Rice (Oryza sativa L.) is an economically important food crop in western Kenya but its production remains very low due to abiotic and biotic constraints. Rice yellow mottle disease (RYMD) caused by Rice yellow mottle virus (RYMV, genus: Sobemovirus) can cause up to 100% yield loss. This study characterized and determined the genetic diversity of RYMV strains in the ten isolates collected in February 2020 from both symptomatic and asymptomatic plants in western Kenya. The samples from the two rice fields A and B had two major common rice varieties of IR; field A (IR 2793) and field B (IR 2793-8-1). Total RNA was extracted using GeneJET Plant RNA Purification Mini Kit followed by RT-PCR using RYMV CP specific primers. The PCR products were sequenced by Sanger sequencing technology. Phylogenetic analysis was done by MEGA X. RYMV presence was confirmed serologically by DAS-ELISA. Isolates Ke_A1, KeB3 and KeB4 are novel sequences. KeB3 and KeB4 isolates clustered uniquely from the other Kenyan sequences depicting new evolutionary diversity. KeB3 and KeB4 shared 99% sequence identity with Ke105 and Ke101, while isolate Ke_A1 shared 98% identity with Ke101 and 99% with Ke105. Phylogenetic analysis of the CP gene sequences revealed that the isolates from Uganda (Ug), Kenya (Ke) and Tanzania (Tz) clustered together by country, implying that there was a possibility of single introduction of the RYMV CP gene in the three East African (EA) countries once, before further local viral diversity occurred in each country with new recombinations for further research.
| Published in | American Journal of Plant Biology (Volume 5, Issue 4) |
| DOI | 10.11648/j.ajpb.20200504.17 |
| Page(s) | 120-124 |
| Creative Commons |
This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited. |
| Copyright |
Copyright © The Author(s), 2024. Published by Science Publishing Group |
Genetic Diversity, Novel Sequences, Rice yellow mottle virus, Western Kenya
| [1] | Lidejere, M. I. (2012). Variations in the Coat Protein Gene of Rice yellow mottle virus isolates from Western Kenya. Msc. Thesis. Masinde Muliro University of Science and Technology, Kenya. |
| [2] | Adego, A. K., Wéré, H. K., Muoma, J., Mukoye, B., Hébrard, E., Pinel-Galzi, A., Poulicard, N. and Fargette, D. (2017). Current status of rice yellow mottle virus in western Kenya. Research Journali's Journal of Agriculture. 4 (9): 1-12. |
| [3] | Kouassi, N. K., N’Guessan, P., Albar, L., Fauquet, C. & Brugidou, C. (2005). Distribution and characterization of Rice yellow mottle virus: a threat to African farmers. Plant Disease. 89: 124-132. |
| [4] | Rakotomalala, M., Vrancken, B., Pinel-Galzi, A., Ramavovololona, P., He´brard, E., Randrianangaly, J. S., Dellicour, S., Lemey, P. and Fargette, D. (2019). Comparing patterns and scales of plant virus phylogeography: Rice yellow mottle virus in Madagascar and in continental Africa. Virus Evolution. 5 (2): vez023. |
| [5] | Ochola, D. & Tusiime, G. (2011). Survey on Incidences and Severity of Rice Yellow Mottle Virus Disease in Eastern Uganda. International Journal of Plant Pathology. 2: 15-25. |
| [6] | Kanyeka, Z. L., Sangu, E., Fargette, D., Pinel-Galzi, A. & Hérbrard, E. (2007). Distribution and diversity of local strains of Rice yellow mottle virus in Tanzania. African Crop Science Journal. 15: 201–209. |
| [7] | Lidejere, M. I. et al., (2012). Variations in the Coat Protein Gene of Rice yellow mottle virus isolates from Western Kenya. Msc. Thesis. Masinde Muliro University of Science and Technology, Kenya. |
| [8] | Ndikumana, I., Pinel-Galzi, A., Fargette, D. & Hebrard, E. (2017). Complete genome sequence of a new strain of Rice yellow mottle virus from Malawi, characterized by a recombinant VPg protein. Genome Announcement. 5: e01198-17. |
