cid=92050510 |doi-access=free}}</ref>
A third subspecies, which is broad-grained and thrives under tropical conditions, was identified based on morphology and initially called ''javanica'', but is now known as ''tropical japonica''. Examples of this variety include the medium-grain 'Tinawon' and 'Unoy' cultivars, which are grown in the high-elevation rice terraces of the Central Cordillera Mountains of northern Luzon, Philippines.<ref>CECAP, PhilRice and IIRR. 2000. "Highland Rice Production in the Philippine Cordillera."</ref>
Glaszmann (1987) used isozymes to sort ''O. sativa'' into six groups: ''japonica'', ''aromatic'', ''indica'', ''aus'', ''rayada'', and ''ashina''.<ref name="Glaszmann 1987">{{cite journal |last1=Glaszmann |first1=J. C. |title=Isozymes and classification of Asian rice varieties |journal=Theoretical and Applied Genetics |date=May 1987 |volume=74 |issue=1 |pages=21–30 |doi=10.1007/BF00290078 |pmid=24241451 |s2cid=22829122}}</ref>
Garris ''et al.'' (2004) used simple sequence repeats to sort ''O. sativa'' into five groups: ''temperate japonica'', ''tropical japonica'' and ''aromatic'' comprise the ''japonica'' varieties, while ''indica'' and ''aus'' comprise the ''indica'' varieties.<ref name="Garris Tai Coburn 2004">{{cite journal |last1=Garris |first1=Amanda J. |last2=Tai |first2=T. H. |last3=Coburn |first3=J. |last4=Kresovich |first4=S. |last5=McCouch |first5=S. |author5-link=Susan McCouch |year=2004 |title=Genetic structure and diversity in ''Oryza sativa'' L. |journal=Genetics |pmid=15654106 |doi=10.1534/genetics.104.035642 |volume=169 |issue=3 |pages=1631–1638 |pmc=1449546}}</ref> The Garris scheme has held up against newer analyses as of 2019,<ref name=civan>{{cite journal |last1=Civáň |first1=Peter |last2=Ali |first2=Sajid |last3=Batista-Navarro |first3=Riza |last4=Drosou |first4=Konstantina |last5=Ihejieto |first5=Chioma |last6=Chakraborty |first6=Debarati |last7=Ray |first7=Avik |last8=Gladieux |first8=Pierre |last9=Brown |first9=Terence A |title=Origin of the Aromatic Group of Cultivated Rice ( Oryza sativa L.) Traced to the Indian Subcontinent |journal=Genome Biology and Evolution |date=2019-03-01 |volume=11 |issue=3 |pages=832–843 |doi=10.1093/gbe/evz039|pmid=30793171 |pmc=6427689 }}</ref> though one 2014 article argues that ''rayada'' is distinct enough to be its own group under ''japonica''.<ref>{{cite journal |last1=Wang |first1=C-H |last2=Zheng |first2=X-M |last3=Xu |first3=Q |last4=Yuan |first4=X-P |last5=Huang |first5=L |last6=Zhou |first6=H-F |last7=Wei |first7=X-H |last8=Ge |first8=S |title=Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm |journal=Heredity |date=May 2014 |volume=112 |issue=5 |pages=489–496 |doi=10.1038/hdy.2013.130|pmid=24326293 |pmc=3998783 |bibcode=2014Hered.112..489W }}</ref>
=== Etymology === The generic name ''Oryza''<ref name="oryza-MW">{{cite Merriam-Webster|oryza}}</ref> is a classical Greek word for rice, while the specific epithet ''sativa'' means "cultivated".<ref name="sativa-dict">{{cite Lexico|sativa}}</ref><ref>{{cite Merriam-Webster|sativa}}</ref>
== Genetics ==
