Syntenic analysis of ACCase loci and target‐site‐resistance mutations in cyhalofop‐butyl resistant Echinochloa crus‐galli var. crus‐galli in Japan.

BACKGROUND: Recently, suspected cyhalofop‐butyl‐resistant populations of allohexaploid weed Echinochloa crus‐galli var. crus‐galli were discovered in rice fields in Aichi Prefecture, Japan. Analyzing the target‐site ACCase genes of cyhalofop‐butyl helps understand the resistance mechanism. However, in E. crus‐galli, the presence of multiple ACCase genes and the lack of detailed gene investigations have complicated the analysis of target‐site genes. Therefore, in this study, we characterized the herbicide response of E. crus‐galli lines and thoroughly characterized the ACCase genes, including the evaluation of gene mutations in the ACCase genes of each line. RESULT: Four suspected resistant lines collected from Aichi Prefecture showed varying degrees of resistance to cyhalofop‐butyl and other FOP‐class ACCase inhibitors but were sensitive to herbicides with other modes of action. Through genomic analysis, six ACCase loci were identified in the E. crus‐galli genome. We renamed each gene based on its syntenic relationship with other ACCase genes in the Poaceae species. RNA‐sequencing analysis revealed that all ACCase genes, except the pseudogenized copy ACCase2A, were transcribed at a similar level in the shoots of E. crus‐galli. Mutations known to confer resistance to FOP‐class herbicides, that is W1999C, W2027C/S and I2041N, were found in all resistant lines in either ACCase1A, ACCase1B or ACCase2C. CONCLUSION: In this study, we found that the E. crus‐galli lines were resistant exclusively to ACCase‐inhibiting herbicides, with a target‐site resistance mutation in the ACCase gene. Characterization of ACCase loci in E. crus‐galli provides a basis for further research on ACCase herbicide resistance in Echinochloa spp. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]