| [9] | Fargette, D., Pinel, A., Halimi, H., Brugidou, C., Fauquet, C. and Van Regenmortel, M. (2002a). Comparison of molecular and immunological typing of the isolates of Rice yellow mottle virus. Archives of Virology. 147: 583-596. |
| [10] | Traoré, O., Sorho, F., Pinel, A., Abubakar, Z., Banwo, O., Maley, J., Hébrard, E., Winter, S., Séré, Y., Konaté, G. & Fargette, D. (2005). Processes of diversification and dispersion of Rice yellow mottle virus inferred from large-scale and high-resolution phylogeographical studies. Molecular Ecology. 14: 2097-2110. |
| [11] | King, A. et al. (2018). Changes to Taxonomy and the International Code of Virus Classification and Nomenclature Ratified by the International Committee on Taxonomy of Viruses. Archives of Virology. 163: 2601–31. |
| [12] | Ling, R. et al. (2013). An Essential Fifth Codon ORF in the Sobemoviruses. Virology. 446: 397–408. |
| [13] | Adego, A. K., Poulicard, N., Pinel-Galzi, A., Mukoye, B., Fargette, D., Wéré, H. K. and Hébrard, E. (2018). Full-length genome sequences of recombinant and non-recombinant sympatric strains of Rice yellow mottle virus from western Kenya. Genome Announcements. 6 (8): e01508-17. |
| [14] | Pinel, A., N’Guessan, P., Bousalem, M. & Fargette, D. (2000). Molecular variability geographically distinct isolates of rice yellow mottle virus in Africa. Archives of Virology. 145: 1621-1638. |
| [15] | 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. |
| [16] | Fargette, D., Pinel, A., Abubakar, Z., Traoré, O., Brugidou, C., Fatogoma, S., Hébrard, E., Choisy, M., Séré, Y., Fauquet, C. & Konaté, G. (2004). Inferring the evolutionary history of rice yellow mottle virus from genomic, phylogenetic, and phylogeographic studies. Journalof Virology. 78: 3252–3261. |
| [17] | Tamura, K. & Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution. 10: 512-526. |
| [18] | Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution. 35: 1547-1549. |
| [19] | Bakker W (1974). Characterisation and ecological aspects of Rice yellow mottle virus in Kenya. Ph. D. Thesis. University of Wageningen, The Netherlands. |
| [20] | Hébrard, E., Pinel-Galzi, A. & Fargette, D. (2008). Virulence domain of the RYMV genome-linked viral protein VPg towards rice rymv1–2-mediated resistance. Archives of Virology. 153: 1161-11648. |
| [21] | Poulicard, N., Pinel-Galzi, A., Hébrard, E. & Fargette, D. (2010). Why Rice yellow mottle virus, a rapidly evolving RNA plant virus, is not efficient at breaking rymv1–2 resistance. Molecular Plant Pathology. 11: 145-154. |
APA Style
Anthony Simiyu Mabele, Benard Mukoye, Denis Misiko Mukhongo. (2020). Serological and Molecular Characterization Detects Unique Rice Yellow Mottle Virus Strains in Kenya. American Journal of Plant Biology, 5(4), 120-124. https://doi.org/10.11648/j.ajpb.20200504.17
ACS Style
Anthony Simiyu Mabele; Benard Mukoye; Denis Misiko Mukhongo. Serological and Molecular Characterization Detects Unique Rice Yellow Mottle Virus Strains in Kenya. Am. J. Plant Biol. 2020, 5(4), 120-124. doi: 10.11648/j.ajpb.20200504.17
AMA Style
Anthony Simiyu Mabele, Benard Mukoye, Denis Misiko Mukhongo. Serological and Molecular Characterization Detects Unique Rice Yellow Mottle Virus Strains in Kenya. Am J Plant Biol. 2020;5(4):120-124. doi: 10.11648/j.ajpb.20200504.17
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Download@article{10.11648/j.ajpb.20200504.17,
author = {Anthony Simiyu Mabele and Benard Mukoye and Denis Misiko Mukhongo},
title = {Serological and Molecular Characterization Detects Unique Rice Yellow Mottle Virus Strains in Kenya},
journal = {American Journal of Plant Biology},
volume = {5},
number = {4},
pages = {120-124},
doi = {10.11648/j.ajpb.20200504.17},
url = {https://doi.org/10.11648/j.ajpb.20200504.17},
eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajpb.20200504.17},
