Diversity of Viruses and Viroids Infecting Taro in Kenya Based on Small RNA Sequencing and PCR Detection
DOI:
https://doi.org/10.47672/aja.1281Keywords:
Diversity, Colocasia esculenta, Small RNA sequencing, Taro Bacilliform Virus (TaBV), sequence variability, viroidsAbstract
Purpose: Viral diseases cause severe yield losses and quality decline in crops worldwide. Despite their economic significance, the occurrence and distribution of the major viruses and viroids infecting Taro in Kenya remain poor, limiting the development of robust disease management strategies to mitigate their spread. This study thus aimed to identify the viruses and viroids infecting Taro in Kenya as a basis for developing effective management strategies to support the prevention and control of Taro viruses.
Methodology: Viral surveys and sampling were conducted across nine Taro-growing counties with diverse agroecological conditions in Kenya to determine the incidence and distribution of viruses affecting Taro. Leaf and whole plant samples of symptomatic edible and wild Taro were collected for PCR, RT-PCR, and small RNA sequencing assays to determine the diversity of viruses and viroids infecting Taro.
Results: Disease-like symptoms, including stunting, leaf rolling, shrinkage, deformed leaves with mosaic and yellow veins, and dwarfism, were observed. An overall mean disease incidence of 32-60% was recorded in all sites surveyed. Small RNA sequencing revealed the presence of both DNA and RNA viruses. Detected DNA viruses included the Taro Bacilliform Virus (TaBV) and Taro Bacilliform CH Virus (TaBCHV), badnaviruses specific to Taro, the sweet potato Badnavirus B, sugarcane bacilliform virus, and sweet potato leaf curl virus. The RNA viruses included the sweet potato feathery mottle and Phaseolus vulgaris alphaendornavirus. A Citrus exocortis viroid was also detected. Interestingly, the wild relatives of Taro displayed very few viral sequence hits. This study reports the Taro viruses and viroids circulating in Kenya and is the first to describe the incidence, distribution, and sequence variability of TaBV in Kenya.
Recommendations: Future studies should focus on developing effective management strategies to support the prevention and control of Taro viruses, including genetic resources for virus-Taro interactions, removing infected crops, controlling insect vectors, and developing virus-free planting materials.
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References
Adams, I.P., Glover, R.H., Monger, W.A., Mumford, R., Jackeviciene, E., Navalinskiene, M., Samuitiene, M., & Boonham, N. (2009) Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol Plant Pathol 10:537–545.
Akwee, P.E., Netondo, G., Kataka, J.A., & Va, P. (2015) A critical review of the role of Taro Colocasia esculenta L. (Schott) to food security: A comparative analysis of Kenya and Pacific Island taro germplasm. Scientia Agriculturae, 9, 101-8.
Anthony, M.B., Marc, L., & Bjoern, U. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, Volume 30, Issue 15, 1, Pages 2114–2120.
Babu, B., Hegde, V., Makeshkumar, T., & Jeeva, M. L. (2011) Detection and identification of Dasheen mosaic virus infecting Colocasia esculenta in India. Indian Journal of Virology, 22 (1), 59–62.
Bhat, A.I., Hohn, T., & Selvarajan, R. (2016). Badnaviruses: The Current Global Scenario. Viruses, 8(6), 177.
Bull, S.E., Briddon, R.W., Sserubombwe, W.S., Ngugi, K., Markham, P.G., & Stanley, J. (2006) Genetic diversity and phylogeography of cassava mosaic viruses in Kenya. J. Gen. Virol. 87:3053-3065.
Coetzee, B., Freeborough, M.J., Maree, H.J., Celton, J.M., Rees, D.J.G., & Burger, J.T. (2010) Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard. Virology 400, 157–163.
Gollifer, D.E., Jackson, G.V.H., & Dabek, A.J. (1977) The occurrence and transmission of viruses of edible aroids in the Solomon Islands and the Southwest Pacific. International Journal of Pest Management, 23, 171–7.
