Oryza sativa
Mature Rice (India) by Augustus Binu.jpg
Mature seed heads
Oryza sativa at Kadavoor.jpg
Inflorescence
Scientific classification edit
Kingdom: Plantae
Clade: Tracheophytes
Clade: Angiosperms
Clade: Monocots
Clade: Commelinids
Order: Poales
Family: Poaceae
Genus: Oryza
Species:
O. sativa
Binomial name
Oryza sativa
Synonyms[1]
List
    • Oryza aristata Blanco
    • Oryza communissima Lour.
    • Oryza denudata (Desv.) Steud.
    • Oryza elongata (Desv.) Steud.
    • Oryza formosana Masam. & Suzuki
    • Oryza glutinosa Lour.
    • Oryza marginata (Desv.) Steud.
    • Oryza montana Lour.
    • Oryza mutica Steud.
    • Oryza palustris Salisb.
    • Oryza parviflora P.Beauv.
    • Oryza perennis Moench
    • Oryza plena (Prain) N.P.Chowdhury
    • Oryza praecox Lour.
    • Oryza pubescens (Desv.) Steud.
    • Oryza pumila Steud.
    • Oryza repens Buch.-Ham. ex Steud.
    • Oryza rubribarbis (Desv.) Steud.
    • Oryza sativa subsp. indica Shig.Kato
    • Oryza sativa subsp. japonica Shig.Kato
    • Oryza segetalis Russell ex Steud.

Oryza sativa, commonly known as Asian rice, is the plant species most commonly referred to in English as rice. It is the type of farmed rice whose cultivars are most common globally, and was first domesticated in the Yangtze River basin in China 13,500 to 8,200 years ago.[2][3][4][5]

Oryza sativa belongs to the genus Oryza of the grass family Poaceae. With a genome consisting of 430 Mbp across 12 chromosomes, it is renowned for being easy to genetically modify and is a model organism for the botany of cereals.

Classification

See also: History of rice cultivation

Oryza sativa contains two major subspecies: the sticky, short-grained japonica or sinica variety, and the nonsticky, long-grained indica [ja] rice variety. Japonica was domesticated in the Yangtze Valley 9-6,000 years ago,[6] 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 8,500-4,500 years ago,[6] and its varieties are mainly lowland rices, grown mostly submerged, throughout tropical Asia. Rice occurs in a variety of colors, including white, brown, black, purple, and red rices.[7][8] Black rice (also known as purple rice) is a range of rice types, some of which are glutinous rice. Varieties include Indonesian black rice and Thai jasmine black rice.[citation needed]

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 Cordillera Mountains of northern Luzon, Philippines.[9]

Glaszmann (1987) used isozymes to sort O. sativa into six groups: japonica, aromatic, indica, aus, rayada, and ashina.[10]

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.[11]

Nomenclature and taxonomy

Rice has been cultivated since ancient times and oryza[12] is a classical Latin word for rice while sativa[13] means "cultivated".

Genetics

SPL14/LOC4345998 is a gene that regulates the overall architecture/growth habit of the plant. Some of its epialleles increase rice yield.[14] An accurate and usable Simple Sequence Repeat marker set was developed and used to generate a high-density map in McCouch et al., 2002.[15] A multiplex high-throughput marker assisted selection system has been developed by Masouleh et al., 2009 but as with other crop HTMAS systems has proven difficult to customize, costly (both directly and for the equipment), and inflexible.[15] Other molecular breeding tools have produced results, producing blast resistant cultivars.[16][17][15] Xu et al., 2014 uses a DNA microarray to substantially advance understanding of hybrid vigor in rice, Takagi et al., 2013 uses QTL sequencing to elucidate seedling vigor, and Yano et al., 2016 performs a GWAS by WGS to investigate various agronomic traits.[15] (Because the correspondence between genotype and phenotype is more easily understood in rice, translation of results from rice to other non-models may require more work. For example grain size and grain weight in wheat were elucidated in this way by Valluru et al., 2014.)[15] Affymetrix offers a 44 thousand pot microarray, a 50 thousand, and a one million, and Illumina has a six thousand and a 50 thousand, all of which have performed well and are commonly used.[15] Rice is one of the earliest uses and validation models for the semi-thermal asymmetric reverse PCR (STARP) method developed in Long et al., 2016.[15] The putative homolog for spindle and kinetochore-associated protein 1OsSka1 – is localized to XP_478114 by Hanisch et al., 2006.[18]

Resistance to Magnaporthe grisea is provided by various resistance genes including Pi1, Pi54, and Pita.[19]

O. sativa has a large number of insect resistance genes specifically for the Brown planthopper.[20] As of 2022 15 R genes among these have been cloned and characterized including Tamura et al., 2014's[21] discovery of Bph2[22][20] Guo et al., 2018's discovery of Bph6,[20] Zhao et al., 2016's discovery of Bph9,[20] Du et al., 2009's discovery of Bph14,[20] and Ji et al., 2016's[23] discovery of Bph18.[22][20]

In total 641 copy number variations are known, the combination of results of Ma and Bennetzen 2004 and Yu et al., 2011.[15] Exome capture often reveals new single nucleotide polymorphisms in rice, due to its large genome and high degree of DNA repetition.[15] There have been two major results of this type, Saintenac et al., 2011 and Henry et al., 2014.[15]

Both abscisic acid and salicylic acid are employed by O. sativa in its regulation of its own immune responses.[24] Jiang et al., 2010 finds SA broadly upregulates and ABA broadly downregulates immunity to Magnaporthe grisea, and success depends on the balance between their levels.[24]

Breeding

This section is an excerpt from Rice breeding

Rice seed collection from IRRI
Rice seed collection from IRRI

While most rice is bred for crop quality and productivity, there are varieties selected for characteristics such as texture, smell, and firmness. There are four major categories of rice worldwide: indica, japonica, aromatic and glutinous. The different varieties of rice are not considered interchangeable, either in food preparation or agriculture, so as a result, each major variety is a completely separate market from other varieties. It is common for one variety of rice to rise in price while another one drops in price.

