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Title: Population analysis of the finger millet blast pathogen Magnaporthe oryzae in Eastern Africa
Author: Shittu, Taiwo Adewale
ISNI:       0000 0004 7967 8833
Awarding Body: University of Bedfordshire
Current Institution: University of Bedfordshire
Date of Award: 2018
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The main aims of the investigation were to develop an in-depth understanding of the genetic diversity, population structure and evolutionary relationships as well as to assess the sexual reproductive capability of the finger millet blast (FMB) pathogen Magnaporthe oryzae in Eastern Africa. A set of 300 M. oryzae isolates collected during 2000 - 2017 from key finger millet growing districts in Kenya, Uganda, Tanzania and Ethiopia were utilised in this study. Two novel molecular markers designated HyP1 and HyP2 were developed in this study and two known phylogenetic markers ITS (internal transcribed spacer) and HIS4 (histone 4 gene) were identified by bioinformatic analysis. Single- and multi-locus analysis provided a clear assessment of the FMB pathogen genotype diversity and distribution pattern. At the regional level in Eastern Africa, ITS and HIS4 revealed 7 - 9 genotypes, whereas HyP1 and HyP2 identified 80 - 85 genotypes reflecting their high resolution. Multi-locus sequence (MLS) analysis revealed 207 genotypes displaying a continuous genetic variation pattern of the FMB pathogen populations in Eastern Africa. Bayesian and reticulate network analyses distinguished the vast majority of genotypes into two sub-populations (designated as Group A and B), which were geographically clustered. Diagnostic PCR revealed the presence of a high proportion of M. oryzae isolates containing the Grasshopper (grh) repeat element in Ethiopia and Tanzania (e.g. 85 %). Reference genome assemblies have been established for two M. oryzae isolates representing the sub-populations identified. Genome resequence data has been developed for sixteen isolates representing the genotype diversity. Comparative analysis provided novel insights into the genomic architecture and evolutionary relationships in the FMB pathogen. Genomic regions and/or genes, putatively isolate specific have been identified. Phylogenomic analysis revealed monophyletic nature of the FMB pathogen in Eastern Africa and Asia suggesting a common origin. Genome-wide single nucleotide polymorphism (SNPs) ranges broadly corresponded to the sub-populations identified. Complete grh sequence has been defined and the presence of at least two versions of the element in the FMB pathogen in Eastern Africa has been shown. Mating type specific PCR assay revealed high proportions of the two mating types MAT 1-1 (56 %) and MAT 1-2 (44 %) in the contemporary population of the FMB pathogen in Eastern Africa and also in the four countries surveyed, albeit at variable levels. Mating culture assays established a high proportion of fertile isolates (60 %) and revealed the dominance of male sexual behaviour followed by hermaphrodite and female isolates. The emerging pattern is indicative of a decrease in the fertility status as well as the level of hermaphrodites and females. Integrated assessment of the mating type and fertility data along with the high genotype diversity and their continuous variation pattern observed is strongly suggestive of a mixed reproductive behaviour including episodic sexual reproduction. The new knowledge and resources generated contribute to the advancement of current understanding of the finger millet blast pathogen biology providing a framework for the effective utilization of host resistance in Eastern Africa as well as a strong platform for further research advances in the field.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: Magnaporthe oryzae ; finger millet ; blast pathogen ; population analysis ; reproductive biology ; genetics ; genomics ; B132 Pathobiology