Functional dissection of NPR3 by genome editing highlights its role in grapevine defense and root symbiosis

Abstract

New Plant Breeding Techniques (NPBTs), and particularly genome editing, represent a powerful avenue to enhance disease resilience in perennial crops. However, their practical implementation in grapevine remains constrained by the species’ complex biology, recalcitrance to transformation, and long breeding cycles. In this study, we explored the potential of targeted genome editing of key susceptibility and regulatory genes to reinforce disease resistance while preserving beneficial plant–microbe interactions. Simultaneous disruption of the mildew susceptibility genes VvMLO6 and VvMLO7 resulted in a marked reduction of powdery mildew incidence, reaching approximately 80% compared with wild-type plants under controlled infection conditions. In parallel, editing of the salicylic acid signaling regulator VvNPR3 led to a substantial decrease in disease severity (up to 70%) and conferred enhanced tolerance to the oomycete pathogen Plasmopara viticola. These resistance phenotypes were associated with pronounced metabolic adjustments, including increased accumulation of stilbenes such as resveratrol and piceid, suggesting a broader reprogramming of defense-related pathways and secondary metabolism. Beyond pathogen resistance, we investigated whether NPR3 also plays a role in modulating interactions with beneficial microorganisms in the root environment. Notably, roots of NPR3-edited lines displayed significantly increased colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis, characterized by a higher abundance of functional arbuscules and a more developed intraradical mycelium. Integrated transcriptomic and metabolomic profiling revealed extensive remodeling of defense signaling networks, cell wall dynamics, and specialized metabolism, collectively contributing to a more permissive root environment for symbiosis establishment.

Consistently, strong induction of the mycorrhizal marker VvPT4, together with the activation of fungal genes involved in nutrient exchange processes, confirmed the establishment of a more efficient symbiotic interface. Overall, our findings identify NPR3 as a central regulatory hub coordinating immune responses and symbiotic compatibility in grapevine, providing a conceptual framework for genome editing strategies that simultaneously enhance disease resistance and beneficial microbial partnerships in this economically and culturally important perennial crop.