Gu, Y.H., Tao, X., Lai, X.J., Wang, H.Y., & Zhang, Y.Z. (2014) Exploring the polyadenylated RNA virome of sweet potato through high-throughput sequencing. PLoS ONE 9: e98884
Ivancic A. (1992) Breeding and genetics of Taro (Colocasia esculenta (L)) Schott Ministry of Agriculture and Lands, Solomon Islands UNDP, Food and Agriculture Organizations of the United Nations, 1-97
Gollifer, D.E. & Jackson, G.V.H. (1975) Disease and pest problems of Taro (Colocasia esculenta L. Schott) in the British Solomon Islands. Pesticide Articles and News Summarie, 21, 45-53
Hadidi A., Sun, L., & Randles, J.W. (2022) Modes of Viroid Transmission. Cells. Feb 18;11(4):719
Hammond, R.W. & Owens, R.A. (2006). Viroids. New and Continuing Risks for Horticultural and Agricultural Crops. APSnet Feature article.
Higgins, C.M., Bejerman, N., Li, M., James, A.P., Dietzgen, R.G., Pearson, M.N., Revill, P.A., & Harding, R.M. (2016) Complete genome sequence of Colocasia bobone disease-associated virus, a putative cytorhabdovirus infecting Taro. Arch. Virol. 161, 745–748.
Jackson, G.V.H. (1978). Alomae and bobone diseases of Taro. South Pacific Commission Advisory Leaflet No. 8
Jackson, G.V.H. (1980) ‘Diseases and pests of taro.’ (SPC: Noumea)
James M., Kenten R.H., Woods, R.D. (1973). Virus-like particles associated with two diseases of Colocasia esculenta (L.) Schott in the British Solomon Islands. Journal of General Virology, 21, 145–153
Jo, Y., Choi, H., Kim, S.-M., Kim, S.-L., Lee, B. C., & Cho, W. K. (2017). The pepper virome: natural co-infection of diverse viruses and their quasispecies. BMC Genomics 18:453.
Jo, Y., Choi, H., Kim, S.-M., Kim, S.-L., Lee, B. C., & Cho, W. K. (2016). Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus. BMC Genomics 17:579.
Jo, Y., Choi, H., Kyong Cho, J., Yoon, J.-Y., Choi, S.-K., & Kyong Cho, W. (2015). In silico approach to reveal viral populations in grapevine cultivar Tannat using transcriptome data. Sci. Rep. 5:15841.
Kazmi, S. A., Yang, Z., Hong, N., Wang, G., & Wang, Y. (2015). Characterization by small RNA sequencing of Taro bacilliform CH Virus (TaBCHV), a novel Badnavirus. PLoS One.
Kashif, M., Pietilä, S., Artola, K., Jones, R. A. C., Tugume, A. K., Makinen, V., et al. (2012). Detection of viruses in sweet potato from Honduras and Guatemala augmented by deep-sequencing of small-RNAs. Plant Dis. 96, 1430–1437.
Kidanemariam, D.B., Sukal, A.C., Abraham, A.D., Stomeo, F., Dale, J.L., James, A.P. & Harding, R.M. (2018) Identification and molecular characterization of Taro bacilliform virus and Taro bacilliform CH virus from East Africa. Plant Pathol. 67, 1977–1986.
Kreuze, J. F., Perez, A., Untiveros, M., Quispe, D., Fuentes, S., Barker, I., & Simon, R. (2009) Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery, and sequencing of viruses.Virology, 388(1), 1–7.
Leke, W.N., Mignouna, D.B., Brown, J.K. et al. (2015) Begomovirus disease complex: emerging threat to vegetable production systems of West and Central Africa. Agric & Food Secur 4, 1
Li, R., Gao, S., Hernandez, A. G., Wechter, W. P., Fei, Z., & Ling, K. S. (2012) Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation. PLoS ONE 7: e37127.
Macanawai, A.R, Ebenebe, A.A, & Hunter, D. (2005) Investigations into the seed and mealybug transmission of Taro bacilliform virus. Australasian Plant Pathology, 34, 73–6.
Maino, M.K. (2003) The development of a serological-based diagnostic test for Dasheen mosaic potyvirus (DsMV). M Sc Thesis, School of Life Sciences, Queensland University of Technology.
Matsumura, E., Coletta-Filho, H., Nouri, S., Falk, B., Nerva, L. & Oliveira, T. (2017) Deep sequencing analysis of RNAs from citrus plants grown in a citrus sudden death-affected area reveals diverse known and putative novel viruses. Viruses 9:92
Natalia, K. & Rosemarie, W.H. (2014) Molecular biology of viroid–host interactions and disease control strategies, Plant Science, Volume 228, Pages 48-60.
Navas-Castillo, J., Fiallo-Olivé, E., & Sánchez-Campos, S. (2011) Emerging virus diseases transmitted by whiteflies. Annu. Rev. Phytopathol. 49, 219–248.
