''Oryza sativa'', commonly known as Asian rice or indica rice, is the plant species most commonly referred to in English as ''

rice Rice is the seed of the grass species '' Oryza sativa'' (Asian rice) or less commonly ''Oryza glaberrima'' (African rice). The name wild rice is usually used for species of the genera '' Zizania'' and '' Porteresia'', both wild and domesticat ...

''. It is the type of farmed rice whose cultivars are most common globally, and was first domesticated in the

Yangtze River The Yangtze or Yangzi ( or ; ) is the longest list of rivers of Asia, river in Asia, the list of rivers by length, third-longest in the world, and the longest in the world to flow entirely within one country. It rises at Jari Hill in th ...

basin in China 13,500 to 8,200 years ago. ''Oryza sativa'' belongs to the genus ''

Oryza ''Oryza'' is a genus of plants in the grass family. It includes the major food crop rice (species ''Oryza sativa'' and ''Oryza glaberrima''). Members of the genus grow as tall, wetland grasses, growing to tall; the genus includes both annual an ...

'' of the grass family Poaceae. With a

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...

consisting of 430 Mbp across 12

chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...

s, it is renowned for being easy to genetically modify and is a model organism for the

botany Botany, also called , plant biology or phytology, is the science of plant life and a branch of biology. A botanist, plant scientist or phytologist is a scientist who specialises in this field. The term "botany" comes from the Ancient Greek w ...

of cereals.

Classification

''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 The Yangtze or Yangzi ( or ; ) is the longest river in Asia, the third-longest in the world, and the longest in the world to flow entirely within one country. It rises at Jari Hill in the Tanggula Mountains (Tibetan Plateau) and flows ...

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 The Ganges ( ) (in India: Ganga ( ); in Bangladesh: Padma ( )). "The Ganges Basin, known in India as the Ganga and in Bangladesh as the Padma, is an international river to which India, Bangladesh, Nepal and China are the riparian states." is ...

8,500-4,500 years ago, and its varieties are mainly lowland rices, grown mostly submerged, throughout tropical Asia. Rice occurs in a variety of colors, including

white White is the lightest color and is achromatic (having no hue). It is the color of objects such as snow, chalk, and milk, and is the opposite of black. White objects fully reflect and scatter all the visible wavelengths of light. White o ...

brown Brown is a color. It can be considered a composite color, but it is mainly a darker shade of orange. In the CMYK color model used in printing or painting, brown is usually made by combining the colors orange and black. In the RGB color model us ...

black Black is a color which results from the absence or complete absorption of visible light. It is an achromatic color, without hue, like white and grey. It is often used symbolically or figuratively to represent darkness. Black and white ...

purple Purple is any of a variety of colors with hue between red and blue. In the RGB color model used in computer and television screens, purples are produced by mixing red and blue light. In the RYB color model historically used by painters, ...

, and

red rice Red rice is a variety of rice that is colored red by its anthocyanin content. It is usually eaten unpolished or partially polished, and has a red bran layer, rather than the more common pale brown. Red rice has a nutty flavor. It has the highe ...

s. 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 Luzon (; ) is the largest and most populous island in the Philippines. Located in the northern portion of the Philippines archipelago, it is the economic and political center of the nation, being home to the country's capital city, Manila, as ...

, Philippines. Glaszmann (1987) used

isozyme In biochemistry, isozymes (also known as isoenzymes or more generally as multiple forms of enzymes) are enzymes that differ in amino acid sequence but catalyze the same chemical reaction. Isozymes usually have different kinetic parameters (e.g. dif ...

s 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 ''Oryza'' is a genus of plants in the grass family. It includes the major food crop rice (species ''Oryza sativa'' and ''Oryza glaberrima''). Members of the genus grow as tall, wetland grasses, growing to tall; the genus includes both annual an ...

'' is a classical Latin word for rice while ''

sativa Sativa, sativus, and sativum are Latin botanical adjectives meaning '' cultivated''. It is often associated botanically with plants that promote good health and used to designate certain seed-grown domestic crops. Usage ''Sativa'' (ending in -a) ...

'' means "cultivated".

