Xanthomonas campestris pv. musacearum : population diversity and the identification of potential sources of resistance from banana accessions representing the Musa diversity worldwide

Abstract

Banana, plantain and enset are economically important crops worldwide, contributing to income and food security. Production of Musa spp. and enset is constrained by several pests and diseases, including Xanthomonas wilt (XW), caused by the bacterium Xanthomonas campestris pv. musacearum (Xcm). The pathogen is transmitted through infected planting materials, contaminated tools and insects visiting the inflorescence. Significant disease management measures include malebud removal to reduce insect transmitted infections, decontaminating farm tools, and using disease-free planting material. As Xcm infects both banana and enset, understanding relationships between the bacterial genotype and the plant host species is important as it might reveal genetic factors that drive host specialization, thus guiding the management options. A clear understanding of the genetic variation existing within and between the Xcm population is essential for tracking the movement of the pathogen through time and space and uncover routes of geographical spread, as well as rate of evolution (emergence of new strains) and patterns of adaptation. Correct identification and differentiation of pathogenic strains and closely related species is essential for development and dissemination of suitable and sustainable disease control measures. Although numerous studies have been performed on the pathogenicity of Xcm on banana and enset, information gaps still exist. No detailed studies have been conducted to understand the population structure or determine the genetic differences among Xcm strains from different countries. Similarly, no study has been conducted to understand why there is differential varietal response among Musa spp. and enset to Xcm. Previous studies to understand the population genetics of Xcm were conducted on a limited (small) number of strains. An analysis of a larger pathogen population could potentially reveal whether or not there is differentiation structured by host specificity or preference, as well as potential routes of pathogen spread from the point of origin and emergence of new strains. Chapter 1 of this thesis reviews literature on the importance of banana and enset, constraints to production with a focus on Xanthomonas campestris pv. musacearum (Xcm), Xcm taxonomy, pathology and pathogenesis, ecology, epidemiology and management options. This review further focuses on pathogenicity and virulence factors present in Xcm, molecular techniques that have been used to explore diversity and concludes by focusing on future prospects, including the need for more comprehensive studies to understand genetic variation using more discriminative molecular and epidemiological tools to better understand patterns of dissemination and adaptation. SNP-based molecular markers have been developed for phylogeographic studies of epidemiology and spread of Xcm. Chapter Two sought to understand levels of genetic diversity within Xcm using SNP-based molecular markers previously developed by Wasukira et al. (2012) in a large Xcm population collected from several East Africa countries. Restriction fragment length polymorphism (RFLP) of fragments derived from single nucleotide polymorphisms (SNP) based markers were used to validate Xcm diversity based on studies previously described by Wasukira et al. (2012). Chapter Three describes the development of new genotyping markers based on multiplelocus variable number of tandem repeat analysis (MLVA) and their use to genotype a collection of Xcm strains. The aim was to produce a highly discriminatory identification scheme suitable for distinguishing between closely related Xcm strains, and to update the knowledge about diversity and structure of African Xcm populations. Chapter Four focused on evaluating banana varieties constituting the entire IITA collection for response to Xcm and identification of potential sources of resistance. Banana varieties representing the major groups within the IITA collection were screened for response to a known virulent Xcm strain to identify potential sources of resistance. Cluster analysis was used to test the hypothesis of whether resistance to Xcm is clustered, that is, restricted to certain areas and banana varieties or is random. This information will be used to identify banana varieties to target for further screening and use in breeding programs. Chapter Five summarises the conclusions and prospects from the different chapters.