Evolution of ACCase‐inhibitor resistance in Chloris virgata is conferred by a Trp2027Cys mutation in the herbicide target site

• Published in: Pest management science 2023-12, Vol.79 (12), p.5220-5229
• Main Authors: Ferreira, Luiz Augusto Inojosa, Oliveira, Rubem Silvério, Constantin, Jamil, Brunharo, Caio
• Format: Article
• Language: English
• Subjects: Amino acid substitution; Amino acids; Biological evolution; Chemical pest control; Chloris virgata; Copy number; Crop production; Evolutionary genetics; Gene expression; Genetic resources; genome annotation; Genomes; genomics; Genotyping; Glyphosate; Grasses; Herbicide resistance; Herbicides; Inhibitors; molecular marker; Mutation; Pest control; Pest resistance; Phenotypes; Populations; Soybeans; Substitutes; target‐site mutation; transcriptome; Tropical environment; Tropical environments; Tryptophan
• ISSN: 1526-498X; 1526-4998
• DOI: 10.1002/ps.7723

BACKGROUND Chloris virgata is a troublesome weed in tropical regions. With the evolution of glyphosate resistance in key grass species, acetyl CoA carboxylase (ACCase) inhibitors have become a commonly used tool in soybean production areas in Brazil. We assessed if suspected resistant populations exhibited cross resistance to the different classes of ACCase inhibitors and investigated the resistance mechanisms in C. virgata. RESULTS Dose–response experiments revealed resistance to haloxyfop‐methyl and pinoxaden, with 432‐ and 3‐fold resistance, respectively, compared to susceptible populations. Due to the lack of genetic resources for C. virgata, we sequenced, assembled, and annotated the genome using short‐read Illumina technology. The k‐mer analysis estimated a genome size of approximately 336 Mbp, with BUSCO completeness of 97%, and over 36 000 gene models were annotated. We examined if ACCase copy number variation and increased gene expression were involved in the resistance phenotype and found no difference when compared to a susceptible population. A mutation was detected in ACCase that encodes for amino acid position 2027, resulting in a tryptophan‐to‐cysteine (Trp2027Cys) substitution. We found the resistant population absorbed 11.4% less herbicide and retained 21% more herbicide on the treated leaf compared to the susceptible population. We developed a genotyping assay targeting the resistance‐endowing Trp2027Cys substitution for quick resistance diagnosis. CONCLUSION A Trp2027Cys amino acid substitution in ACCase confers resistance to haloxyfop and pinoxaden in C. virgata. We provide important insights into the evolutionary history of C. virgata and a draft genome as a useful resource to further our understanding of the biology in the genus Chloris. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. We identified populations that evolved resistance to acetyl CoA carboxylase (ACCase) inhibitors, generated a draft genome, elucidated the phylogenetic relationship with other important grass species, performed an extensive characterization of the resistance mechanisms, and developed a genetic assay for rapid resistance identification of Chloris virgata populations.