{{visible anchor|SPL14}}/{{visible anchor|LOC4345998}} is a gene that regulates the overall architecture/growth habit of the plant. Some of its epialleles increase rice yield.<ref name="Stange-et-al-2021">{{cite journal |last1=Stange |first1=Madlen |last2=Barrett |first2=Rowan D. H. |last3=Hendry |first3=Andrew P. |title=The importance of genomic variation for biodiversity, ecosystems and people |journal=Nature Reviews Genetics |publisher=Nature Portfolio |volume=22 |issue=2 |date=February 2021 |issn=1471-0056 |doi=10.1038/s41576-020-00288-7 |pages=89–105 |pmid=33067582 |s2cid=223559538|id=MS ORCID [http://orcid.org/0000-0002-4559-2535 0000-0002-4559-2535]). (RDHB ORCID [http://orcid.org/0000-0003-3044-2531 0000-0003-3044-2531])}}</ref> An accurate and usable simple sequence repeat marker set was developed and used to generate a high-density map.<ref name="Rasheed-et-al-2017" /> A multiplex high-throughput marker assisted selection system has been developed but as with other crop HTMAS systems has proven difficult to customize, costly (both directly and for the equipment), and inflexible.<ref name="Rasheed-et-al-2017">{{cite journal|publisher=Elsevier|last1=Rasheed |first1=Awais |last2=Hao |first2=Yuanfeng |last3=Xia |first3=Xianchun |last4=Khan |first4=Awais |last5=Xu |first5=Yunbi |last6=Varshney |first6=Rajeev K. |last7=He |first7=Zhonghu |title=Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives |journal=Molecular Plant|id=Chinese Academy of Sciences+Chinese Society for Plant Biology+Shanghai Institutes for Biological Sciences|volume=10|issue=8|year=2017 |issn=1674-2052 |doi=10.1016/j.molp.2017.06.008 |pages=1047–1064 |s2cid=33780984 |pmid=28669791|doi-access=free |bibcode=2017MPlan..10.1047R }}</ref> Other molecular breeding tools have produced rice blast resistant cultivars.<ref name="Miah-et-al-2012">{{cite journal |last1=Miah |first1=G. |last2=Rafii |first2=M. Y. |last3=Ismail |first3=M. R. |last4=Puteh |first4=A. B. |last5=Rahim |first5=H. A. |last6=Asfaliza |first6=R. |last7=Latif |first7=M. A. |title=Blast resistance in rice: a review of conventional breeding to molecular approaches |journal=Molecular Biology Reports |publisher=Springer Science+Business Media |volume=40 |issue=3 |date=2012-11-27 |issn=0301-4851 |doi=10.1007/s11033-012-2318-0 |pages=2369–2388|pmid=23184051 |s2cid=8922855 |url=http://psasir.upm.edu.my/id/eprint/29230/1/29230.pdf }}</ref><ref name="Rao-et-al-2014">{{cite journal |last1=Rao |first1=Yuchun |last2=Li |first2=Yuanyuan |last3=Qian |first3=Qian |title=Recent progress on molecular breeding of rice in China |journal=Plant Cell Reports |publisher=Springer Science+Business Media |volume=33 |issue=4 |date=2014-01-19 |issn=0721-7714 |doi=10.1007/s00299-013-1551-x |pages=551–564|pmid=24442397 |pmc=3976512 |bibcode=2014PCelR..33..551R }}</ref><ref name="Rasheed-et-al-2017" /> DNA microarray has been used to advance understanding of hybrid vigor in rice, QTL sequencing has been used to elucidate seedling vigor, and genome wide association study (GWAS) by whole genome sequencing (WGS) has been used to investigate various agronomic traits.<ref name="Rasheed-et-al-2017" />
In total, 641 copy number variations are known.<ref name="Rasheed-et-al-2017" /> Exome capture often reveals new single nucleotide polymorphisms in rice, due to its large genome and high degree of DNA repetition.<ref name="Rasheed-et-al-2017" />
