DNA-based detection of grapevine trunk-disease from environmental spore samples

Authors: Fujiyoshi, Phillip; LAWRENCE, DANIEL - University Of California, Davis; TRAVADON, RENAUD - University Of California, Davis; Baumgartner, Kendra

Submitted to: MethodsX
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/18/2021
Publication Date: 8/20/2021
Citation: Fujiyoshi, P.T., Lawrence, D.P., Travadon, R., Baumgartner, K. 2021. DNA-based detection of grapevine trunk-disease from environmental spore samples. MethodsX. 8. Article 101494. https://doi.org/10.1016/j.mex.2021.101494.
DOI: https://doi.org/10.1016/j.mex.2021.101494

Interpretive Summary: In California vineyards, spore dispersal of fungi that cause grapevine trunk diseases Botryosphaeria dieback and Eutypa dieback occurs with winter rains. Spores infect through cuts in the wood made when the vines are pruned in winter. Better timing of practices that prevent infection may benefit from trapping the fungal spores in the vineyard, which could pinpoint site-specific time frames of disease spread. To speed pathogen detection from spore traps, we identified species-specific molecular markers (i.e., PCR primers) and protocols. Then we compared the traditional culture-based method versus our new DNA-based method. PCR primers for Botryosphaeria-dieback pathogen Neofusicoccum parvum and Eutypa-dieback pathogen Eutypa lata were confirmed species-specific, through extensive testing of related species (in families Botryosphaeriaceae and Diatrypaceae, respectively), other trunk diseases, and saprophytic fungi that sporulate in vineyards. Consistent detection of N. parvum was achieved from spore suspensions used fresh or stored at -20°C, whereas consistent detection of E. lata was achieved only with a new spore-lysis method, using zirconia/silica beads in a FastPrep homogenizer (MP Biomedicals; Solon, Ohio, USA), and only from spore suspensions used fresh. Freezing E. lata spores at -20°C made detection inconsistent. From environmental samples, spores of E. lata were detected only via PCR, whereas spores of N. parvum were detected both via PCR and in culture.

Technical Abstract: In California vineyards, spore dispersal of fungi that cause grapevine trunk diseases Botryosphaeria dieback and Eutypa dieback occurs with winter rains. Spores infect through pruning wounds made to the woody structure of the vine in winter. Better timing of preventative practices that minimize infection may benefit from routine spore-trapping, which could pinpoint site-specific time frames of spore dispersal. To speed pathogen detection from environmental spore samples, we identified species-specific PCR primers and protocols. Then we compared the traditional culture-based method versus our new DNA-based method. PCR primers for Botryosphaeria-dieback pathogen Neofusicoccum parvum and Eutypa-dieback pathogen Eutypa lata were confirmed species-specific, through extensive testing of related species (in families Botryosphaeriaceae and Diatrypaceae, respectively), other trunk diseases, and saprophytic fungi that sporulate in vineyards. Consistent detection of N. parvum was achieved from spore suspensions used fresh or stored at -20°C, whereas consistent detection of E. lata was achieved only with a new spore-lysis method, using zirconia/silica beads in a FastPrep homogenizer (MP Biomedicals; Solon, Ohio, USA), and only from spore suspensions used fresh. Freezing E. lata spores at -20°C made detection inconsistent. From environmental samples, spores of E. lata were detected only via PCR, whereas spores of N. parvum were detected both via PCR and in culture.