<i> Rice yellow mottle virus </i> (RYMV) is the most important disease of rice in Africa. The disease was first observed in1966 inKenya but has now spread in all rice-growing countries of Sub-Saharan Africa. In Tanzania, its distribution has been restricted to the major rice-growing regions. However, the knowledge on RYMV genetic diversity relies on a limited number of coat protein sequences. Previous studies revealed the presence of the phylotypes S4lv, S4lm and strain S5 in Mwanza, Mbeya and Morogoro regions, respectively, and strain S6 in Kilimanjaro region and Pemba Island. Surveys were conducted during the cropping seasons 2013-2014 in eight rice-growing regions of Tanzania to determine geographical variations and phylotypes of RYMV and the influence of environment factors on its distribution and diversity. A total of 185 rice fields were surveyed. Results indicate that prevalence, severity and phylotypes of RYMV varied significantly with rainfall intensity, temperature and relative humidity (P ≤ 0.01). The highest prevalence was found in Morogoro (82%), Mbeya (80%) and Arusha (67.33%) regions whereas Kigoma (9.33%), Rukwa (11.33%) and Shinyanga (18.67%) had the lowest RYMV prevalence. In each region, RYMV prevalence was higher in 2014 than in 2013. The phylotypes S4lm and new determined phylotypes (S6 c and S6 w ) were highly adapted to low temperature (13.3°C) and rainfall (13.7 mm) areas. For the first time, strains from the phylotype S4ug were found outside Uganda, in Kilimanjaro region. Strain S4lv (phylotype Lake Victoria) was found for the first time in Arusha region. The strain S4lm was found in Mbeya, Morogoro and Rukwa regions. Strains S4lm and S4lv were also found in Shinyanga and Kigoma regions, respectively. The strain S5 was still restricted to Morogoro but extended to new locations such as Ulanga district. Strain S6 was found in several new areas and new phylotypes of S6 (S6c and S6w) are reported in this study.
International Rice Research Institute, Eds. (2002) Standard Evaluation System for Rice. 5th Edition, Inger. Genetic Resources Center, IRRI, Manila, Philippines, 27 p.
Kouassi, N.K., N’Guessan, P., Albar, L., Fauquet, C.M. and Brugidou, C. (2005) Distribution and Characterization of Rice Yellow Mottle Virus: A Threat to African Farmers. Plant Disease, 89, 124-133. https://doi.org/10.1094/PD-89-0124
Matsumura, K., Hijmans, R.J., Chemin, Y., Elvidge, C.D., Sugimoto, K., Wu, W., Lee, Y. and Shibasaki, R. (2009) Mapping the Global Supply and Demand Structure of Rice. Sustainability Science, 4, 301. https://doi.org/10.1007/s11625-009-0077-1
Luzi-Kihupi, A., Zakayo, J.A., Tusekelege, H., Mkuya, M., Kibanda, N.J.M., Khatib, K.J. and Maerere, A. (2009) Mutation Breeding for Rice Improvement in Tanzania. In: Induced Plant Mutations in the Genomics Era, Food and Agriculture Organization of the United Nations, Rome, 385-387.
Awoderu, Y.A. (1991) Rice Yellow Mottle Virus Situation in West Africa. Journal of Basic Microbiology, 31, 91-99. https://doi.org/10.1002/jobm.3620310204
Mghase, J.J., Shiwachi, H., Nakasone, K. and Takahashi, H. (2010) Agronomic and Socio-Economic Constraints to High Yield of Upland Rice in Tanzania. African Journal of Agriculture Research, 5, 150-158.
Taylor, D.R., Fofie, A.S. and Suma, M. (1990) Natural Infection of Rice Yellow Mottle Virus Disease (RYMV) on Rice in Sierra Leone. International Rice Research Newsletter, 15, 5-19.
Kanyeka, Z.L., Kibanda, J.M. and Mbapila, J. (1996) Rice Yellow Mottle Virus in Tanzania. Proceedings of the Potential and Constraints for Improvement of Rice Cultivation Seminar, Kilimanjaro Agricultural Training Center, Moshi (KATC), Tanzania, 11-15 March 1996, 17-22.
