Incidence of Groundnut Rosette Disease (GRD) and Genetic Diversity of Groundnut Rosette Assistor Virus (GRAV) in Western Kenya
International Journal of Genetics and Genomics
Volume 7, Issue 4, December 2019, Pages: 98-102
Received: Sep. 11, 2019; Accepted: Oct. 4, 2019; Published: Oct. 16, 2019
Views 512      Downloads 131
Benard Mukoye, Department of Biological Sciences, School of Natural Sciences, Masinde Muliro University of Science and Technology (MMUST), Kakamega, Kenya; Department of Biosafety and Phytosanitary Services, Kenya Plant Health Inspectorate Service (KEPHIS), Nairobi, Kenya
Millicent Florence Owuor Ndonga, Department of Biological Sciences, School of Natural Sciences, Masinde Muliro University of Science and Technology (MMUST), Kakamega, Kenya
Hassan Karakacha Were, Department of Agriculture and Land Use Management (ALUM), School of Agriculture, Veterinary Science and Technology, Masinde Muliro University of Science and Technology (MMUST), Kakamega, Kenya
Article Tools
Follow on us
This study determined the incidence of groundnut rosette disease (GRD) and genetic diversity of groundnut rosette assistor virus (GRAV, genus Luteovirus) in western Kenya. The diseases is a major constraint of groundnuts in Sub-Saharan Africa (SSA) causing up to 100% yield losses in severe cases. Among the GRD associated viruses, GRAV plays a crucial role in vector transmission of the other viruses. Therefore understanding the genetics of GRAV across SSA could enhance development of resistance to the disease. In Kenya, groundnuts are mainly grown in western region, however, the yields are poor mainly due to GRD. Information on occurrence and distribution of GRD in western Kenya was not documented and little was known about the characteristics of associated viruses. Two diagnostic surveys were conducted in six counties; Bungoma, Busia, Homabay, Kakamega, Siaya and Vihiga. Symptomatic and asymptomatic groundnut were collected in RNAlater® solution for laboratory analysis. Total RNA was extracted from the leaf samples using RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocol and used for double stranded cDNA synthesis using the SuperScript II kit. The cDNA was column-purified with the DNA Clean & ConcentratorTM-5 – DNA kit. The samples were then processed with the transposon-based chemistry library preparation kit (Nextera XT, Illumina) following manufacturer’s instructions. The fragment sizes structure of the DNA libraries was assessed using the Agilent 2100 Bioanalyzer. The indexed denatured DNA libraries were sequenced (200-bp paired-end sequencing) on the Illumina MiSeq platform (Illumina). Reads quality check was done using FastQC. Trimmed reads were used for de novo assembly and contigs aligned to the viral genomes database using CLC Genomics Workbench 10.1.2. The assembled contigs were subjected to a BLASTn search against the GenBank database. Phylogenetic analyses and comparisons were performed using the MEGA X. Average incidence was 53% and 41% in the short and long rain seasons, respectively. Chlorotic rosette was the dominant symptom followed by Green rosette and Mosaic. The GRAV coat protein (GRAV-CP) gene sequences revealed 97-100% identity with GeneBank isolates showing very slight variations across SSA. The study concludes that GRD incidence is high in western Kenya and that GRAV is highly conserved across SSA. The study recommends an urgent need to curb GRD, possibly through the exploitation of pathogen derived resistance (PDR) with GRAV as the suitable candidate.
Incidence, GRAV, Kenya, Diversity
To cite this article
Benard Mukoye, Millicent Florence Owuor Ndonga, Hassan Karakacha Were, Incidence of Groundnut Rosette Disease (GRD) and Genetic Diversity of Groundnut Rosette Assistor Virus (GRAV) in Western Kenya, International Journal of Genetics and Genomics. Vol. 7, No. 4, 2019, pp. 98-102. doi: 10.11648/j.ijgg.20190704.12
Copyright © 2019 Authors retain the copyright of this article.
This article is an open access article distributed under the Creative Commons Attribution License ( which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Kumar, P. L. & Waliyar, F., (Ed). (2007). Diagnosis and detection of viruses infecting ICRISAT mandate crops: Methods Manual. Patancheru 502 324, Andhra Pradesh, India; International Crops Research Institute for the Semi-Arid Tropics. 133pp.
Kidula, N., Okoko, N., Bravo-Ureta, B. E., Thuo, M. & Wasilwa, L. (2010). A preliminary analysis of yield differences in groundnuts between research and non-research farmers in Kenya. In paper presented at the 12th KARI biennial scientific conference, 8-12 November 2010, Naiobi Kenya.
Okello, D. K., Birima, M. & Deom, C. M., (2010). Overview of groundnut research in Uganda: Post, present and future. Afr. J. Biotechnol. 9: 6448-6459.
Kayondo, S. I., Rubaihayo, P. R., Ntare, B. R., Gibson, P. I., Edema, R., Ozimati, A. & Okello, D. K. (2014). Genetics of resistance to groundnut rosette virus disease: African crop science journal, 22: 21-29. ISSN: 1021-9730/2014.