abstract = {Rice (Oryza sativa L.) is an economically important food crop in western Kenya but its production remains very low due to abiotic and biotic constraints. Rice yellow mottle disease (RYMD) caused by Rice yellow mottle virus (RYMV, genus: Sobemovirus) can cause up to 100% yield loss. This study characterized and determined the genetic diversity of RYMV strains in the ten isolates collected in February 2020 from both symptomatic and asymptomatic plants in western Kenya. The samples from the two rice fields A and B had two major common rice varieties of IR; field A (IR 2793) and field B (IR 2793-8-1). Total RNA was extracted using GeneJET Plant RNA Purification Mini Kit followed by RT-PCR using RYMV CP specific primers. The PCR products were sequenced by Sanger sequencing technology. Phylogenetic analysis was done by MEGA X. RYMV presence was confirmed serologically by DAS-ELISA. Isolates Ke_A1, KeB3 and KeB4 are novel sequences. KeB3 and KeB4 isolates clustered uniquely from the other Kenyan sequences depicting new evolutionary diversity. KeB3 and KeB4 shared 99% sequence identity with Ke105 and Ke101, while isolate Ke_A1 shared 98% identity with Ke101 and 99% with Ke105. Phylogenetic analysis of the CP gene sequences revealed that the isolates from Uganda (Ug), Kenya (Ke) and Tanzania (Tz) clustered together by country, implying that there was a possibility of single introduction of the RYMV CP gene in the three East African (EA) countries once, before further local viral diversity occurred in each country with new recombinations for further research.},
year = {2020}
}
TY - JOUR T1 - Serological and Molecular Characterization Detects Unique Rice Yellow Mottle Virus Strains in Kenya AU - Anthony Simiyu Mabele AU - Benard Mukoye AU - Denis Misiko Mukhongo Y1 - 2020/11/30 PY - 2020 N1 - https://doi.org/10.11648/j.ajpb.20200504.17 DO - 10.11648/j.ajpb.20200504.17 T2 - American Journal of Plant Biology JF - American Journal of Plant Biology JO - American Journal of Plant Biology SP - 120 EP - 124 PB - Science Publishing Group SN - 2578-8337 UR - https://doi.org/10.11648/j.ajpb.20200504.17 AB - Rice (Oryza sativa L.) is an economically important food crop in western Kenya but its production remains very low due to abiotic and biotic constraints. Rice yellow mottle disease (RYMD) caused by Rice yellow mottle virus (RYMV, genus: Sobemovirus) can cause up to 100% yield loss. This study characterized and determined the genetic diversity of RYMV strains in the ten isolates collected in February 2020 from both symptomatic and asymptomatic plants in western Kenya. The samples from the two rice fields A and B had two major common rice varieties of IR; field A (IR 2793) and field B (IR 2793-8-1). Total RNA was extracted using GeneJET Plant RNA Purification Mini Kit followed by RT-PCR using RYMV CP specific primers. The PCR products were sequenced by Sanger sequencing technology. Phylogenetic analysis was done by MEGA X. RYMV presence was confirmed serologically by DAS-ELISA. Isolates Ke_A1, KeB3 and KeB4 are novel sequences. KeB3 and KeB4 isolates clustered uniquely from the other Kenyan sequences depicting new evolutionary diversity. KeB3 and KeB4 shared 99% sequence identity with Ke105 and Ke101, while isolate Ke_A1 shared 98% identity with Ke101 and 99% with Ke105. Phylogenetic analysis of the CP gene sequences revealed that the isolates from Uganda (Ug), Kenya (Ke) and Tanzania (Tz) clustered together by country, implying that there was a possibility of single introduction of the RYMV CP gene in the three East African (EA) countries once, before further local viral diversity occurred in each country with new recombinations for further research. VL - 5 IS - 4 ER -
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