Distribution and Molecular Characterization of Cassava Mosaic Geminiviruses and associated DNA Satellites in Kenya

Abstract

ABSTRACT

CMD was widely distributed in the country with an average incidence of 57.3 Cassava (Manihot esculenta Crantz) is an important food crop in Kenya. It is popular with communities in Western, Nyanza, part of Eastern and Coast provinces. It is an important source of dietary carbohydrates and cushions these communities against hunger due to its drought tolerance characteristics. However, the crop has come under severe attack by various diseases of which viral diseases have had a very devastating effect on the overall yields. An epidemic of Cassava mosaic disease (CMD) caused by Cassava mosaic geminiviruses (CMG’s) severely hindered cassava production across eastern and central Africa which led to farmers giving up on the crop especially in western Kenya.

Although quite some work has been done on the identification of plant viral diseases, not much has been done on the molecular characterization, genetic diversity and distribution in all cassava growing areas in the country. This study builds on the previous studies by determining the cassava mosaic geminiviruses infecting cassava and the associated DNA satellites in all cassava growing regions of the country.

A countrywide survey was carried out in four distinct regions which are also administrative regions namely provinces. The provinces under survey were Eastern, Nyanza, Western and Coast provinces. A total of 94 cassava fields were surveyed with 350 leaf samples of suspected CMG’s and associated DNA satellites were collected and assayed by PCR molecular techniques for detection and identification of viruses and the associated DNA satellites. Sequence diversity for CMG’s and the associated DNA satellites were determined. Whitefly counts were also done on all visited farm fields to determine the method of virus transmission % with Coast province recording the highest (73.8%) incidence. The prevalence of CMD countrywide was 84.6% with Nyanza province recording the highest (96.2%) prevalence. Sequence identity and phylogenetic analysis revealed less variability within the viral species African cassava mosaic virus (ACMV). However variability amongst isolates in the species East African cassava mosaic virus (EACMV) was more distinct. The Kenyan ACMV isolates under study were closely related to ACMV isolates from Kenya, Uganda and Namibia with sequence identities of 97%-98%. Sequence identity and phylogenetic analysis for EACMV indeed showed that the Kenyan EACMV isolates are closely related to the Ugandan isolates. Sequence analysis of the DNA satellites associated with Cassava mosaic begomoviruses showed greater variability amongst themselves and the DNA satellites from the gene bank. Most of the DNA satellite sequences determined in this study had a low similarity to the NCBI genebank sequences of begomoviruses associated DNA III satellites from Tanzania and the Mentha leaf satellite DNAII from India at only 30% sequence similarity for both.

These results have shown emergence of ACMV in coast and eastern provinces with 20% cases of dual infection between ACMV and EACMV species of CMGs. Breeding programmes for resistance or tolerance to these CMG’s need to take into considerations the possibility of inter and intra species recombination. There is need also to evaluate yield losses due to the symptom severity of cases where CMG’s and their associated DNA satellites have been identified.