Choosing the Molecular Substrate: DNA-versus-RNA Target Selection Logic in CRISPR-Based Plant Pathology

In CRISPR-based plant pathology, the choice of molecular substrate (DNA versus RNA) determines the framework of biological inference before any technical decision is made. This narrative review argues that the central question should not be "which editing system is more suitable," but rather "which substrate aligns with the temporal horizon, host-pathogen interaction dynamics, and the type of biological claim under consideration." DNA targeting, by creating stable genomic changes, enables durable reprogramming, long-term causal fixation, and phenotypic evaluation across developmental, environmental, and transgenerational scales. This substrate is ideal for validating susceptibility genes, engineering durable resistance, and understanding structural roles in defense networks, although it carries risks of pleiotropic, compensatory, and delayed effects. In contrast, RNA targeting, through time-restricted and reversible intervention, enables precise interrogation of stage-dependent roles, early responses, and transient dynamics while minimizing developmental noise-making it particularly effective for investigating rapid defense processes and context-dependent interactions. By presenting a conceptual framework, comparative tables, and schematic models, this article demonstrates that misalignment between the chosen substrate and the nature of the biological question is a source of many apparent contradictions in the literature. Substrate choice is not a downstream technical decision but an upstream epistemological variable that shapes the type of evidence, interpretive clarity, phenotypic attribution validity, and the scope of scientific claims. In gray zones, a combinatorial or staged logic (RNA for initial interrogation and DNA for final fixation) is proposed. This approach elevates study design from tool-centric logic to inference-centric architecture and introduces the language of substrate-aware design. The article's primary contribution is providing practical conceptual guidance for informed substrate selection that enhances reproducibility, interpretive validity, and alignment between biological questions and molecular interventions. This framework can contribute to standardizing reporting and designing more effective research in plant disease management using CRISPR technology.

کلیدواژه ها:

CRISPR-Cas systems ، DNA targeting ، RNA targeting ، molecular substrate selection ، substrate-aware design ، biological inference ، host-pathogen dynamics ، durable resistance ، transient gene silencing ، genome editing in plants ، phenotypic attribution ، interpretive resolution ، staged intervention logic