Oryza sativa explained

Oryza sativa, having the common name Asian cultivated rice [1], 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.[2] [3] [4] [5]

Oryza sativa belongs to the genus Oryza and the BOP clade in the grass family Poaceae. With a genome consisting of 430Mbp 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.[6]

Description

O. sativa has an erect stalk stem that grows tall, with a smooth surface. The leaf is lanceolate, long, and grows from a ligule long.[7]

Classification

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

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

Oryza sativa contains two major subspecies: the sticky, short-grained japonica or sinica variety, and the nonsticky, long-grained rice variety. Japonica was domesticated in the Yangtze Valley 9–6,000 years ago,[8] 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, 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.[9] [10]

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.[11]

Glaszmann (1987) used isozymes to sort O. sativa into six groups: japonica, aromatic, indica, aus, rayada, and ashina.[12]

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.[13] The Garris scheme has held up against newer analyses as of 2019,[14] though one 2014 article argues that rayada is distinct enough to be its own group under japonica.[15]

Genetics

/ is a gene that regulates the overall architecture/growth habit of the plant. Some of its epialleles increase rice yield.[16] An accurate and usable simple sequence repeat marker set was developed and used to generate a high-density map. 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.[17] Other molecular breeding tools have produced rice blast resistant cultivars.[18] [19] 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.

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

Resistance to the rice blast fungus Magnaporthe grisea is provided by various resistance genes including , , and .[20] 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.[21] [22]

O. sativa has a large number of insect resistance genes specifically for the brown planthopper.[23], 15 R genes have been cloned and characterized.

