Diversity of cassava mosaic disease causal viruses in Kenya
Abstract
Cassava Mosaic Disease (CMD) caused by Cassava Mosaic Begomoviruses (CMBs) causes poor Cassava (Mannihot esculenta Crantz.) production in Kenya. Lack of genomic characterization of CMBs hampers control and management of the disease. This study was conducted to determine the diversity and distribution of begomoviruses causing CMD in Kenya. A survey of CMD was conducted in the counties of Bungoma, Busia, Siaya, Kakamega, Kilifi, Kwale, Machakos and Kisii. The DNA was extracted from 60 leaf samples using Cetyltrimethlammonium bromide protocol. Specific primers targeting all EACMV and ACMV viruses were then used to amplify DNA fragments of CMD pathogens. PCR products were prepared and sequenced using Sanger sequencing platform. The sequences were assembled BLAST searched against NCBI database using BLASTn. Phylogenetic trees were constructed based on automatic Neighbor Joining Tree and Maximum Likelihood method of nucleotides substitution by Kimura 2 Parameter with Invariant Plus Gamma. ACMV isolates from Busia and Kakamega
clustered together in group I while the rest clustered in group II. They were more similar to each other and to Ugandan isolate implying common ancestry than with the other isolate from Kisii. The EACMV isolate from Kisii and a weed Leonotis leonarus from Bungoma clustered together with EACMV-UG isolate from Bungoma western Kenya while another was quite similar to an EACMV-Ke isolate from Makueni eastern Kenya. An isolate from Kisumu County was very similar to another isolate from Non-cassava plant Makhamia zanzibarica. These findings imply that the occurrence of CMD Begomoviruses in non-cassava plants may have a role in CMD epidemiology
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