Species of plant
Oryza sativa , also known as 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.
[2]
[3]
[4]
[5]
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
cereals and
monocots .
[6]
Botany
The species has an erect and stout or slender 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.
[7]
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,
[8] 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,
[8] 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 .
[9]
[10]
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.
[11]
Glaszmann (1987) used
isozymes to sort O. sativa into six groups:
japonica , aromatic , indica , aus , rayada , and ashina .
[12]
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.
[13]
Nomenclature and taxonomy
Rice has been cultivated since ancient times and
oryza
[14] is a classical Latin word for rice while
sativa
[15] 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.
[16] An accurate and usable
Simple Sequence Repeat marker set was developed and used to generate a
high-density map .
[17] 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.
[17] Other
molecular breeding tools have produced
rice blast resistant cultivars.
[18]
[19]
[17]
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 .
[17]
Rice is one of the earliest uses and validation models for the semi-thermal asymmetric reverse PCR (STARP) method developed in 2016.
[17]
Resistance to the rice blast fungus
Magnaporthe grisea is provided by various
resistance genes including Pi1 , Pi54 , and Pita .
[20]
O. sativa has a large number of
insect resistance genes specifically for the
Brown planthopper .
[21] As of 2022
[update] , 15
R genes have been cloned and characterized.
[21]
In total, 641
copy number variations are known.
[17]
Exome capture often reveals new
single nucleotide polymorphisms in rice, due to its large genome and high degree of DNA repetition.
[17]
The plant hormones
abscisic acid and
salicylic acid are employed by O. sativa for regulation of immune responses.
[22] Salicylic acid broadly stimulate and abscisic acid suppresses immunity to the rice blast fungus M. grisea , and success depends on the balance between their levels.
[22]
Breeding
Rice seed collection from
IRRI
The
International Rice Research Institute maintains the International Rice Genebank, which holds over 100,000 rice varieties. Much of southeast Asia grows
sticky or glutinous rice varieties. High-yield cultivars of rice suitable for cultivation in Africa, called the
New Rice for Africa (NERICA), have been developed to improve
food security and alleviate poverty in Sub-Saharan Africa.
The complete
genome of rice was
sequenced in 2005, making it the first crop plant to reach this status.
Since then, the genomes of hundreds of types of rice, both wild and cultivated, and including both Asian and African rice species, have been sequenced.
A triple
introgression of
resistance genes against
Magnaporthe grisea —and actual
field resistance —have been developed.
[20] This is a
marker-assisted backcross of the genes
Pi1 ,
Pi54 , and
Pita into an
aromatic cultivar using
SSR- and
STS-markers .
[20] Pi21 is a gene that confers broad-spectrum non-race-specific rice blast resistance against several strains.
[23]
Gallery
See also
References
^
"Oryza sativa L."
Plants of the World Online . Board of Trustees of the Royal Botanic Gardens, Kew. 2017. Retrieved December 21, 2020 .
^ Normile, Dennis (1997). "Yangtze seen as earliest rice site". Science . 275 (5298): 309–310.
doi :
10.1126/science.275.5298.309 .
S2CID
140691699 .
^ Vaughan, DA; Lu, B; Tomooka, N (2008).
"The evolving story of rice evolution" . Plant Science . 174 (4): 394–408.
doi :
10.1016/j.plantsci.2008.01.016 .
^ Harris, David R. (1996). The Origins and Spread of Agriculture and Pastoralism in Eurasia . Psychology Press. p. 565.
ISBN
978-1-85728-538-3 .
^ Zhang, Jianping; Lu, Houyuan; Gu, Wanfa; Wu, Naiqin; Zhou, Kunshu; Hu, Yayi; Xin, Yingjun; Wang, Can; Kashkush, Khalil (December 17, 2012).
"Early Mixed Farming of Millet and Rice 7800 Years Ago in the Middle Yellow River Region, China" . PLOS ONE . 7 (12): e52146.
Bibcode :
2012PLoSO...752146Z .
doi :
10.1371/journal.pone.0052146 .
PMC
3524165 .
PMID
23284907 .
^ Haberer, Georg; Mayer, Klaus FX; Spannagl, Manuel (April 1, 2016).
"The big five of the monocot genomes" . Current Opinion in Plant Biology . SI: 30: Genome studies and molecular genetics. 30 : 33–40.
doi :
10.1016/j.pbi.2016.01.004 .
ISSN
1369-5266 .
^ Catindig, J.L.A.; Lubigan, R.T.; Johnson, D. (n.d.).
"Oryza sativa" . Rice Knowledge Bank .
International Rice Research Institute . Retrieved June 29, 2023 .
^
a
b Purugganan, Michael D.; Fuller, Dorian Q. (2009). "The nature of selection during plant domestication".
Nature . 457 (7231).
Nature Research : 843–848.
Bibcode :
2009Natur.457..843P .
doi :
10.1038/nature07895 .
ISSN
0028-0836 .
PMID
19212403 .
S2CID
205216444 .
^ Oka (1988)
^ Mohammadi Shad, Z.; Atungulu, G. (March 2019).
"Post-harvest kernel discoloration and fungi activity in long-grain hybrid, pureline and medium-grain rice cultivars as influenced by storage environment and antifungal treatment" . Journal of Stored Products Research . 81 : 91–99.
doi :
10.1016/j.jspr.2019.02.002 .
S2CID
92050510 .
^ CECAP, PhilRice and IIRR. 2000. "Highland Rice Production in the Philippine Cordillera."
^ Glaszmann, J. C. (May 1987). "Isozymes and classification of Asian rice varieties". Theoretical and Applied Genetics . 74 (1): 21–30.
doi :
10.1007/BF00290078 .
PMID
24241451 .
S2CID
22829122 .
^ Garris, Amanda J.; Tai, T. H.; Coburn, J.; Kresovich, S.;
McCouch, S. (2004).
"Genetic structure and diversity in Oryza sativa L."
Genetics . 169 (3): 1631–1638.
doi :
10.1534/genetics.104.035642 .
PMC
1449546 .
PMID
15654106 .
^
"oryza" .
Merriam-Webster.com Dictionary .
^
^ 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 .
^
a
b
c 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 .
^
Li, Wei; Deng, Yiwen; Ning, Yuese; He, Zuhua; Wang, Guo-Liang (2020).
"Exploiting Broad-Spectrum Disease Resistance in Crops: From Molecular Dissection to Breeding" .
Annual Review of Plant Biology . 71 (1).
Annual Reviews : 575–603.
doi :
10.1146/annurev-arplant-010720-022215 .
ISSN
1543-5008 .
PMID
32197052 .
S2CID
214600762 .
External links