Resistance to ACCase-inhibiting herbicides conferred by the Ile-1781-Val mutation in Leptochloa fusca and visual detection of target mutations by RAA-CRISPR/Cas12a.

Background: Leptochloa fusca is a new dominant grass weed in paddy ecosystem of local region in China. The extensive herbicide application has selected the cyhalofop-butyl-resistant L. fusca populations. Here, we aimed to (i) characterize the target-site resistance mechanisms to ACCase inhibitors, and (ii) establish an efficient and rapid method for detecting mutations.

Results: The L. fusca population (SFC-R) was resistant to cyhalofop-butyl (RF = 5.4), metamifop (RF = 5.5), and fenoxaprop-P-ethyl (RF = 6.8). Gene sequencing revealed that the Ile-1781-Val mutation was the molecular basis of resistance. A recombinase-aided amplification (RAA) combined with CRISPR/Cas12a method was successfully developed, which could rapidly and visually detect the single nucleotide variation underling the Ile-1781-Val substitution in L. fusca.

Conclusion: This study confirmed that target-site mutation (Ile-1781-Val) endowed resistance to ACCase inhibitors in L. fusca, and represented the first report of applying the RAA-CRISPR/Cas12a assay for mutation detection in resistant weeds. Considering its simplicity and specificity, this technique may be used in monitoring and early warning of resistant weeds. © 2025 Society of Chemical Industry.