Chickpeas (Cicer arietinum) act as an important source of nutrition in many developing countries. In recent years, the productivity of the chickpea crop has been negatively impacted by Fusarium oxysporum f. sp. ciceri. To address this problem, efforts have been made to find resistance genes present in chickpea germplasm to combat this disease. This project is focused on improving genomic resources in chickpea with the goal of identifying a resistance gene that was predicted previously in a quantitative trait locus (QTL) study. Three cultivated accessions were sequenced and analyzed for structural and genetic differences and an assay was designed for fine mapping the QTL region conferring disease resistance. The sequencing resulted in improvement of the reference genome and expansion of chickpea genomic resources. The assay design will be applied in further research in an attempt to identify the causal gene for Fusarium wilt resistance which can be applied to breeding efforts to deploy more resistant cultivars.

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.

Nitrogen fixation efficiency is a desired trait in agriculture. Here we study nitrogen fixation traits in chickpea (Cicer arietium), which has special relevance given the crop’s predominance as an important source of protein and nutrition in the developing world. This study seeks to understand the relevance of genetic and transcriptional diversity of both the crop (C. arietinum), its two wild relatives C. reticulatum and C. echinospermum, and their cognate symbiotic microbes Mesorhizobium mediterraneum and M. ciceri. The experiments test the hypothesis that local adaptation is an ecological mechanism operating in wild systems to optimize biological nitrogen fixation, by quantifying biomass gain and nodulation phenotypes in a network of naturally-occurring host and bacterial genotype combinations. Plant biomass gain was greater for native (homologous) compared to non-native (heterologous) plant-bacteria combinations, leading to the conclusion that nitrogen fixation per se is more effective in co-evolved plant-microbe pairs, providing strong evidence of local adaptation in natural systems. C. echinospermun has effective symbiosis with its native, homologous symbiont M. ciceri and it is incompatible (nod-) with the heterologous symbiont M. mediterraneum. Conversely, C. reticulatum has more effective symbiosis with its native, homologous symbiont M. mediterraneum compared to heterologous M. ciceri. Interestingly, C. reticulatum has similar nodulation phenotypes with both bacterial species, and thus increased biomass gain in the homologous interaction is interpreted as greater efficiency of nitrogen fixation. The analysis of recombinant inbred lines derived from C. echinospermum X C. arietinum inoculated with either M. mediterraneum or M. ciceri document genetic segregation of symbiotic specificity, providing the basis for molecular genetic studies. Transcriptional profiling analysis of compatible and incompatible symbiotic pairs revealed responses to nitrogen (symbiotic and inorganic) that are both common and different among plant species. In particular, enhanced transcription of genes related to carbon metabolism and plastid-related functions is characteristic of M. ciceri nodules, while interaction with M. mediterraneum is associated with upregulation a diversity of processes, including nitrogen related gene expression, but largely exclusive of carbon metabolism. Whole genome analyses were used to characterize bacterial strains associated with chickpea cultivation in Pakistan and strains from the wild’s center of origin in South-Eastern Turkey. The analysis focused, in particular, on the provenance of genes involved in Type III secretion and Nod factor synthesis, informing us about the evolution of bacterial symbiosis in chickpea and bacterial loci relevant in the host-microbe interaction. The understanding gained from these studies informs fundamental questions about Cicer-Mesorhizobium co-evolution, and also has two broad practical implications: (1) for breeding of modern cultivars with improved biological nitrogen fixation, and (2) for developing improved microbial inoculants.

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