Oryza sativa
Oryza sativa, commonly known as Asian rice, is the plant species most commonly referred to in English as rice. It is the type of farmed rice whose cultivars are most common globally, and was first domesticated in the Yangtze River basin in China 13,500 to 8,200 years ago. "Oryza sativa" is a grass with a genome consisting of 430Mb across 12 chromosomes. It is renowned for being easy to genetically modify and is a model organism for the botany 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 9-6,000 years ago, and its varieties are usually 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 occurs in a variety of colors, including white, brown, black, purple, and red rices. 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. 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. / 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 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 tools "have" produced results, producing blast resistant cultivars. 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. (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.) 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 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. 15 R genes 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 variations 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.