Identification of effector genes for the spinach Fusarium wilt pathogen, Fusarium oxysporum f. ap. spinaciae

Alexander M. Batson

The maritime Pacific Northwest is the only region in the United States that is suitable for spinach seed production, where mild and dry summers with long day length are necessary for high yields of quality seed. Spinach Fusarium wilt caused by Fusarium oxysporum f. sp. spinaciae is the greatest biotic limitation to spinach seed production in this region. Management strategies for Fusarium wilt in spinach seed crops in this region are limited as they only partially or transiently suppress the pathogen. Little is known about what defines the causal agent of spinach Fusarium wilt as a pathogen of spinach genetically. However, host-specificity of other F. oxysporum ff. spp. is associated with unique combinations of effector genes, which are important for pathogenicity. In this study, Fusarium isolates were characterized phenotypically for pathogenicity to spinach and genotypically for a group of putative pathogenicity genes known as the Secreted in Xylem (SIX) genes. Thirty-nine isolates of F. oxysporum f. sp. spinaciae were identified and characterized into two pathogenicity groups based on wilt severity observed on three proprietary inbred spinach parent lines with differing levels of resistance to Fusarium wilt. SIX8 and/or SIX14 were detected in all F. oxysporum f. sp. spinaciae isolates identified; however, the profile of SIX genes did not differentiate F. oxysporum f. sp. spinaciae from other F. oxysporum isolates that did not cause wilt of spinach. Illumina and PacBio platforms were used to sequence the genomes of seven F. oxysporum f. sp. spinaciae isolates and five spinach associated F. oxysporum isolates. Effector genes were predicted from the genome assemblies with a previously described software pipeline, which differentiated F. oxysporum f. sp. spinaciae isolates from non-pathogens of spinach. Furthermore, the two pathogenicity groups of F. oxysporum f. sp. spinaciae were differentiated based on predicted effector gene profiles. Further characterization of the predicted effector genes and other regions of the genome of F. oxysporum f. sp. spinaciae will aid in understanding mechanisms of pathogenicity, developing molecular tools for rapid detection and quantification of this pathogen, and breeding spinach cultivars and parent lines with increased resistance to Fusarium wilt.

Identification of effector genes for the spinach Fusarium wilt pathogen, Fusarium oxysporum f. ap. spinaciae

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