Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring

Abstract

Background Development and application of DNA-based methods to distinguish highly virulent isolates of Fusarium oxysporum f. sp. koae [Fo koae; cause of koa wilt disease on Acacia koa (koa)] will help disease management through early detection, enhanced monitoring, and improved disease resistance-breeding programs. Results This study presents whole genome analyses of one highly virulent Fo koae isolate and one non-pathogenic F. oxysporum (Fo) isolate. These analyses allowed for the identification of putative lineage-specific DNA and predicted genes necessary for disease development on koa. Using putative chromosomes and predicted gene comparisons, Fo koae-exclusive, virulence genes were identified. The putative lineage-specific DNA included identified genes encoding products secreted in xylem (e. g., SIX1 and SIX6) that may be necessary for disease development on koa. Unique genes from Fo koae were used to develop pathogen-specific PCR primers. These diagnostic primers allowed target amplification in the characterized highly virulent Fo koae isolates but did not allow product amplification in low-virulence or non-pathogenic isolates of Fo. Thus, primers developed in this study will be useful for early detection and monitoring of highly virulent strains of Fo koae. Isolate verification is also important for disease resistance-breeding programs that require a diverse set of highly virulent Fo koae isolates for their disease-screening assays to develop disease-resistant koa. Conclusions These results provide the framework for understanding the pathogen genes necessary for koa wilt disease and the genetic variation of Fo koae populations across the Hawaiian Islands.

Fusarium spp. diversity associated with symptomatic Acacia koa in Hawaiʽi

“…High‐resolution genetic markers could monitor/assess pathogen spread more precisely at the species/sub‐species level, and pathogenicity tests on koa are needed to establish pathogenicity of the untested Fusarium spp. Genetic tools are valuable for identifying pathogenic strains of Fusarium and reducing the need for lengthy greenhouse virulence trials (Dobbs et al 2020). Development of tools to identify diverse pathogenic genotypes of Fusarium would greatly aid breeding programmes in the development of robust, disease‐resistant koa and improve forest health by reintroducing koa to regions under potentially high disease conditions.…”

“…Isolates for this study were provided by the Hawaiʽi Agriculture Research Center (HARC) from five islands (Kauai, Oahu, Maui, Lanai, and Hawaiʽi) and also included collections from a survey conducted in 2018 by Colorado State University on symptomatic koa roots from three islands, Kauai, Oahu and Hawaiʽi (Dobbs et al 2020). Isolates were grown on ¼‐strength Potato Dextrose Agar (PDA) in Petri dishes in the dark for 7 days before they were putatively identified as Fusarium species based on colony morphology (Nelson et al, 1983).…”

“…(Rozas et al, 2017). A statistical parsimony (TCS) haplotype network was constructed based on the tef1 sequence data using PopART with a 95% genetic cut‐off, similar to that used in Dobbs et al (2020).…”

“…oxysporum strains have been identified on all islands where koa is grown and planted (Dobbs et al. 2020). Possible inter‐ and intra‐island introductions of pathogenic Fo koae may be responsible for the increased genetic variation observed among Fo koae strains, and increased genetic variation may exacerbate disease damage, especially within tree populations that lack natural resistance to new Fo koae strains.…”

The identification and pathogenicity of Fusarium oxysporum causing acacia seedling wilt disease

“…koae, f. sp. nov. (Gardner 1980;Dobbs et al 2020). Furthermore, F. oxysporum was reported to have attacked A. nilotica (L.) P. J. H. Hurter & McNabb seedlings in the greenhouse of the Forest Research Institute, India (Kapoor et al 2004).…”