Learning from fungicide resistance: Evolutionary insights to guide RNAi-based control of fungal crop pathogens
Abstract
Crop protection against fungal pathogens is essential to prevent crop losses and maintain food security. Current crop protection relies heavily on chemical fungicides. However, rapid evolution of fungicide resistance, the constant appearance of new pathogens, and legislation against chemical pesticides due to concerns regarding their impact on human health and the environment, mean new crop protection strategies are urgently required. One elegant solution is double-stranded RNA-based crop protection, which aims to silence selected genes in the pathogen to reduce crop damage. This technology brings the promise of targeting specific genes, which could be chosen to maximise protection, minimize off-target effects and reduce the risk of resistance evolution. Here we discuss strategies for successful use of this novel technology based on lessons learned from fungicide resistance and recent discoveries in fungal evolution derived from genome-sequencing.
What the paper shows and why it matters
(AI-generated)
Control of fungal crop diseases relies mainly on chemical fungicides. Resistance has repeatedly undermined these products, and some have been banned, so new methods are needed. One candidate is double-stranded RNA (dsRNA) sprayed onto crops. It is built to match, and so switch off, chosen genes of the pathogen (RNA interference, RNAi). Proponents expect high specificity, a short life in the environment and a lower risk of resistance, which is a reasonable hope. But any treatment that lowers a pathogen’s fitness favours less susceptible variants, and it has not been worked out how lessons from fungicide resistance and knowledge of fungal genomes should guide the choice of targets and the use of this technology.
The paper argues that sprayed double-stranded RNA against fungal crop pathogens needs to be designed with pathogen evolution in mind to stay effective, because high specificity does not by itself protect against resistance. Fungicide history shows the trade-off: products acting on many sites carry a lower risk of resistance but a higher risk of harming non-target organisms, whereas precise single-site products are vulnerable to resistance through small genetic changes. Silencing essential genes gives strong control but also strong selection. The paper therefore recommends targets that balance safety for non-target organisms against resistance risk. It suggests, as possible routes, several dsRNAs aimed at genes far apart in the genome, or genes involved in causing disease rather than in survival, though each has drawbacks. Adaptation can also proceed by routes beyond point mutations, such as mobile DNA, gene duplication and gene loss. RNAi adds its own risks: mutations that weaken the match to the target and, most seriously, loss of dsRNA uptake or of the RNAi machinery. Some fungi already take up little or no dsRNA or have lost RNAi.
The argument means that durability has to be planned from the start rather than repaired after resistance appears. The paper places dsRNA within integrated pest management. It lists what is missing: laboratory selection experiments, knowledge of how much sequence mismatch RNAi tolerates and why some fungi do not take up dsRNA, and, in Europe, a regulatory framework that includes resistance monitoring. It concludes that, with focused research, careful implementation and open communication, RNAi can become a valuable addition to integrated crop protection.