Resistance to the rice blast fungus ''Magnaporthe grisea'' is provided by various resistance genes including ''{{visible anchor|Pi1}}'', ''{{visible anchor|Pi54}}'', and ''{{visible anchor|Pita}}''.<ref name="Mehta-et-al-2019">{{cite book |editor-last=Wani |editor-first=Shabir Hussain |title=Disease Resistance in Crop Plants: Molecular, Genetic and Genomic Perspectives |publisher=Springer |year=2019 |isbn=978-3-030-20727-4 |oclc=1110184027 |pages=83–112/xii+307 |chapter=5 Rice, Marker-Assisted Breeding, and Disease Resistance |last1=Mehta |first1=Sahil |last2=Singh |first2=Baljinder |last3=Dhakate |first3=Priyanka |last4=Rahman |first4=Mehzabin |last5=Islam |first5=Muhammad Aminul}}</ref> ''O. sativa'' uses the plant hormones abscisic acid and salicylic acid to regulate immune responses. Salicylic acid broadly stimulates, and abscisic acid suppresses, immunity to ''M. grisea''; success depends on the balance between their levels.<ref>{{cite journal |last1=Pieterse |first1=Corné M.J. |last2=Van der Does |first2=Dieuwertje |last3=Zamioudis |first3=Christos |last4=Leon-Reyes |first4=Antonio |last5=Van Wees |first5=Saskia C.M. |title=Hormonal Modulation of Plant Immunity |journal=Annual Review of Cell and Developmental Biology |publisher=Annual Reviews |volume=28 |issue=1 |date=2012-11-10 |issn=1081-0706 |doi=10.1146/annurev-cellbio-092910-154055 |pages=489–521 |s2cid=18180536 |pmid=22559264|hdl=1874/274421 |url=https://dspace.library.uu.nl/handle/1874/274421 |ref=none}} |{{cite journal|publisher=Oxford University Press |last1=Atkinson |first1=Nicky J. |last2=Urwin |first2=Peter E. |title=The interaction of plant biotic and abiotic stresses: from genes to the field |journal=Journal of Experimental Botany |volume=63 |issue=10 |date=2012-03-30 |issn=0022-0957 |doi=10.1093/jxb/ers100 |pages=3523–3543 |s2cid=205195661 |pmid=22467407|doi-access=free}}</ref><ref>{{cite journal |last1=Liu |first1=Wende |last2=Liu |first2=Jinling |last3=Triplett |first3=Lindsay |last4=Leach |first4=Jan E. |last5=Wang |first5=Guo-Liang |title=Novel Insights into Rice Innate Immunity Against Bacterial and Fungal Pathogens |journal=Annual Review of Phytopathology |publisher=Annual Reviews |volume=52 |issue=1 |date=2014-08-04 |issn=0066-4286 |doi=10.1146/annurev-phyto-102313-045926 |pages=213–241 |s2cid=9244874 |pmid=21380629|bibcode=2014AnRvP..52..213L }}</ref>
''O. sativa'' has a large number of insect resistance genes specifically for the brown planthopper.<ref name="Wang-Han-2022">{{cite journal |last1=Wang |first1=Changsheng |last2=Han |first2=Bin |title=Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics |journal=Molecular Plant |publisher=Cell Press |volume=15 |issue=4 |year=2022 |issn=1674-2052 |doi=10.1016/j.molp.2022.03.009 |pmid=35331914 |pages=593–619|s2cid=247603925 |doi-access=free |bibcode=2022MPlan..15..593W }}</ref> {{As of|2022}}, 15 R genes have been cloned and characterized.<ref name="Wang-Han-2022" />
== See also == * Domesticated plants and animals of Austronesia * International Code of Nomenclature for Cultivated Plants * Traceability of genetically modified organisms
== References ==
{{reflist|30em}}
== External links == * {{Wikispecies-inline|Oryza sativa}} * {{Commons category-inline|Oryza sativa}}
{{Rice}} {{Taxonbar|from=Q161426}} {{Authority control}}
sativa Category:Crops originating from Asia Category:Flora of China Category:Plants described in 1753 Category:Rice Category:Botanical taxa named by Carl Linnaeus