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

Abstract

BackgroundRecently, 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.ResultFour 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‐seq 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, i.e. W1999C, W2027S/S and I2041N, were found in all resistant lines in either ACCase1A, ACCase1B or ACCase2C.ConclusionIn 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.This article is protected by copyright. All rights reserved.

Differential Resistance to Acetyl-CoA Carboxylase Inhibitors in Rice: Insights from Two Distinct Target-Site Mutations

“…However, the application of APP herbicide fenoxaprop- P -ethyl in rice fields is constrained by its marginal safety profiles and a heightened risk of pesticide damage. Moreover, several pernicious weed species prevalent in paddy fields, such as Leptochloa spp., Echinochloa spp., and Digitaria spp., have exhibited resistance to commonly used ACCase-inhibiting herbicides, including cyhalofop-butyl and metamifop. − Therefore, the development of rice varieties or germplasm resistant to ACCase inhibitor herbicides is crucial, not only to expand the repertoire of herbicides usable in rice fields but also to effectively mitigate the prevalence and impact of weeds. To obtain herbicide-resistant rice, three primary methodologies are employed: mutant screening, transgenesis, and gene editing. − Both chemical mutagenesis, tissue culture-mediated mutant screening, and gene editing technologies have been instrumental in the development of rice varieties resistant to ACCase inhibitors. − …”