Detection of Cassava Viruses from Elite Genotypes and Characterization of Cassava mosaic begomoviruses from farmers’ fields in Kenya

Abstract

Cassava is an important cash crop in the tropics that is recognized as a food security crop for over 300 million people in sub-Saharan Africa. In Kenya, it is grown for income and food covering a spread of 69,169 ha with an output of 892,122 tons. The crop faces several production challenges among which include diseases. The objectives of this study were; to determine the reaction of elite cassava genotypes to infection by Cassava mosaic disease (CMD) and Cassava brown streak disease (CBSD) in Kenya, to determine the geographical distribution and genetic diversity of cassava begomoviruses in Kenya. Five elite cassavagenotypes (08/363, F10-30-R2, Nl, Tajirika, Ex-mariakani), susceptible genotype (Kibandameno) and a local check/control (Shibe) were grown under natural disease. The populations of the whitefly vector, Bemisia tabaci (Gennadis), severity and incidence of cassava mosaic virus were recorded during the growth period at 3, 6 and 9 months after planting (MAP). Infection was determined through disease severity, incidence, Enzyme linked immunosorbent assay (ELISA) and Polymerase Chain Reaction (PCR) assays. In another study to determine the incidence, symptom severity, prevalence and geographical distribution of cassava begomoviruses, a diagnostic survey was conducted in 2013. A total of 24 fields in Nyanza, 22 in Western, 22 in Coast and 20 in Eastern were sampled. Species specific primers were used in laboratory analysis to detect the viruses present in cassava growing regions of Kenya. The sampled regions included Coast, Nyanza, Eastern and Western areas of Kenya. Genetic diversity of cassava begomoviruses was also done through sequencing. The highest CMD incidence was recorded in Western region with 60.19% and lowest in Eastern with 34.66%. Disease prevalence was highest in Nyanza, Western (100%) and lowest in Eastern (65%) respectively. Significant differences (p=<0.001) in CMD severity was recorded amongst the surveyed regions. The highest CMD severity was recorded with a mean of 1.8 in Western and lowest being 1.2 in Coast region of Kenya. PCR detected five begomoviruses namely; East African mosaic virus (EACMV), East African cassava mosaic Ugandan variant (EACMV-UgV), African cassava mosaic virus (ACMV), East African cassava mosaic Kenyan variant (EACMV-KE) and DNA satellites in the four regions under survey. The highest EACMV detection occurred in Nyanza region with 70.6% and the lowest being Western Kenya that recorded 36.6% detection. In EACMV-KE, the highest detections were recorded in Nyanza region with 26.5%, and lowest in Coast with 4.3%. However, EACMV-KE in this study was not found in Western Kenya. The highest ACMV detections were found in Nyanza with 29.4% with no detection of ACMV in the Eastern region of Kenya. EACMV-UgV was recorded in all regions surveyed in this study with Nyanza province having the highest disease detection with 41.2%. Comparison between coat protein (CP) of the Kenyan EACMV isolates showed that there was wide genetic variability in nucleotide identity forming 2 independent clusters. On the other hand, EACMV-KE Kenyan isolates did not reveal great genetic variability within themselves forming asingle clade with bootstrap value of 99%. When compared with sequences in the NCBI database, the Kenyan isolates were closely related to an isolate from Tanzania (AY795988.1). The study showed high cassava mosaic begomoviruses infections in Nyanza, a cause for concern for policy makers. Urgent strategies focusing on this area can be deployed to contain the viruses. In this case strategies such as phytosanitation, breeding and promotion of disease resistant genotypes should be implemented to control crop losses. This study also tested the presence of viruses in elite genotypes through multiple detection methods namely; visual observation, serological and molecular. The Cassava mosaic and Cassava brown streak diseases incidence was highest in Kibanda meno (>70%) and lowest in Shibe and Tajirika. Mean CMD/CBSD severities in the tested genotypes was highest in Kibanda meno (>1.5). Both ELISA and PCR detected CMD and CBSD in asymptomatic and symptomatic cassava samples. Genotypes 08/363 and F10-30-R2 had greater resistance to cassava mosaic and cassava brown streak disease while Kibandameno and Ex-mariakani were highly susceptible. Further tests can also be done focusing on the virus load in order to develop a correlation between symptom severity and virus load in the cassava genotypes.