Genetics

/ is a gene that regulates the overall architecture/growth habit of the plant. Some of its

epiallele An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution. ::"The chrom ...

s increase rice yield. An accurate and usable Simple Sequence Repeat marker set was developed and used to generate a high-density map in McCouch ''et al.'', 2002. 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. Other

molecular breeding Molecular breeding is the application of molecular biology tools, often in plant breedingVoosen P (2009Molecular Breeding Makes Crops Hardier and More Nutritious Markers, knockouts and other technical advances improve breeding without modifying gen ...

tools ''have'' produced results, producing blast resistant cultivars. Xu ''et al.'', 2014 uses a DNA microarray to substantially advance understanding of

hybrid vigor Heterosis, hybrid vigor, or outbreeding enhancement is the improved or increased function of any biological quality in a hybrid offspring. An offspring is heterotic if its traits are enhanced as a result of mixing the genetic contributions o ...

in rice, Takagi ''et al.'', 2013 uses QTL sequencing to elucidate

seedling vigor A seedling is a young sporophyte developing out of a plant embryo from a seed. Seedling development starts with germination of the seed. A typical young seedling consists of three main parts: the radicle (embryonic root), the hypocotyl (embryo ...

, and Yano ''et al.'', 2016 performs a

GWAS In genomics, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an observational study of a genome-wide set of genetic variants in different individuals to see if any varian ...

by WGS to investigate various agronomic traits. (Because the correspondence between genotype and

phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological pr ...

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.) 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. 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. The putative

homolog In biology, homology is similarity due to shared ancestry between a pair of structures or genes in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats and birds, the arms of prima ...

for '' spindle and kinetochore-associated protein 1'' ' is localized to by Hanisch ''et al.'', 2006. Resistance to '' Magnaporthe grisea'' is provided by various resistance genes including ', ', and '. ''O. sativa'' has a large number of insect resistance genes specifically for the

Brown planthopper The brown planthopper (BPH), ''Nilaparvata lugens'' (Stål) (Hemiptera: Delphacidae) is a planthopper species that feeds on rice plants (''Oryza sativa'' L.). These insects are among the most important pests of rice, which is the major staple cr ...

. 15

R gene Resistance genes (R-Genes) are genes in plant genomes that convey plant disease resistance against pathogens by producing R proteins. The main class of R-genes consist of a nucleotide binding domain (NB) and a leucine rich repeat (LRR) dom ...

s among these have been cloned and characterized including Tamura ''et al.'', 2014's discovery of ' Guo ''et al.'', 2018's discovery of ', Zhao ''et al.'', 2016's discovery of ', Du ''et al.'', 2009's discovery of ', and Ji ''et al.'', 2016's discovery of '. In total 641

copy number variation Copy number variation (CNV) is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals. Copy number variation is a type of structural variation: specifically, it is a type of ...

s are known, the combination of results of Ma and Bennetzen 2004 and Yu ''et al.'', 2011. Exome capture often reveals new single nucleotide polymorphisms in rice, due to its large genome and high degree of DNA repetition. There have been two major results of this type, Saintenac ''et al.'', 2011 and Henry ''et al.'', 2014. Both abscisic acid and salicylic acid are employed by ''O. sativa'' in its regulation of its own immune responses. 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.

Breeding

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.

Gallery

Image:Kerbau Jawa.jpg,

Water buffalo The water buffalo (''Bubalus bubalis''), also called the domestic water buffalo or Asian water buffalo, is a large bovid originating in the Indian subcontinent and Southeast Asia. Today, it is also found in Europe, Australia, North America, So ...

being used to plough

rice fields A paddy field is a flooded field of arable land used for growing semiaquatic crops, most notably rice and taro. It originates from the Neolithic rice-farming cultures of the Yangtze River basin in southern China, associated with pre-Aust ...

Java Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's mos ...

File:Jumli Marshi Oryza sativa Rice.jpg, Jumli Marshi, brown rice from Nepal File:Niyamgiri rice.jpg, Traditional rice of Niyamgiri Hills, India File:Medicinal Rice.jpg, Rice from Chhattisgarh File:Koeh-232.jpg, ''O. sativa'' File:RiceStemcs400x1.jpg, Rice stem cross section magnified 400 times

References

External links

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Crops originating from Asia Flora of China Plants described in 1753 Rice Taxa named by Carl Linnaeus