Oryza sativa

Oryza sativa contains two major subspecies: the sticky, short-grained japonica or sinica variety, and the nonsticky, long-grained indica [zh] 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.

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]

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

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 1 – OsSka1 – 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]

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]

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  Water buffalo being used to plough rice fields in Java
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  Jumli Marshi, brown rice from Nepal
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  Traditional rice of Niyamgiri Hills, India
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  Rice from Chhattisgarh
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  O. sativa
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  Rice stem cross section magnified 400 times

• Black rice
• Domesticated plants and animals of Austronesia
• International Code of Nomenclature for Cultivated Plants
• Japonica rice
• Maratelli rice
• Oryza glaberrima (African rice)
• Traceability of genetically modified organisms