See also

Notes and References

  1. Web site: Oryza sativa (Asian cultivated rice) . National Library of Medicine . 24 July 2024 .
  2. Normile . Dennis . 1997 . Yangtze seen as earliest rice site . Science . 275 . 5298 . 309–310 . 10.1126/science.275.5298.309 . 140691699.
  3. Vaughan . D.A. . Lu . B. . Tomooka . N. . 2008 . The evolving story of rice evolution . Plant Science . 174 . 4 . 394–408 . 10.1016/j.plantsci.2008.01.016.
  4. Book: Harris, David R. . The Origins and Spread of Agriculture and Pastoralism in Eurasia . Psychology Press . 1996 . 978-1-85728-538-3 . 565.
  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 . 2012PLoSO...752146Z . 10.1371/journal.pone.0052146 . 3524165 . 23284907 . free.
  6. Haberer . Georg . Mayer . Klaus F.X. . Spannagl . Manuel . 2016-04-01 . The big five of the monocot genomes . Current Opinion in Plant Biology . SI: 30: Genome studies and molecular genetics . 30 . 33–40 . 10.1016/j.pbi.2016.01.004 . 1369-5266.
  7. Web site: Catindig . J.L.A. . Lubigan . R.T. . Johnson . D. . n.d. . Oryza sativa . Rice Knowledge Bank . . 29 June 2023.
  8. Purugganan . Michael D. . Fuller . Dorian Q. . The nature of selection during plant domestication . . . 457 . 7231 . 2009 . 0028-0836 . 10.1038/nature07895 . 843–848 . 19212403 . 2009Natur.457..843P . 205216444 .
  9. Oka (1988)
  10. Mohammadi Shad . Z. . Atungulu . G. . 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 . March 2019 . 81 . 91–99 . 10.1016/j.jspr.2019.02.002 . 92050510 . free.
  11. CECAP, PhilRice and IIRR. 2000. "Highland Rice Production in the Philippine Cordillera."
  12. Glaszmann . J. C. . Isozymes and classification of Asian rice varieties . Theoretical and Applied Genetics . May 1987 . 74 . 1 . 21–30 . 10.1007/BF00290078 . 24241451 . 22829122.
  13. Garris . Amanda J. . Tai . T. H. . Coburn . J. . Kresovich . S. . McCouch . S. . Susan McCouch . 2004 . Genetic structure and diversity in Oryza sativa L. . . 15654106 . 10.1534/genetics.104.035642 . 169 . 3 . 1631–1638 . 1449546.
  14. Civáň . Peter . Ali . Sajid . Batista-Navarro . Riza . Drosou . Konstantina . Ihejieto . Chioma . Chakraborty . Debarati . Ray . Avik . Gladieux . Pierre . Brown . Terence A . Origin of the Aromatic Group of Cultivated Rice (Oryza sativa L.) Traced to the Indian Subcontinent . Genome Biology and Evolution . 2019-03-01 . 11 . 3 . 832–843 . 10.1093/gbe/evz039.
  15. Wang . C-H . Zheng . X-M . Xu . Q . Yuan . X-P . Huang . L . Zhou . H-F . Wei . X-H . Ge . S . Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm . Heredity . May 2014 . 112 . 5 . 489–496 . 10.1038/hdy.2013.130. 3998783 .
  16. Stange . Madlen . Barrett . Rowan D. H. . Hendry . Andrew P. . The importance of genomic variation for biodiversity, ecosystems and people . . . 22 . 2 . February 2021 . 1471-0056 . 10.1038/s41576-020-00288-7 . 89–105 . 33067582 . 223559538. MS ORCID 0000-0002-4559-2535). (RDHB ORCID 0000-0003-3044-2531).
  17. Elsevier. Rasheed . Awais . Hao . Yuanfeng . Xia . Xianchun . Khan . Awais . Xu . Yunbi . Varshney . Rajeev K. . He . Zhonghu . Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives . Molecular Plant. Chinese Academy of Sciences+Chinese Society for Plant Biology+Shanghai Institutes for Biological Sciences. 10. 8. 2017 . 1674-2052 . 10.1016/j.molp.2017.06.008 . 1047–1064 . 33780984 . 28669791. free .
  18. Miah . G. . Rafii . M. Y. . Ismail . M. R. . Puteh . A. B. . Rahim . H. A. . Asfaliza . R. . Latif . M. A. . Blast resistance in rice: a review of conventional breeding to molecular approaches . . . 40 . 3 . 2012-11-27 . 0301-4851 . 10.1007/s11033-012-2318-0 . 2369–2388. 23184051 . 8922855 .
  19. Rao . Yuchun . Li . Yuanyuan . Qian . Qian . Recent progress on molecular breeding of rice in China . . . 33 . 4 . 2014-01-19 . 0721-7714 . 10.1007/s00299-013-1551-x . 551–564. 24442397 . 3976512 .
  20. Book: Wani . Shabir Hussain . Disease Resistance in Crop Plants: Molecular, Genetic and Genomic Perspectives . . 2019 . 978-3-030-20727-4 . 1110184027 . 83–112/xii+307 . 5 Rice, Marker-Assisted Breeding, and Disease Resistance . Mehta . Sahil . Singh . Baljinder . Dhakate . Priyanka . Rahman . Mehzabin . Islam . Muhammad Aminul.
  21. Pieterse . Corné M.J. . Van der Does . Dieuwertje . Zamioudis . Christos . Leon-Reyes . Antonio . Van Wees . Saskia C.M. . Hormonal Modulation of Plant Immunity . . . 28 . 1 . 2012-11-10 . 1081-0706 . 10.1146/annurev-cellbio-092910-154055 . 489–521 . 18180536 . 22559264. 1874/274421 . none. |. Atkinson . Nicky J. . Urwin . Peter E. . The interaction of plant biotic and abiotic stresses: from genes to the field . . 63 . 10 . 2012-03-30 . 0022-0957 . 10.1093/jxb/ers100 . 3523–3543 . 205195661 . 22467407. free.
  22. Liu . Wende . Liu . Jinling . Triplett . Lindsay . Leach . Jan E. . Wang . Guo-Liang . Novel Insights into Rice Innate Immunity Against Bacterial and Fungal Pathogens . . . 52 . 1 . 2014-08-04 . 0066-4286 . 10.1146/annurev-phyto-102313-045926 . 213–241 . 9244874 . 21380629.
  23. Wang . Changsheng . Han . Bin . Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics . . . 15 . 4 . 2022 . 1674-2052 . 10.1016/j.molp.2022.03.009 . 35331914 . 593–619. 247603925 . free .

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