Genome mapping coupled with CRISPR gene editing reveals a P450 gene confers avermectin resistance in the beet armyworm

Authors: ZUO, YAYUN - Nanjing Agricultural University; SHI, YU - Nanjing Agricultural University; ZHANG, FENG - Nanjing Agricultural University; GUAN, FANG - Nanjing Agricultural University; ZHANG, JIANPENG - Nanjing Agricultural University; FEYEREISEN, RENEE - University Of Copenhagen; Fabrick, Jeffrey; YANG, YIHUA - Nanjing Agricultural University; WU, YIDONG - Nanjing Agricultural University

Submitted to: PLoS Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/23/2021
Publication Date: 7/12/2021
Citation: Zuo, Y., Shi, Y., Zhang, F., Guan, F., Zhang, J., Feyereisen, R., Fabrick, J.A., Yang, Y., Wu, Y. 2021. Genome mapping coupled with CRISPR gene editing reveals a P450 gene confers avermectin resistance in the beet armyworm. PLoS Genetics. 17(7). Article e1009680. https://doi.org/10.1371/journal.pgen.1009680.
DOI: https://doi.org/10.1371/journal.pgen.1009680

Interpretive Summary: Insecticides are important in the global process of managing insect pests. However, the evolution of resistance limits insecticide efficacy and is an increasingly intractable problem affecting crop production worldwide. Two avermectins, emamectin benzoate (EB) and abamectin, are relatively new pesticides with reduced environmental risk that target a wide number of insect pests, including the beet armyworm, Spodoptera exigua, an important global pest of many crops. Because of the extreme genetic diversity found in insects and the large numbers of genes involved in insecticide detoxification, better tools are needed to quickly identify and validate the involvement of putative resistance genes. Here, an ARS scientist at Maricopa, AZ and collaborators coupled genome sequencing with CRISPR/Cas9 gene editing and mapped avermectin resistance in the beet armyworm to a specific chromosomal region harboring several cytochrome P450 genes. Specific knockout of the cytochrome P450 CYP9A186 gene by CRISPR/Cas9 gene editing fully restored insecticide susceptibility, implicating this gene in avermectin resistance. These results were further verified by in vitro functional assays where the CYP9A186 protein harboring a natural substitution (F116V) was produced in cultured insect cells and showed enhanced metabolism of EB and abamectin. Hence, the combined approach of coupling gene editing with whole genome DNA sequencing allows for the rapid identification of metabolic resistance genes responsible for insecticide resistance.

Technical Abstract: The evolution of insecticide resistance represents a global constraint to agricultural production. Because of the extreme genetic diversity found in insects and the large numbers of genes involved in insecticide detoxification, better tools are needed to quickly identify and validate the involvement of putative resistance genes for improved monitoring, management, and countering of field evolved insecticide resistance. The avermectins, emamectin benzoate (EB) and abamectin are relatively new pesticides with reduced environmental risk that target a wide number of insect pests, including the beet armyworm, Spodoptera exigua, an important global pest of many crops. Unfortunately, field resistance to avermectins recently evolved in the beet armyworm, threatening the sustainable use of this class of insecticides. Here, we report a high-quality chromosome-level assembly of the beet armyworm genome and use bulked segregant analysis (BSA) to identify the locus of avermectin resistance, which mapped on 15–16 Mbp of chromosome 17. Knockout of the CYP9A186 gene that maps within this region by CRISPR/Cas9 gene editing fully restored EB susceptibility, implicating this gene in avermectin resistance. Heterologous expression and in vitro functional assays further confirm that a natural substitution (F116V) found in the substrate recognition site 1 (SRS1) of the CYP9A186 protein results in enhanced metabolism of EB and abamectin. Hence, the combined approach of coupling gene editing with BSA allows for the rapid identification of metabolic resistance genes responsible for insecticide resistance, which is critical for effective monitoring and adaptive management of insecticide resistance.