Abubakar, Z., Ali, F., Pinel, A., Traoré, O., N’Guessan, P., Notteghem, J., Kimmins, F., Konaté, G. and Fargette, D. (2003) Phylogeography of Rice Yellow Mottle Virus in Africa. Journal of General Virology, 84, 733-743. https://doi.org/10.1099/vir.0.18759-0
Abo, M.E., Sy, A.A. and Alegbejo, S.M. (1998) Rice Yellow Mottle Virus (RYMV) in Africa: Evolution, Distribution, Economic Significance and Sustainable Rice Production and Management Strategies. Journal of Sustainable Agriculture, 11, 85-111. https://doi.org/10.1300/J064v11n02_08
Bakker, W. (1970) Rice Yellow Mottle, a Mechanically Transmissible Virus Disease of Rice in Kenya. Netherlands Journal of Plant Pathology, 76, 53-63. https://doi.org/10.1007/BF01974433
Konaté, G., Sarra, S. and Traoré, O. (2001) Rice Yellow Mottle Virus Is Seedborne but Not Seed Transmitted in Rice. European Journal of Plant Pathology, 107, 361-364. https://doi.org/10.1023/A:1011295709393
Tamm, T. and Truve, E. (2000) Sobemovirus (Minireview). Journal of Virology, 74, 6231-6231. https://doi.org/10.1128/JVI.74.14.6231-6241.2000
Fargette, D., Pinel, A., Halimi, H., Brugidou, C., Fauquet, C. and Van Regenmortel, M. (2002) Comparison of Molecular and Immunological Typing of Isolates of Rice Yellow Mottle Virus. Archives of Virology, 147, 583-596. https://doi.org/10.1007/s007050200008
Mpunami, A., Ndikumana, I., Hubert, J., Pinel-Galzi, A., Kibanda, N., Mwalyego, F., Tembo, P., Kola, B., Mkuya, M., Kanyeka, Z., Mutegi, R., N’chimbi Msolla, S., Njau, P., Séré, Y., Fargette, D. and Hébrard, E. (2012) Tanzania, Biodiversity Hotspot of Rice Yellow Mottle Virus. Arusha, Tanzania, 97-101.
Banwo, O.O., Alegbejo, M.D. and Abo, M.E. (2004) Rice Yellow Mottle Virus Genus Sobemovirus: A Continental Problem in Africa. Journal of Plant Protection Science, 40, 26-36.
Kanyeka, Z.L., Sangu, E., Fargette, D., Pinel-Galzi, A. and Hébrard, E. (2007) Distribution and Diversity of Local Strains of Rice Yellow Mottle Virus in Tanzania. African Journal of Crop Science, 15, 201-209.
Jones, R.A.C. (2016) Future Scenarios for Plant Virus Pathogens as Climate Change Progresses. Advances in Virus Research, 95, 87-147.
Traoré, O., Galzi-Pinel, A., Poulicard, N., Hébrard, E., Konaté, G. and Fargette, D. (2008) Rice Yellow Mottle Virus Diversification Impact on the Genetic Control of RYMV. Plant Disease Journal, 5, 1-4.
Rakotomalala, M., Pinel-Galzi, A., Albar, L., Ghesquière, A., Rabenantoandro, Y., Ramavovololona, P. and Fargette, D. (2008) Resistance to Rice Yellow Mottle Virus in Rice Germplasm in Madagascar. European Journal of Plant Pathology, 122, 277-286. https://doi.org/10.1007/s10658-008-9282-5
N’Guessan, P., Pinel, A., Caruana, M.L., Frutos, R., Sy, A., Ghesquière, A. and Fargette, D. (2000) Evidence of the Presence of Two Serotypes of Rice Yellow Mottle Sobemovirus in Côte d’Ivoire. European Journal of Plant Pathology, 106, 167-178. https://doi.org/10.1023/A:1008792109954
Ardales, E.Y., Leung, H., Vera Cruz, C.M., Mew, T.W., Leach, J.E. and Nelson, R.J. (1996) Hierarchical Analysis of Spatial Variation of the Rice Bacterial Blight Pathogen across Diverse Agroecosystems in the Philippines. Phytopathology, 86, 241-252. https://doi.org/10.1094/Phyto-86-241
Bekeko, Z., Hussien, T. and Tessema, T. (2012) Distribution, Incidence, Severity and Effect of the Rust (Puccinia abrupta var. partheniicola) on Parthenium hysterophorus L. in Western Hararghe Zone, Ethiopia. African Journal of Plant Science, 6, 337-345. https://doi.org/10.5897/AJPS12.040
Nwilene, F.E., Traore, A.K., Asidi, A.N., Sere, Y., Onasanya, A. and Abo, M.E. (2009) New Records of Insect Vectors of Rice Yellow Mottle Virus (RYMV) in Cote d’Ivoire, West Africa. Journal of Entomology, 6, 198-206. https://doi.org/10.3923/je.2009.198.206
Finninsa, C. (2003) Relationship between Common Bacterial Blight Severity and Bean Yield Loss in Pure Stand and Bean-Maize Intercropping Systems. International Journal of Pest Management, 49, 177-185. https://doi.org/10.1080/0967087021000049269
William, H.A., Darrell, J.C. and Girish, B. (1990) Use of the Arcsine and Square Root Transformations for Subjectively Determined Percentage Data. Journal of Weed Science, 38, 452-458.
