View source for Rice yellow mottle virus

{{Short description|Species of virus}}
{{Virusbox
| image = 
| image_alt = 
| image_caption = 
| parent = Sobemovirus
| species = Rice yellow mottle virus
| subdivision_ranks = 
| subdivision_ref = 
| subdivision = 
| synonyms = rice yellow mottle sobemovirus, pale yellow mottle disease
| synonyms_ref = 
}}

'''Rice yellow mottle virus''' ('''RYMV''') is a plant [[pathogenic virus]], belonging to the [[genus]] [[Sobemovirus]]. The genome is a [[RNA virus|positive-sense single strand]] [[RNA]] of 4450 [[nucleotides]] in length and is not [[Polyadenylation|polyadenylated]].<ref name=":1">{{cite journal |last1=Yassi |first1=M. N. A |last2=Ritzenthaler |first2=C. |last3=Brugidou |first3=C. |last4=Fauquet |first4=C. |last5=Beachy |first5=R. N. |title=Nucleotide sequence and genome characterization of rice yellow mottle virus RNA |journal=Journal of General Virology |date=1 February 1994 |volume=75 |issue=2 |pages=249–257 |doi=10.1099/0022-1317-75-2-249|pmid=8113745 }}</ref> It was first reported in Kenya in 1966<ref name = "Bakker_1974">{{cite thesis | vauthors = Bakker W | degree= Ph.D. | title = Characterization and ecological aspects of rice yellow mottle virus in Kenya. | date = 1974 | publisher = Wageningen University | url = https://library.wur.nl/WebQuery/wurpubs/423049 }}</ref> in one of Africa's first cultivation intensification schemes, due to RYMV's association with intensification,<ref group="P" name="1966-Kenya">p.{{spaces}}7, "RYMV was first detected in 1966 near Kisumu in Kenya along the north-east shore of Lake Victoria [21]. This report coincided with the development of one of the first major intensive rice production schemes in Africa. Since then, most epidemics have been associated with rice intensificiation."</ref> but DNA analysis of its evolutionary history shows it to have evolved in [[East Africa]] in the 19th century.<ref group="T" name="19th">Abstract, "Diversification and spread of RYMV has been concomitant with an extension of rice cultivation in Africa since the 19th century."</ref><ref group="P" name="19th">Abstract, "In East Africa, RYMV emerged in the 19{{sup|th}} century after rice intensification along the Indian Ocean coast, and later spread inland concomitantly with rice introduction."</ref><ref group="P" name="evo-e-w-19th">p.{{spaces}}9, "The pattern of genetic diversity of RYMV has been interpreted as resulting from a concomitant diversification and spread of the virus from East to West Africa since the 19th century [19]. It is shown here that, at a finer scale of spatial resolution, the geographic distribution of the strains has been shaped by the history of rice cultivation in Africa."</ref> Since its identification in Kenya it has been detected in many countries in [[sub-Saharan Africa]].<ref name="Abo_1997">{{cite journal |last1=Abo |first1=M. E. |last2=Sy |first2=A. A. |last3=Alegbejo |first3=M. D. |title=Rice Yellow Mottle Virus (RYMV) in Africa: Evolution, Distribution, Economic Significance on Sustainable Rice Production and Management Strategies |journal=Journal of Sustainable Agriculture |date=4 December 1997 |volume=11 |issue=2–3 |pages=85–111 |doi=10.1300/J064v11n02_08 |bibcode=1997JSusA..11b..85A}}</ref> It has also been detected in [[Central Africa]], but has yet to be seen outside the continent.<ref name=":0">{{cite journal |last1=Fargette |first1=Denis |last2=Pinel |first2=Agnès |last3=Abubakar |first3=Zakia |last4=Traoré |first4=Oumar |last5=Brugidou |first5=Christophe |last6=Fatogoma |first6=Sorho |last7=Hébrard |first7=Eugénie |last8=Choisy |first8=Marc |last9=Séré |first9=Yacouba |last10=Fauquet |first10=Claude |last11=Konaté |first11=Gnissa |title=Inferring the Evolutionary History of Rice Yellow Mottle Virus from Genomic, Phylogenetic, and Phylogeographic Studies |journal=Journal of Virology |date=April 2004 |volume=78 |issue=7 |pages=3252–3261 |doi=10.1128/JVI.78.7.3252-3261.2004 |pmid=15016846 |pmc=371063}}</ref> The genomic organization of RYMV is most similar to that of ''[[Cocksfoot mottle sobemovirus]].''<ref name=":0" /> RYMV is one of the better-studied plant-virus [[pathosystem]]s.<ref group="T" name="better-studied">p.{{spaces}}258-9, "The RYMV {{emdash}} rice pathosystem is one of the few plant-virus pathosystems to have been subjected to detailed studies involving both field and molecular epidemiology."</ref><ref name="Lefeuvre-et-al-2019" />

