Oryza sativa

Oryza sativa
Mature seed heads
Inflorescence
Scientific classification Edit this classification
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, having the common name Asian cultivated rice,[2] 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.[3][4][5][6]

Oryza sativa belongs to the genus Oryza and the BOP clade in 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 study of the biology of cereals and monocots.[7]

Description

O. sativa has an erect stalk stem that grows 80–120 cm (30–45 in) tall, with a smooth surface. The leaf is lanceolate, 15–30 cm (5+7⁄8–11+3⁄4 in) long, and grows from a ligule 10–20 mm (3⁄8–3⁄4 in) long.[8]

Classification

See also: History of rice cultivation and List of rice varieties

The generic name Oryza[9] is a classical Latin word for rice, while the specific epithet sativa means "cultivated".[10][11]

Oryza sativa contains two major subspecies: the sticky, short-grained japonica or sinica variety, and the nonsticky, long-grained indica [籼稻 [zh]] [インディカ米 [ja]] rice variety. Japonica was domesticated in the Yangtze Valley 9–6,000 years ago,[12] 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,[12] 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.[13][14]

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.[15]

Glaszmann (1987) used isozymes to sort O. sativa into six groups: japonica, aromatic, indica, aus, rayada, and ashina.[16]

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.[17] The Garris scheme has held up against newer analyses as of 2019,[18] though one 2014 article argues that rayada is distinct enough to be its own group under japonica.[19]

Genetics

SPL14/LOC4345998 is a gene that regulates the overall architecture/growth habit of the plant. Some of its epialleles increase rice yield.[20] An accurate and usable simple sequence repeat marker set was developed and used to generate a high-density map.[21] 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.[21] Other molecular breeding tools have produced rice blast resistant cultivars.[22][23][21] 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.[21]

In total, 641 copy number variations are known.[21] Exome capture often reveals new single nucleotide polymorphisms in rice, due to its large genome and high degree of DNA repetition.[21]

Resistance to the rice blast fungus Magnaporthe grisea is provided by various resistance genes including Pi1, Pi54, and Pita.[24] 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.[25][26]

O. sativa has a large number of insect resistance genes specifically for the brown planthopper.[27] As of 2022, 15 R genes have been cloned and characterized.[27]

