UC Davis

Fusarium oxysporum is a fungal pathogen responsible for wilt and root rot diseases in over 100plant species. An estimated 30% of yield losses are attributed to F. oxysporum in Ethiopian chickpea cultivation. As a result, breeding resistant chickpea varieties has become a key strategy in disease management. Historically, germplasm, perceived as resistant, has succumbed to Fusarium wilt when deployed across Ethiopia. This dissertation explores the genetic diversity of F. oxysporum in Ethiopia and investigates the mechanisms driving this diversity.

The dissertation begins by examining the role of bioinformatic methods in delineating clonalgroups. Two pipelines are evaluated for their effectiveness to successively delineate clonal groups across four different evolutionary models. Leveraging the 320-isolate genome sequencing effort, we assess the clonal diversity of F. oxysporum within Ethiopia and genomes deposited on NCBI. Subsequently, we study the nucleotide diversity and population genetics of this population. Despite a genetically narrow population, there is substantial genotypic diversity driving both the core and dispensable genomic compartments. Our findings suggest that meiotically-driven recombination is critical in structuring the foundational F. oxysporum population followed by multiple clonal outbreaks. In the final chapter, we investigate the role of structural variation and pangenomic variation in shaping genomic diversity. We identify a large pangenome, driven primarily by accessory chromosomes and large insertions near chromosomal ends. Multiple mechanisms appear to drive a highly compartmentalized, but highly dynamic, pangenome.

Overall, this research provides new insights into the biology and ecology of F. oxysporum inEthiopia. We hope that these findings will lead to practical solutions that improve disease management and strengthen breeding efforts against F. oxysporum.