McDonald, J.H. (2014) Biological Statistics: Data Transformation. http://www.biostathandbook.com/transformation.html
Pinel, A., N’Guessan, P., Bousalem, M. and Fargette, D. (2000) Molecular Variability of Geographically Distinct Isolates of Rice Yellow Mottle Virus in Africa. Archives Virology, 145, 1621-1638. https://doi.org/10.1007/s007050070080
Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position Specific Gap Penalties and Weight Matrix Choice. Journal of Nucleic Acids Research, 22, 4673-4680. https://doi.org/10.1093/nar/22.22.4673
Gouy, M., Guindon, S. and Gascuel, O. (2010) SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building. Molecular Biology and Evolution, 27, 221-224. https://doi.org/10.1093/molbev/msp259
Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W. and Gascuel, O. (2010) New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Systematic Biology, 59, 307-321. https://doi.org/10.1093/sysbio/syq010
Pinel, A. and Fargette, D. (2006) First Report of Rice Yellow Mottle Virus in Rice in Uganda. Plant Disease Journal, 90, 683.2-683.2.
Ochola, D., Issaka, S., Rakotomalala, M., Pinel-Galzi, A., Ndikumana, I., Hubert, J., Hébrard, E., Séré, Y., Tusiime G. and Fargette, D. (2015) Emergence of Rice Yellow Mottle Virus in Eastern Uganda: Recent and Singular Interplay Between Strains in East Africa and in Madagascar. Virus Research, 195, 64-72.
Fargette, D., Pinel, A., Abubakar, Z., Traoré, O., Brugidou, C., Fatogoma, S., Hébrard, E., Choisy, M., Séré, Y., Fauquet, C. and Konaté, G. (2004) Inferring the Evolutionary History of Rice Yellow Mottle Virus from Genomic, Phylogenetic, and Phylogeographic Studies. Journal of Virology, 78, 3252-3261. https://doi.org/10.1128/JVI.78.7.3252-3261.2004
Rakotomalala, M., Pinel-Galzi, A., Mpunami, A., Randrianasolo, A., Ramavovololona, P., Rabenantoandro, Y. and Fargette, D. (2013) Rice Yellow Mottle Virus in Madagascar and in the Zanzibar Archipelago; Island Systems and Evolutionary Time Scale to Study Virus Emergence. Virus Research, 171, 71-79.
Abo, M.E., Alegbejo, M.D., Sy, A.A. and Misari, S.M. (2000) An Overview of the Mode of Transmission, Host Plants and Methods of Detection of Rice Yellow Mottle Virus. Journal of Sustainable Agriculture, 17, 19-36. https://doi.org/10.1300/J064v17n01_04
Traoré, O., Pinel-Galzi, A., Sorho, F., Sarra, S., Rakotomalala, M., Sangu, E., Kanyeka, Z., Séré, Y., Konaté, G., Fargette, D. (2009) A Reassessment of the Epidemiology of Rice Yellow Mottle Virus Following Recent Advances in Field and Molecular Studies. Journal of Virus Research, 141, 258-267.
Fargette, D., Konate, G., Fauquet, C., Muller, E., Peterschmitt, M., Thresh, J.M. (2006) Molecular Ecology and Emergence of Tropical Plant Viruses. Annual Review of Phytopathology, 44, 235-260. https://doi.org/10.1146/annurev.phyto.44.120705.104644
Traoré, M.D., Traoré, V.S.E., Galzi-Pinel, A., Fargette, D., Konate, G., Traore, A.S. and Traoré, O. (2008) Abiotic Transmission of Rice Yellow Mottle Virus through Soil and Contact between Plants. Pakistan Journal of Biological Sciences, 11, 900-904. https://doi.org/10.3923/pjbs.2008.900.904
Harrington, R.B. (2002) The Heat Is on Barley Yellow Dwarf Disease: Recent Advances and Future Strategies, CIMMYT, México, D.F., 34-39.
Traoré, O., Pinel, A., Fargette, D. and Konate, G. (2001) First Report and Characterization of Rice Yellow Mottle Virus in Central Africa. Plant Disease Journal, 85, 920.1.
Sarra, S., Oevering, P., Guindo, S. and Peters, D. (2004) Wind-Mediated Spread of Rice Yellow Mottle Virus (RYMV) in Irrigated Rice Crops. Plant Pathology, 53, 148-153. https://doi.org/10.1111/j.0032-0862.2004.00981.x
Uke, A., Tibanyendela, N., Ikeda, R., Fujiie, A. and Natsuaki, K.T. (2014) Modes of Transmission and Stability of Rice Yellow Mottle Virus. Journal of Plant Protection Research, 54, 363-366. https://doi.org/10.2478/jppr-2014-0054
Trovao, N.S., Baele, G., Vrancken, B., Bielejec, F., Suchard, M.A., Fargette, D. and Lemey, P. (2015) Host Ecology Determines the Dispersal Patterns of a Plant Virus. Virus Evolution Journal, 1, vev016. https://doi.org/10.1093/ve/vev016