Genetic diversity, evolutionary history and epigenetic analysis of East African highland bananas
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Genetic variation describes naturally occurring genetic differences among individuals of the same species and permits flexibility and survival of a population in the face of changing environmental circumstances, diseases and pests. Genomic variation develops from a combination of evolutionary influences, among them, mutation process and demographic history. Understanding in greater detail the basis of the tremendous phenotypic variability in East African Highland bananas subgroup that are apparently clonal variants of a single original seedling is essential for developing improved breeding strategies for this subgroup. While genetic diversity studies have included cultivars from this subgroup, intra- population structure and phylogenetic relationships per se are still unknown. In addition, none of these studies have attempted to study the evolutionary history and epigenetic polymorphism in this subgroup. In this thesis, I have used EAHB cultivars to assess the genetic variation, population structure and evolutionary history. I focus on the role of DNA methylation as an epigenetic mark that contributes to phenotypic diversity and determine inheritance of DNA methylation patterns in sexual and vegetative propagation models. The results show that despite being phenotypically distinct, these cultivars are strikingly genetically similar with a narrow genetic base. While DNA methylation polymorphisms are common amongst EAHB cultivars, MSAP does not detect any obvious relationship between DNA methylation variation and phenotypic variation in East African Highland bananas. This study demonstrates that the EAHB subgroup has low mutation rates, show past population expansion but may have suffered a genetic bottleneck that may have led to the low genetic diversity. Extensive linkage disequilibrium and balancing selection were observed. Finally, I discovered that EAHB cultivars and Zebrina (wild AA cultivar) underwent a speciation event 928 thousand years and their most recent common ancestor dates back 2980 thousand years ago.