Rice cultivars also fall into groups according to environmental conditions, season of planting, and season of harvest, called ecotypes. Some major groups are the Japan-type (grown in Japan), "buly" and "tjereh" types (Indonesia); sali (or aman—main winter crop), ahu (also aush or ghariya, summer), and boro (spring) (Bengal and Assam). Cultivars exist that are adapted to deep flooding, and these are generally called "floating rice".

A triple introgression of resistance genes against Magnaporthe grisea - and actual field resistance - have been demonstrated by Khan et al., 2018. This is a marker-assisted backcross of Pi1, Pi54, and Pita into an aromatic cultivar using SSR- and STS-markers.[19]

Gallery

See also

References

  1. ^ "Oryza sativa L." Plants of the World Online. Board of Trustees of the Royal Botanic Gardens, Kew. 2017. Retrieved December 21, 2020.
  2. ^ Normile, Dennis (1997). "Yangtze seen as earliest rice site". Science. 275 (5298): 309–310. doi:10.1126/science.275.5298.309. S2CID 140691699.
  3. ^ Vaughan, DA; Lu, B; Tomooka, N (2008). "The evolving story of rice evolution". Plant Science. 174 (4): 394–408. doi:10.1016/j.plantsci.2008.01.016.
  4. ^ Harris, David R. (1996). The Origins and Spread of Agriculture and Pastoralism in Eurasia. Psychology Press. p. 565. ISBN 978-1-85728-538-3.
  5. ^ Zhang, Jianping; Lu, Houyuan; Gu, Wanfa; Wu, Naiqin; Zhou, Kunshu; Hu, Yayi; Xin, Yingjun; Wang, Can; Kashkush, Khalil (December 17, 2012). "Early Mixed Farming of Millet and Rice 7800 Years Ago in the Middle Yellow River Region, China". PLOS ONE. 7 (12): e52146. Bibcode:2012PLoSO...752146Z. doi:10.1371/journal.pone.0052146. PMC 3524165. PMID 23284907.
  6. ^ a b Purugganan, Michael D.; Fuller, Dorian Q. (2009). "The nature of selection during plant domestication". Nature. Nature Research. 457 (7231): 843–848. Bibcode:2009Natur.457..843P. doi:10.1038/nature07895. ISSN 0028-0836. PMID 19212403. S2CID 205216444.
  7. ^ Oka (1988)
  8. ^ Mohammadi Shad, Z; Atungulu, G. (March 2019). "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 of Stored Products Research. 81: 91–99. doi:10.1016/j.jspr.2019.02.002. S2CID 92050510.
  9. ^ CECAP, PhilRice and IIRR. 2000. "Highland Rice Production in the Philippine Cordillera."
  10. ^ Glaszmann, J. C. (May 1987). "Isozymes and classification of Asian rice varieties". Theoretical and Applied Genetics. 74 (1): 21–30. doi:10.1007/BF00290078. PMID 24241451. S2CID 22829122.
  11. ^ Garris; Tai, TH; Coburn, J; Kresovich, S; McCouch, S; et al. (2004). "Genetic structure and diversity in Oryza sativa L." Genetics. 169 (3): 1631–8. doi:10.1534/genetics.104.035642. PMC 1449546. PMID 15654106.
  12. ^ "oryza". Merriam-Webster Dictionary.
  13. ^
  14. ^ Stange, Madlen; Barrett, Rowan D. H.; Hendry, Andrew P. (February 2021). "The importance of genomic variation for biodiversity, ecosystems and people". Nature Reviews Genetics. Nature Portfolio. 22 (2): 89–105. doi:10.1038/s41576-020-00288-7. ISSN 1471-0056. PMID 33067582. S2CID 223559538. (MS ORCID 0000-0002-4559-2535). (RDHB ORCID 0000-0003-3044-2531).
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  16. ^ Miah, G.; Rafii, M. Y.; Ismail, M. R.; Puteh, A. B.; Rahim, H. A.; Asfaliza, R.; Latif, M. A. (November 27, 2012). "Blast resistance in rice: a review of conventional breeding to molecular approaches" (PDF). Molecular Biology Reports. Springer. 40 (3): 2369–2388. doi:10.1007/s11033-012-2318-0. ISSN 0301-4851. PMID 23184051. S2CID 8922855.
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  18. ^ Cheeseman, Iain M.; Desai, Arshad (2008). "Molecular architecture of the kinetochore–microtubule interface". Nature Reviews Molecular Cell Biology. Nature Portfolio. 9 (1): 33–46. doi:10.1038/nrm2310. ISSN 1471-0072. PMID 18097444. S2CID 34121605.
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  24. ^ a b