Mutegi, C. K. (2010). The extend of aflatoxin and aspergillus section flavi, penicillium spp. and Rhizopus spp. contamination of peanuts from households in Western Kenya and the causative factors of contamination. PhD dissertation, University of Kwazulu-Natal, Pietermaritzburg. South Africa.
Waliyar, F., Kumar, P. L., Ntare, B. R., Monyo, E., Nigam, S. N., Reddy, A. S., Osiru, M. & Diallo, A. T. (2007). A Century of Research on Groundnut Rosette Disease and its Management. Information Bulletin no. 75. Patancheru 502 324, Andhra Pradesh, India. International Crops Research Institute for the Semi-Arid Tropics, 40 pp. ISBN 978-92-9066-501-4.
Taliansky, M. E. & Robinson, D. J. (2003). Molecular Biology of umbraviruses: Phantom warriors. J. Gen. Virol. 84: 1951-1960.
Naidu, R. A., Robinson, D. J., & Kimmins, F. M. (1998a). Detection of each of the causal agents of groundnut rosette disease in plants and vector aphids by RT-PCR. J. Virol. Methods 76: 9-18.
Deom, C. M., Naidu, R. A., Chiyembekeza, A. J., Ntare, B. R. & Subrahmanyam, P. (2000). Sequence diversity with the three agents of groundnut rosette disease. Phytopathol. 90: 214-219. doi: 10.1094/PHYTO.2000.90.3.214
Murant, A. F., & Kumar, I. K. (1990). Different variants of the satellite RNA of groundnuts rosette virus are responsible for the chlorotic and green forms of groundnut rosette disease. Ann. Appl. Biol. 117: 85-92.
Scott, K. P., Farmer, M. J., Robinson, D. J., Torrence, L. & Murant, A. F. (1996). Comparison of the coat protein of groundnut rosette assistor virus with those of other luteovirus. Ann. Appl. Biol. 128: 77-83.
Mugisa, I. O., Karungi, J., Akello, B., Ochwo-Ssemakula, M. K. N., Biruma, M., Okello, D. K. & Otim, G. (2016). Determinants of groundnut rosette virus disease occurrence in Uganda. Elseviercropprotectionjournal.
Okello, D. V, Akello, L. B, Tukamuhabwa, P., Odongo, T. L, Ochwo-Ssemakula, M., Adriko, J. & Deom, C. M. (2014). Groundnut rosette disease symptom types, distribution and management of the disease in Uganda. African journal of plant science. 8: 153-163.
Wangai, A. W., Pappu, S. S., Pappu, H. R., Okoko, N., Deom, C. M. & Naidu, R. A. (2001). Distribution and characteristics of groundnut rosette disease in Kenya. Plant Disease, 85: 470-474.
Reddy, D. V. R. (1991). Groundnut viruses and virus diseases; Distribution, identification and control. Rev. Plant Pathol. 70: 665-678.
Haas B. J, Papanicolaou A, Yassour M, Grabherr M, Blood P. D, Bowden J, Couger M. B, Eccles D, Li B, Lieber M, MacManes M. D, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey C. N, Henschel R, LeDuc R. D, Friedman N, Regev A. (2013). De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8: 1494–1512.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol 215: 403– 410.
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.
Were, H. K., Kabira, J. N., Kinyua, Z. M., Olubayo, F. M., Karinga, J. K., Aura, J., Lees, A. K., Cowan, G. H. & Torrance, L. (2013). Occurrence and Distribution of Potato Pests and Diseases in Kenya. Potato Research 56: 325–342.
Misari, S. M., Abraham, J. M., Demski J. W., Ansa, O. A., Kuhn, C. W, Casper, R. & Breyel, E. (1988a). Aphid transmission of the viruses causing chlorotic and green rosette diseases of peanut in Nigeria. Plant Disease 72: 250-253.
Blok, V. C., Ziegler, A., Robinson, D. J. & Murant, A. F. (1994). Sequences of 10 variants of the satellite- like RNA -3 of groundnut rosette virus. Virology 202: 25-32.
Mukoye, B., Mangeni, B. C., Sue, J., Ndonga, M. F. O., & Were, H. K. (2018). Next Generation Sequencing as a tool in modern pest diagnosis. A case study of groundnuts (Arachis hypogaea) as a potential host of new viruses in western Kenya. Conference proceedings: The 2nd Phytosanitary Conference, 4th – 8th June, 2018 at KEPHIS-Nairobi, Kenya.
Appiah, A. S., Sossah, L. F., Tegg, S. R., Offei, K. S. & Wilson, R. C. (2017). Assessing sequence diversity of goundnut rosette disease agents and the distribution of groundnut rosette assistor virus in major groundnut-producing regions of Ghana. Trop. Plant Pathol. Doi: 10.1007/s40858-017-0140-x.
Science Publishing Group
1 Rockefeller Plaza,
10th and 11th Floors,
New York, NY 10020
Tel: (001)347-983-5186