== Virology ==

=== Structure ===
RYMV is a [[(+)ssRNA|single-stranded positive-sense RNA virus]]. There is a high level of genetic diversity with the RYMV nucleotides, which is roughly 14%.<ref>{{Cite journal|last=Abubakar|first=Z.|date=2003-03-01|title=Phylogeography of Rice yellow mottle virus in Africa|journal=Journal of General Virology|volume=84|issue=3|pages=733–743|doi=10.1099/vir.0.18759-0|pmid=12604826|issn=0022-1317|doi-access=free}}</ref> RYMV is a ''[[sobemovirus]]''.<ref>{{cite journal |last1=Yassi |first1=M. N. |last2=Ritzenthaler |first2=C. |last3=Brugidou |first3=C. |last4=Fauquet |first4=C. |last5=Beachy |first5=R. N. |title=Nucleotide sequence and genome characterization of rice yellow mottle virus RNA |journal=The Journal of General Virology |date=February 1994 |volume=75 (Pt 2) |issue=2 |pages=249–257 |doi=10.1099/0022-1317-75-2-249 |pmid=8113745 |issn=0022-1317|doi-access=free }}</ref>

=== Impact on plants ===
RYMV has a massive impact on rice crops. Streaking, [[Mottle|mottling]], discoloration and malformation of leaves as well as death of infected young plants are all typical signs of RYMV infection.<ref name = "Bakker_1974" /><ref name=":2">{{Cite journal|last1=Uke|first1=Ayaka|last2=Tibanyendela|first2=Naswiru|last3=Ikeda|first3=Ryoichi|last4=Fujiie|first4=Azusa|last5=Natsuaki|first5=Keiko Teresa|date=2014-12-30|title=Modes of transmission and stability of Rice yellow mottle virus|journal=Journal of Plant Protection Research|volume=54|issue=4|pages=363–366|doi=10.2478/jppr-2014-0054|issn=1899-007X|doi-access=free}}</ref>  Crop losses can be 25–100%.<ref name=":6">{{Cite journal|title=Plantwise Knowledge Bank {{!}} Resistant rice against rice yellow mottle virus|url=https://www.plantwise.org/KnowledgeBank/factsheetforfarmers/20147801019|date=2016|journal=Plantwiseplus Knowledge Bank|doi=10.1079/pwkb.20147801019 |archive-url=|archive-date=|access-date=2020-05-22 |last1=Kija |first1=E. D. |last2=Mziray |first2=M. I. |volume=Factsheets for Farmers |doi-access=free }}</ref> It is believed that RYMV has begun to spread since the introduction of the exotic rice (''[[Oryza sativa]]'') from Asia into the African continent.<ref name = "Abo_1997" /> Indigenous rices that are from the African area tend to be more tolerant of the virus.<ref name = "Abo_1997" /> The natural host of the virus tends to remain in the [[Oryzeae]] tribe of plants.<ref name=":0" />  The virus only impacts a few plant species, including certain rice species and wild grasses.<ref name=":5">{{Cite journal|title=Distribution and diversity of local strains of rice yellow motile virus in Tanzania |url=https://tspace.library.utoronto.ca/bitstream/1807/47429/1/cs07021.pdf |last1=Kanyeka |first1=ZI |last2=Sangu |first2=E |last3=Fargette |first3=D |last4=Panel-Galzi |first4=A |last5=Hérbrard |first5=E |date=2007 |journal=African Crop Science Journal |hdl=1807/47429 }}</ref> The only way for plants to be confirmed of having RYMV is by performing a [[serological test]].<ref name=":1" />

=== Symptoms of infection ===
Younger seedlings (3–4 leaf growth stage) are the most susceptible – older plants generally exhibit less obvious foliar symptoms and less stunting than younger siblings. Symptoms appear initially as yellow-green linear spots on the base of the youngest leaves.<ref name=":7">{{Cite journal|title=Plantwise Knowledge Bank {{!}} Rice yellow mottle disease|url=https://www.plantwise.org/KnowledgeBank/pmdg/20167800983|last=|first=|date=2018|journal=Plantwiseplus Knowledge Bank|volume=Pest Management Decision Guides |doi=10.1079/pwkb.20167800983 |archive-url=|archive-date=|access-date=2020-05-22|doi-access=free}}</ref> As the infection grows the spots expand parallel to leaf veins and appear as yellow or orange streaks; these can vary in width, but can be continuous up to 10 cm.<ref name=":7" /> 

