''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 ''Oryza glaberrima'', commonly known as African rice, is one of the two domesticated rice species. It was first domesticated and grown i ...

''. 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 Poaceae () or Gramineae () is a large and nearly ubiquitous family of monocotyledonous flowering plants commonly known as grasses. It includes the cereal grasses, bamboos and the grasses of natural grassland and species cultivated in lawns an ...

. 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 ge ...

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 A model organism (often shortened to model) is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workin ...

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 ...

cereal A cereal is any Poaceae, grass cultivated for the edible components of its grain (botanically, a type of fruit called a caryopsis), composed of the endosperm, Cereal germ, germ, and bran. Cereal Grain, grain crops are grown in greater quantit ...

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 on ...

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 used ...

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 have o ...

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, pu ...

, 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 highes ...

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 repeat A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome. ...

s 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 chro ...

s increase rice yield. An accurate and usable

Simple Sequence Repeat A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome. ...

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 A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to ...

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 of ...

in rice, Takagi ''et al.'', 2013 uses

QTL sequencing DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The ...

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 Single-nucleotide polymorphism, genetic variants in different i ...

by WGS to investigate various

agronomic trait Plant breeding is the science of changing the traits of plants in order to produce desired characteristics. It has been used to improve the quality of nutrition in products for humans and animals. The goals of plant breeding are to produce cro ...

s. (Because the correspondence between

genotype The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the alleles or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a ...

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 proper ...

is more easily understood in rice, translation of results from rice to other non-

models A model is an informative representation of an object, person or system. The term originally denoted the plans of a building in late 16th-century English, and derived via French and Italian ultimately from Latin ''modulus'', a measure. Models c ...

may require more work. For example grain size and grain weight in wheat were elucidated in this way by Valluru ''et al.'', 2014.)

Affymetrix Affymetrix is now Applied Biosystems, a brand of DNA microarray products sold by Thermo Fisher Scientific that originated with an American biotechnology research and development and manufacturing company of the same name. The Santa Clara, Califor ...

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 ''Magnaporthe grisea'', also known as rice blast fungus, rice rotten neck, rice seedling blight, blast of rice, oval leaf spot of graminea, pitting disease, ryegrass blast, Johnson spot, neck blast, wheat blast, and Imochi (Japanese:稲熱) is a ...

'' is provided by various resistance genes including ', ', and '. ''O. sativa'' has a large number of

insect resistance gene Plant defense against herbivory or host-plant resistance (HPR) describes a range of adaptations Evolution, evolved by plants which improve their fitness (biology), survival and reproduction by reducing the impact of herbivores. Plant perception ...

s 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 cro ...

. 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 d ...

s are known, the combination of results of Ma and Bennetzen 2004 and Yu ''et al.'', 2011. Exome capture often reveals new

single nucleotide polymorphism In genetics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a sufficiently larg ...

s 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 Abscisic acid (ABA) is a plant hormone. ABA functions in many plant developmental processes, including seed and bud dormancy, the control of organ size and stomatal closure. It is especially important for plants in the response to environmental s ...

and

salicylic acid Salicylic acid is an organic compound with the formula HOC6H4CO2H. A colorless, bitter-tasting solid, it is a precursor to and a metabolite of aspirin (acetylsalicylic acid). It is a plant hormone, and has been listed by the EPA Toxic Substance ...

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 ''

'', and success depends on the balance between their levels.

Breeding

A triple

introgression Introgression, also known as introgressive hybridization, in genetics is the transfer of genetic material from one species into the gene pool of another by the repeated backcrossing of an interspecific hybrid with one of its parent species. Intr ...

of resistance genes against ''

''—and actual field resistance—have been demonstrated by Khan ''et al.'', 2018. This is a marker-assisted backcross of '' Pi1'', '' Pi54'', and ''

Pita Pita ( or ) or pitta (British English), is a family of yeast-leavened round flatbreads baked from wheat flour, common in the Mediterranean, Middle East, and neighboring areas. It includes the widely known version with an interior pocket, als ...

'' 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 List ...

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 Chhattisgarh (, ) is a landlocked state in Central India. It is the ninth largest state by area, and with a population of roughly 30 million, the seventeenth most populous. It borders seven states – Uttar Pradesh to the north, Madhya Prade ...

File:Koeh-232.jpg, ''O. sativa'' File:RiceStemcs400x1.jpg, Rice stem cross section magnified 400 times

References

External links

{{Authority control

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