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. ^ "Oryza sativa (Asian cultivated rice)". National Library of Medicine. Retrieved July 24, 2024.
  3. ^ Normile, Dennis (1997). "Yangtze seen as earliest rice site". Science. 275 (5298): 309–310. doi:10.1126/science.275.5298.309. S2CID 140691699.
  4. ^ Vaughan, D.A.; Lu, B.; Tomooka, N. (2008). "The evolving story of rice evolution". Plant Science. 174 (4): 394–408. Bibcode:2008PlnSc.174..394V. doi:10.1016/j.plantsci.2008.01.016.
  5. ^ Harris, David R. (1996). The Origins and Spread of Agriculture and Pastoralism in Eurasia. Psychology Press. p. 565. ISBN 978-1-85728-538-3.
  6. ^ 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.
  7. ^ Haberer, Georg; Mayer, Klaus F.X.; Spannagl, Manuel (April 1, 2016). "The big five of the monocot genomes". Current Opinion in Plant Biology. SI: 30: Genome studies and molecular genetics. 30: 33–40. Bibcode:2016COPB...30...33H. doi:10.1016/j.pbi.2016.01.004. ISSN 1369-5266. PMID 26866569.
  8. ^ Catindig, J.L.A.; Lubigan, R.T.; Johnson, D. (n.d.). "Oryza sativa". Rice Knowledge Bank. International Rice Research Institute. Retrieved June 29, 2023.
  9. ^ "oryza". Merriam-Webster.com Dictionary. Merriam-Webster.
  10. ^ "sativa". Lexico UK English Dictionary. Oxford University Press. n.d.
  11. ^ "sativa". Merriam-Webster.com Dictionary. Merriam-Webster.
  12. ^ a b Purugganan, Michael D.; Fuller, Dorian Q. (2009). "The nature of selection during plant domestication". Nature. 457 (7231). Nature Research: 843–848. Bibcode:2009Natur.457..843P. doi:10.1038/nature07895. ISSN 0028-0836. PMID 19212403. S2CID 205216444.
  13. ^ Oka (1988)
  14. ^ 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.
  15. ^ CECAP, PhilRice and IIRR. 2000. "Highland Rice Production in the Philippine Cordillera."
  16. ^ 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.
  17. ^ Garris, Amanda J.; Tai, T. H.; Coburn, J.; Kresovich, S.; McCouch, S. (2004). "Genetic structure and diversity in Oryza sativa L." Genetics. 169 (3): 1631–1638. doi:10.1534/genetics.104.035642. PMC 1449546. PMID 15654106.
  18. ^ Civáň, Peter; Ali, Sajid; Batista-Navarro, Riza; Drosou, Konstantina; Ihejieto, Chioma; Chakraborty, Debarati; Ray, Avik; Gladieux, Pierre; Brown, Terence A (March 1, 2019). "Origin of the Aromatic Group of Cultivated Rice ( Oryza sativa L.) Traced to the Indian Subcontinent". Genome Biology and Evolution. 11 (3): 832–843. doi:10.1093/gbe/evz039. PMC 6427689. PMID 30793171.
  19. ^ Wang, C-H; Zheng, X-M; Xu, Q; Yuan, X-P; Huang, L; Zhou, H-F; Wei, X-H; Ge, S (May 2014). "Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm". Heredity. 112 (5): 489–496. doi:10.1038/hdy.2013.130. PMC 3998783. PMID 24326293.
  20. ^ Stange, Madlen; Barrett, Rowan D. H.; Hendry, Andrew P. (February 2021). "The importance of genomic variation for biodiversity, ecosystems and people". Nature Reviews Genetics. 22 (2). Nature Portfolio: 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).
  21. ^ a b c d e f Rasheed, Awais; Hao, Yuanfeng; Xia, Xianchun; Khan, Awais; Xu, Yunbi; Varshney, Rajeev K.; He, Zhonghu (2017). "Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives". Molecular Plant. 10 (8). Elsevier: 1047–1064. doi:10.1016/j.molp.2017.06.008. ISSN 1674-2052. PMID 28669791. S2CID 33780984. Chinese Academy of Sciences+Chinese Society for Plant Biology+Shanghai Institutes for Biological Sciences.
  22. ^ 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. 40 (3). Springer Science+Business Media: 2369–2388. doi:10.1007/s11033-012-2318-0. ISSN 0301-4851. PMID 23184051. S2CID 8922855.
  23. ^ Rao, Yuchun; Li, Yuanyuan; Qian, Qian (January 19, 2014). "Recent progress on molecular breeding of rice in China". Plant Cell Reports. 33 (4). Springer Science+Business Media: 551–564. doi:10.1007/s00299-013-1551-x. ISSN 0721-7714. PMC 3976512. PMID 24442397.
  24. ^ Mehta, Sahil; Singh, Baljinder; Dhakate, Priyanka; Rahman, Mehzabin; Islam, Muhammad Aminul (2019). "5 Rice, Marker-Assisted Breeding, and Disease Resistance". In Wani, Shabir Hussain (ed.). Disease Resistance in Crop Plants: Molecular, Genetic and Genomic Perspectives. Springer. pp. 83–112/xii+307. ISBN 978-3-030-20727-4. OCLC 1110184027.
  25. ^ Pieterse, Corné M.J.; Van der Does, Dieuwertje; Zamioudis, Christos; Leon-Reyes, Antonio; Van Wees, Saskia C.M. (November 10, 2012). "Hormonal Modulation of Plant Immunity". Annual Review of Cell and Developmental Biology. 28 (1). Annual Reviews: 489–521. doi:10.1146/annurev-cellbio-092910-154055. hdl:1874/274421. ISSN 1081-0706. PMID 22559264. S2CID 18180536. |Atkinson, Nicky J.; Urwin, Peter E. (March 30, 2012). "The interaction of plant biotic and abiotic stresses: from genes to the field". Journal of Experimental Botany. 63 (10). Oxford University Press: 3523–3543. doi:10.1093/jxb/ers100. ISSN 0022-0957. PMID 22467407. S2CID 205195661.
  26. ^ Liu, Wende; Liu, Jinling; Triplett, Lindsay; Leach, Jan E.; Wang, Guo-Liang (August 4, 2014). "Novel Insights into Rice Innate Immunity Against Bacterial and Fungal Pathogens". Annual Review of Phytopathology. 52 (1). Annual Reviews: 213–241. doi:10.1146/annurev-phyto-102313-045926. ISSN 0066-4286. PMID 21380629. S2CID 9244874.
  27. ^ a b Wang, Changsheng; Han, Bin (2022). "Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics". Molecular Plant. 15 (4). Cell Press: 593–619. doi:10.1016/j.molp.2022.03.009. ISSN 1674-2052. PMID 35331914. S2CID 247603925.