Affected plants have yellow or orange leaves at the early stage of the crop. In severe cases, leaves roll up and dry. Other symptoms are stunting, reduced tillering and poor panicle filling. This results in low or no seed production and poor grain quality.<ref name=":6" />

=== Transmission ===
RYMV located in the [[Rice hulls|rice husks]] in the plants.<ref name=":3">{{Cite journal|last1=Abo|first1=M. E.|last2=Alegbejo|first2=M. D.|last3=Sy|first3=A. A.|last4=Misari|first4=S. M.|date=2000-11-27|title=An Overview of the Mode of Transmission, Host Plants and Methods of Detection of Rice Yellow Mottle Virus|journal=Journal of Sustainable Agriculture|volume=17|issue=1|pages=19–36|doi=10.1300/j064v17n01_04|bibcode=2000JSusA..17a..19A |s2cid=83755820|issn=1044-0046}}</ref> The virus is transmissible by animals, by wind-mediated leaf contact, and by abiotic factors (e.g. irrigation water).<ref name=":2" /> It can be transmitted by leaf beetles or rats,<ref name=":0" /> or from plant to plant through leaf debris, empty rice spikelets, intertwining roots, leaf contact, rice stubble, contaminated hands, and from closely spaced plants.<ref name=":3" /> This virus is not seed-borne, nor is it transmitted by [[nematode]]s. [[Tettigoniidae|Long-horned grasshoppers]] (''[[Conocephalus]]'') were found to be a possible vector of RYMV in Uganda.<ref name=":2" />

=== Adaptability and resistance ===
A few rice [[cultivar]]s exhibit a high resistance to RYMV characterized by an absence of symptoms and no viral detection. The [[inheritance]] of this high resistance is [[Dominance (genetics)|recessive]]. The resistance gene ''RYMV1'' was identified as an ''eIF(iso)4G'' gene. Four ''rymv1'' resistance [[allele]]s have been characterized, one in ''[[Oryza sativa|O. sativa]]'' (''rymv1-2'') and three in ''O. glaberrima'' cultivars (''rymv1-3'', ''rymv1-4, rymv1-5'').<ref>{{Cite journal|last1=Poulicard|first1=Nils|last2=Pinel-Galzi|first2=Agnès|last3=Traoré|first3=Oumar|last4=Vignols|first4=Florence|last5=Ghesquière|first5=Alain|last6=Konaté|first6=Gnissa|last7=Hébrard|first7=Eugénie|last8=Fargette|first8=Denis|date=2012-01-26|title=Historical Contingencies Modulate the Adaptability of Rice Yellow Mottle Virus|journal=PLOS Pathogens|volume=8|issue=1|pages=e1002482|doi=10.1371/journal.ppat.1002482|pmid=22291591|pmc=3266926|issn=1553-7374 |doi-access=free }} * [[File:CC-BY icon.svg|50px]] Material was copied from this source, which is available under a Creative Commons License.</ref> Resistance of ''rymv1–3'' is caused by a deletion of codons 322–324 in the same domain of ''eIF(iso)4G''.<ref name=":4">{{cite journal |last1=Traoré |first1=Oumar |last2=Pinel-Galzi |first2=Agnès |last3=Issaka |first3=Souley |last4=Poulicard |first4=Nils |last5=Aribi |first5=Jamel |last6=Aké |first6=Séverin |last7=Ghesquière |first7=Alain |last8=Séré |first8=Yacouba |last9=Konaté |first9=Gnissa |last10=Hébrard |first10=Eugénie |last11=Fargette |first11=Denis |title=The adaptation of Rice yellow mottle virus to the eIF(iso)4G-mediated rice resistance |journal=Virology |date=December 2010 |volume=408 |issue=1 |pages=103–108 |doi=10.1016/j.virol.2010.09.007|pmid=20888025 }}</ref>

