Advancing RNAi-Based Strategies Against Downy Mildews: Insights Into dsRNA Uptake and Gene Silencing

Gol, Deniz ORCID: https://orcid.org/0000-0002-6527-2598, Okechukwu, Emeka Chibuzor ORCID: https://orcid.org/0000-0003-0840-4950, Unal, Gizem ORCID: https://orcid.org/0000-0001-9366-9683, Webb, A. ORCID: https://orcid.org/0000-0001-8263-1997, Wood, T. ORCID: https://orcid.org/0000-0002-4637-9955, Hong, Yiguo ORCID: https://orcid.org/0000-0002-3352-9686, Sherif, S. ORCID: https://orcid.org/0000-0002-2801-0679, Wacker, T. ORCID: https://orcid.org/0000-0002-1789-2346, Studholme, D. ORCID: https://orcid.org/0000-0002-3010-6637, McDowell, John ORCID: https://orcid.org/0000-0002-9070-4874 and Tör, M. ORCID: https://orcid.org/0000-0002-4416-5048 (2025) Advancing RNAi-Based Strategies Against Downy Mildews: Insights Into dsRNA Uptake and Gene Silencing. bioRxiv. pp. 1-46. ISSN 2692-8205

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Abstract

Downy mildew (DMs) dieases are caused by destructive obligate pathogens with limited control options, posing a significant threat to global agriculture. RNA interference (RNAi) has emerged as a promising, environmentally sustainable strategy for disease management. In this study, we evaluated the efficacy of dsRNA-mediated RNAi in suppressing key biological functions in DM pathogens of Arabidopsis thaliana, pea and lettuce DM pathogens, Hyaloperonospora arabidopsidis (Hpa), Peronospora viciae f. sp. pisi (Pvp) and Bremia lactucae (Bl), respectively. We specifically targeted the cellulose synthase 3 (CesA3) and the beta tubulin (BTUB) genes. Silencing CesA3 impaired spore germination and infection across multiple species, while BTUB silencing reinforced the potential of dsRNA-mediated inhibition. Reduction in gene expression levels correlated well with the sporulation assays confirming the effectiveness of dsRNA-mediated gene silencing. We used dsRNAs that were chemically synthesized, in vitro transcribed (IVT) or produced in E. coli. We found that the length and concentration of these dsRNAs significantly affected uptake efficiency, spore germination, and sporulation, with higher concentrations enhancing inhibitory effects. Confocal microscopy using Cy-5-labelled short-synthesized dsRNA (SS-dsRNA) provided direct evidence of spore uptake, confirming the potential of SS-dsRNA for pathogen control. However, species-specific sequence variations influenced dsRNA efficacy, underscoring the importance of target sequence design. Multiplexed RNAi impacted silencing synergisticly, further reducing germination and sporulation in Hpa. Additionally, we demonstrated that SS-dsRNA-mediated gene silencing is sustained over time, with a significant reduction in gene expression level at 4, 7, 10 and 11dpi. This indicates the durability and efficacy of this approach. Taken together, these findings demonstrate the potential of dsRNA-mediated gene silencing as a precision tool for managing DM pathogens.

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