Oryza Sativa

Oryza sativa
	Mature seed heads
	Inflorescence
Scientific classification
Kingdom:	Plantae
Clade:	Tracheophytes
Clade:	Angiosperms
Clade:	Monocots
Clade:	Commelinids
Order:	Poales
Family:	Poaceae
Genus:	Oryza
Species:	O. sativa
Binomial name
	Oryza sativa; L.
Synonyms
	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 is much the 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.

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.

Botany

The species 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.

Classification

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

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.

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

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.

Nomenclature and taxonomy

Rice has been cultivated since ancient times and oryza is a classical Latin word for rice while sativa 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. 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. Other molecular breeding tools have produced rice blast resistant cultivars. 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.

Rice is one of the earliest uses and validation models for the semi-thermal asymmetric reverse PCR (STARP) method developed in 2016.

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

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

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.

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 the rice blast fungus M. grisea; success depends on the balance between their levels.

Gallery

Water buffalo ploughing, Java
Jumli Marshi, brown rice from Nepal
Traditional rice of Niyamgiri Hills, India
From Chhattisgarh
Stem cross section magnified 400 times

References

^ 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).

^ ^a ^b ^c ^d ^e ^f ^g 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.

^ 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.

^ 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.

^ 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. Cham, Switzerland: Springer. pp. 83–112/xii+307. ISBN 978-3-030-20727-4. OCLC 1110184027.

^ ^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.

^ ^a ^b

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.
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.

External links

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