== Management ==

=== Prevention ===
Resistant and tolerant varieties are available.<ref name=":6" /><ref name=":8">{{Cite journal|title=Plantwise Knowledge Bank {{!}} Rice yellow mottle (Ikivejuru)|url=https://www.plantwise.org/KnowledgeBank/factsheetforfarmers/20127801765|date=2016|journal=Plantwiseplus Knowledge Bank|doi=10.1079/pwkb.20127801765 |archive-url=|archive-date=|access-date=2020-05-24 |last1=Kajuga |first1=J. |last2=Nkima |first2=G. |volume=Factsheets for Farmers |doi-access=free }}</ref><ref>{{Cite journal|title=Plantwise Knowledge Bank {{!}} Rice Yellow Mottle Virus (RYMV) -Rwanda|url=https://www.plantwise.org/KnowledgeBank/pmdg/20147801479|date=2018|journal=Plantwiseplus Knowledge Bank|doi=10.1079/pwkb.20147801479 |archive-url=|archive-date=|access-date=2020-05-24 |last1=Muhigirwa |first1=J. C. |last2=Nkima |first2=G. |volume=Pest Management Decision Guides |doi-access=free }}</ref>

Using nursery sites which haven't been infected previously or direct sowing in the field can also help prevent the spread of the virus.<ref name=":9">{{Cite journal|title=Plantwise Knowledge Bank {{!}} Rice yellow mottle disease - Malawi|url=https://www.plantwise.org/KnowledgeBank/pmdg/20177800434|date=2018|journal=Plantwiseplus Knowledge Bank|doi=10.1079/pwkb.20177800434 |archive-url=|archive-date=|access-date=2020-05-24 |last1=Chilasa |first1=S. R. |last2=Masangwa |first2=J. I. G. |last3=Shaibu |first3=Y. A. |volume=Pest Management Decision Guides |doi-access=free }}</ref>

[[Centre for Agriculture and Bioscience International|CABI]] recommends planting the crop as early as possible can avoid the peak period of insect vectors of the virus. In addition, synchronising the planting in different fields can prevent the virus from spreading to younger crops.<ref name=":7" />

Maintaining weeds to control other hosts of the virus and clearing bushes around fields to control breeding sites for insect vectors can also prevent RYMV spread.<ref name=":8" /><ref name=":9" /><ref name=":10">{{Cite journal|title=Plantwise Knowledge Bank {{!}} Yellow mottle disease of rice - Ghana|url=https://www.plantwise.org/KnowledgeBank/pmdg/20167800971|date=2018|journal=Plantwiseplus Knowledge Bank|doi=10.1079/pwkb.20167800971 |archive-url=|archive-date=|access-date=2020-05-24 |last1=Moses |first1=E. |last2=Brentu |first2=F. C. |last3=Nyarko |first3=F. A. |volume=Pest Management Decision Guides |doi-access=free }}</ref>

Sanitation procedures can reduce the spread of RYMV. CABI recommends cleaning weeds from irrigation canals and around rice fields, especially during the off season, to remove the virus and its insect vectors  will remove the virus and insect vectors.<ref name=":7" /> Cleaning of farm machinery can reduce spread prevent mechanical spread. This also applies to cleaning any farm machinery after each use.<ref name=":7" /><ref name=":9" />

=== Control ===
RYMV will completely kill susceptible varieties; if detected, removing infected plants and destroying them can prevent further spread. It has also been recommended by CABI to reduce the application of fertiliser on infected plants.<ref name=":7" />

There are no chemical control methods to directly stop the spread of RYMV. However, there are available insecticides to control vectors of the virus in some countries;<ref name=":6" /><ref name=":10" /> suitable chemicals vary depending on country specific guidelines.

== Epidemiology ==
{{As of|2019}} RYMV is still considered an "emerging" disease because there is still a great deal of range expansion ongoing and expected in the future.<ref name="Lefeuvre-et-al-2019">{{cite journal |last1=Lefeuvre |first1=Pierre |last2=Martin |first2=Darren P. |last3=Elena |first3=Santiago F. |last4=Shepherd |first4=Dionne N. |last5=Roumagnac |first5=Philippe |last6=Varsani |first6=Arvind |date=2019-07-16 |title=Evolution and ecology of plant viruses |journal=[[Nature Reviews Microbiology]] |publisher=[[Nature Research]] |volume=17 |issue=10 |pages=632–644 |doi=10.1038/s41579-019-0232-3 |issn=1740-1526 |pmid=31312033 |s2cid=197402034 |quote=Key examples of viruses that are responsible for well-studied emerging diseases are ... sobemoviruses such as rice yellow mottle virus{{super|106}}. |quote-page=639}}</ref>

