Genomic Diversity of Chickpea Wilt Pathogen (Fusarium oxysporium f.sp ciceris) in Ethiopia

Fusarium wilt caused by Fusarium oxysporum f. sp. ciceris (Foc) is the most serious disease of chickpea throughout the world, causing 100% loss under conditions favorable to the pathogen. Foc is both soil and seed borne and difficult to eradicate from infested fields because fungal chlamydospores survive in soils for many years even in the absence of the host plant. Variation in pathogen populations has been previously inferred based on differential host responses, but such inferences are indirect. To better understand geographic patterns of pathogen virulence and genomic variation of Foc in Ethiopia, a GPS-based survey was conducted in the 2014 and 2015 cropping season. Fusaria were isolated from symptomatic plants in a total of 373 fields, representing 6 regions that encompass 90 major chickpea growing districts. Pure strains were derived from single spore isolation and purified strains were assessed for virulence on susceptible chickpea genotypes. A phenol chloroform extraction protocol was preferred to commercial DNA extraction kits as a means to derive DNA of suitable quality for construction of genome sequencing libraries. We present results of phylogenetic and genomic analyses for an initial set of strains. Based on a combination of pathogen virulence, host specificity, genomic variation and the agro- ecology of collection sites, we will select a subset of Fusarium isolates to begin systematic testing of wild introgression populations and popular elite genotypes of chickpea, with the eventual goal of breeding for resistance to the diversity of Foc present in Ethiopia.