Ndabikunze, B.K., Talwana, H.A.L., Mongi, R.J. et al. (2011) Proximate and mineral composition of cocoyam (Colocasia esculenta L. and Xanthosoma sagittifolium L.) grown along the Lake Victoria Basin in Tanzania and Uganda. African Journal of Food Science, 5, 248– 54.
Okoń, S., Ociepa, T., Nucia, A., Cieplak, M., & Kowalczyk, K. (2021) Is Every Wild Species a Rich Source of Disease Resistance? Avena fatua L.-Potential Donor of Resistance to Powdery Mildew. Plants (Basel, Switzerland), 10(3), 560.
Onyeka, J. (2014) Status of Cocoyam (Colocasia esculenta and Xanthosoma spp) in West and Central Africa: Production, Household Importance and the Threat from Leaf Blight. Lima (Peru). CGIAR Research Program on Roots, Tubers and Bananas (RTB).
Owens, R.A. & Verhoeven, J.Th.J. (2009) Potato spindle tuber. The Plant Health Instructor. DOI: 10.1094/PHI-I-2009-0804-01. Reviewed 2015.
Revill, P., Jackson, G., Hafner, G. (2005) Incidence and distribution of viruses of Taro (Colocasia esculenta) in Pacific Island countries. Australasian Plant Pathology, 35, 327–31.
Rodoni, B.C, Dale, J.L., & Harding, R.M. (1994) Review of alomae disease of Taro. Papua New Guinea Journal of Agriculture, Forestry and Fisheries, 37, 14-18
Sano, T., Barba, M., Li, S.F., & Hadidi, A. (2010) Viroids and RNA silencing: mechanism, role in viroid pathogenicity and development of viroid-resistant plants. GM Crops. Mar-Apr;1(2):80-6.
Shaw, D.E, Plumb, R.T., &Jackson G.V.H. (1979) Virus diseases of Taro (Colocasia esculenta) and Xanthosoma spp. in Papua New Guinea. Papua New Guinea Agriculture Journal, 30, 71-97
Shen, W., Le, S., Li, Y., & Hu, F. (2016) SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS One. 11(10): e0163962.
Singh, D., Jackson, D., Hunter, D., Fullerton R., Lebot, V., Tailor, M., Josef, T., et al. (2012). Taro Leaf Blight - A threat to food security. Open access Agriculture, 2, 182-203
Talwana, H.A.L., Serem, A,K., & Ndabikunze, B.K. (2009) Production Status and Prospects of Cocoyam (Colocasia esculenta (L.) Schott.) in East Africa. Journal of Root Crops, 35, 98–107.
Thresh, J.M., Otim-Nape, G.W., Legg, J.P., & Fargette, D. (1997) African cassava mosaic virus disease: the magnitude of the problem. African Journal of Root and Tuber Crops. 2 (1/2), 13-19.
Wanyama, D. & Mardell, G. (2006) Community of taro producers. (www. Sustainable kenya.info page 1. Accessed on 27th October, 2012.
Wylie, S. J., Li, H., Saqib, M., & Jones, M.G.K. (2014). The global trade in fresh produce and the vagility of plant viruses: a case study in garlic. PLoS ONE 9: e105044.
Wu, Q.F., Ding, S.W., Zhang, Y, J., & Zhu, S.F. (2015) Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms. Annu Rev Phytopathol, 53:425–444.
Yang, I.C., Hafner, G.J., Revill, P.A., Dale, J.L., & Harding, R.M. (2003b) Sequence diversity of South Pacific isolates of Taro bacilliform virus and the development of a PCR-based diagnostic test. Archives of Virology, 148, 1957– 68.
Yusop, M.S.M., Saad, M.F.M., Talip, N., Baharum, S.N., & Bunawan, H. (2019) A Review on Viruses Infecting Taro (Colocasia esculenta (L.) Schott). Pathogens.8(2):56.
Zettler, F.W. & Hartman, R.D. (1986) Dasheen mosaic virus and its’ control in cultivated aroids. Extension Bulletin, ASPAC Food and Fertilizer Technology Centre for the Asian and Pacific region, Taipei. No. 233, 13.
Zettler, F.W. & Hartman, R.D. (1987) Dasheen mosaic virus as a pathogen of cultivated aroids and control of the virus by Tissue culture. Plant Disease, 71, 958–963.
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