== Sources ==
{{Free-content attribution
| title = Plantwise Factsheets for Farmers: Resistant rice against rice yellow mottle virus
| author = Jubilant JN Mwangi, Edith D. Kija Mariam I. Mziray
| publisher = CABI
| page numbers = 
| source = 
| documentURL = https://www.plantwise.org/KnowledgeBank/factsheetforfarmers/20147801019
| license statement URL = https://www.cabi.org/terms-and-conditions/
| license = CC-BY-SA
| howto = off
}}

{{Free-content attribution
| title = PMDG: Green List - Rice Yellow Mottle Virus
| author = Plantwise
| publisher = CABI
| page numbers = 
| source = 
| documentURL = https://www.plantwise.org/KnowledgeBank/pmdg/20167800983
| license statement URL = https://www.cabi.org/terms-and-conditions/
| license = CC-BY-SA
| howto = off
}}

{{Free-content attribution
| title = Plantwise Factsheets for Farmers: Rice yellow mottle (Ikivejuru)
| author = Joelle Kajuga, Germain Nkima
| publisher = CABI
| page numbers = 
| source = 
| documentURL = https://www.plantwise.org/KnowledgeBank/factsheetforfarmers/20127801765
| license statement URL = https://www.cabi.org/terms-and-conditions/
| license = CC-BY-SA
| howto = off
}}

{{Free-content attribution
| title = PMDG: Rice Yellow Mottle virus - Rwanda
| author = J. Chrysostome Muhigirwa & Germain Nkima
| publisher = CABI
| page numbers = 
| source = 
| documentURL = https://www.plantwise.org/KnowledgeBank/pmdg/20147801479
| license statement URL = https://www.cabi.org/terms-and-conditions/
| license = CC-BY-SA
| howto = off
}}

{{Free-content attribution
| title = PMDG: Rice Yellow Mottle Virus - Malawi
| author = Chilasa S.L,  J.I.G. Masangwa, Shaibu Y.A.
| publisher = CABI
| page numbers = 
| source = 
| documentURL = https://www.plantwise.org/KnowledgeBank/pmdg/20177800434
| license statement URL = https://www.cabi.org/terms-and-conditions/
| license = CC-BY-SA
| howto = off
}}

{{Free-content attribution
| title = PMDG: Rice Yellow Mottle Virus - Ghana
| author = E. Moses, F. C. Brentu & F.A. Nyarko
| publisher = CABI
| page numbers = 
| source = 
| documentURL = https://www.plantwise.org/KnowledgeBank/pmdg/20167800971
| license statement URL = https://www.cabi.org/terms-and-conditions/
| license = CC-BY-SA
}}

== References ==
{{Reflist}}
*{{cite journal | last1=Pinel-Galzi | first1=Agnès | last2=Traoré | first2=Oumar | last3=Séré | first3=Yacouba | last4=Hébrard | first4=Eugénie | last5=Fargette | first5=Denis | title=The biogeography of viral emergence: ''rice yellow mottle virus'' as a case study | journal=[[Current Opinion in Virology]] | publisher=[[Elsevier]] | volume=10 | year=2015 | issn=1879-6257 | doi=10.1016/j.coviro.2014.12.002 | pages=7–13 | s2cid=45136868 | pmid=25544357}}
{{reflist | group="P"}}
*{{cite journal | last1=Traoré | first1=O. | last2=Pinel-Galzi | first2=A. | last3=Sorho | first3=F. | last4=Sarra | first4=S. | last5=Rakotomalala | first5=M. | last6=Sangu | first6=E. | last7=Kanyeka | first7=Z. | last8=Séré | first8=Y. | last9=Konaté | first9=G. | last10=Fargette | first10=D. | title=A reassessment of the epidemiology of ''Rice yellow mottle virus'' following recent advances in field and molecular studies | journal=[[Virus Research]] | publisher=[[Elsevier]] | volume=141 | issue=2 | year=2009 | issn=0168-1702 | doi=10.1016/j.virusres.2009.01.011 | pages=258–267 | s2cid=25049549 | pmid=19195488}}
{{reflist | group="T"}}

== External links ==
*[https://web.archive.org/web/20070708104034/http://phene.cpmc.columbia.edu/ICTVdB//00.067.0.01.005.htm ICTVdB - The Universal Virus Database: Rice yellow mottle virus]
*[http://www.virology.net/Big_Virology/BVFamilyGroup.html Family Groups - The Baltimore Method]

{{Taxonbar|from=Q7323121}}

{{DEFAULTSORT:Rice Yellow Mottle Virus}}
[[Category:Sobemoviruses]]
[[Category:Viral plant pathogens and diseases]]