Phenotypic and Genotypic Diversity of Xanthomonas axonopodis pv. manihotis Causing Cassava Bacterial Blight Disease in Kenya

Abstract

Cassava bacterial blight (CBB), caused by Xanthomonas axonopodis pv. manihotis (Xam) is a vascular disease that can cause up to 100% yield losses in cassava growing regions in Kenya. There is no information available on the phenotypic and genetic variability of Xam isolates from Kenya. The objective of the present study was to determine the diversity of Xam isolates from different cassava growing regions of Kenya using phenotypic characteristics and DNA polymerase chain reaction-based fingerprinting (rep-PCR) using repetitive extragenic palindromic (rep) primers. Thirty three leaf samples showing symptoms of cassava bacterial blight disease were collected from major cassava growing regions in Kenya. Xam was isolated from the leaf samples and subjected to morphological and molecular characterization. A total of 26 bacterial isolates which produced mucoidal colonies on semi-selective media were obtained from 33 samples collected from farmer’s fields. All the 26 bacterial isolates produced mucoidal colonies on YPGA-CC selective media. Biochemical tests of the 26 bacterial isolates indicated that all the isolates produced Gram-negative mucoidal thread-like rods in 3% potassium hydroxide (KOH). A dendrogram generated from analysis of phenotypic characteristics of the isolates produced two major clusters at 75% similarity level. Analysis of 19 isolates with repetitive extragenic palindromic (rep) PCR yielded characteristic fingerprint pattern with bands ranging between 400 and 2000 bp in size and their numbers ranged from 1 to 6 bands per isolate. Cluster analysis using unweighted pair group method with arithmetic averages (UPGMA) did not reveal any significant differences in clustering and relationship to the geographical origin, with exception of a single isolate that had unique fingerprints. These findings indicate that Xam population in Kenya evolved from the same origin and is a uniform population, and this may prove useful in future breeding programmes. The high genetic homogeneity indicates that development and use of resistant varieties will effectively control the disease.