Genome-wide exploration of metabolic-based pyrethroid resistance mechanism in Helicoverpa armigera

To elucidate the deltamethrin resistance mechanism in Helicoverpa armigera, we explored mutations at the deltamethrin target site, genomic level variations between insecticide-susceptible and -resistant strains, and differences in gene expression patterns between the strains. Known pyrethroid resistance-associated point mutations within the voltage-gated sodium channel were undetected in the cDNA and gDNA of resistant strains or field populations. The whole-genome de novo assembly of a Korean resistant strain was performed (GCA_026262555.1), and 13 genomes of susceptible and resistant individuals were re-sequenced using field populations. Approximately 3,369,837 variants (SNPs and indels) were compared with our reference H. armigera genome, and 1,032,689 variants were identified from open reading frames. A resistance-specific CYP3 subfamily gene with five variants (CYP321A1v1-v5) was identified in the resistant strains, indicating the potential role of these variants in resistance. RNA-seq analysis identified 36,720 transcripts from 45 Illumina RNA-seq datasets of the fat body, gut, and the rest of the body. Differential gene expression analysis revealed some differently overexpressed detoxification enzyme genes in the resistant strains, particularly cytochrome P450 genes. This finding was consistent with the results of bioassay tests using PBO-based synergists, further supporting the role of detoxification enzymes in resistance. Therefore, H. armigera may acquire deltamethrin resistance through a combination of actions, including the overexpression of various detoxification enzymes, such as CYP3 subfamilies (CYP321A5) and cuticular proteins. The five variants of CYP321A subfamily identified in this study may serve as a basis for understanding insecticide resistance at the molecular level and can be applied as diagnostic markers for resistance. Key MessagesO_LIKnown resistance-related mutations were undetected in all the resistant strains or field populations. C_LIO_LINo specific resistance-associated variations were identified at the genomic level. C_LIO_LIThe expression pattern of the CYP3 subfamily genes was strongly correlated with the level of resistance. C_LIO_LIGenes other than CYP337B3 are also involved in the development of high-level resistance. C_LIO_LIResistance developed as a result of changes in the expression of detoxification genes rather than target site modification through mutation. C_LI