GENOMIC ANALYSIS OF INSECTICIDE RESISTANCE CANDIDATE GENES IN THE COLORADO POTATO BEETLE, LEPTINOTARSA DECEMLINEATA

Abstract

Since the advent of modern agriculture, humans have continuously developed and deployed chemical compounds with novel modes of action to manage pest populations, while insects have repeatedly responded by evolving resistance. To date, at least 625 arthropod species have evolved resistance to over 360 pesticidal technologies. As a global super pest, the Colorado potato beetle (CPB) has developed resistance to at least 56 different insecticidal active ingredients. Comprehensive genomic scanning of resistance candidate genes can facilitate downstream applications, including mode-of-action analysis, functional interpretation of resistance mutations, development of molecular resistance monitoring tools, and the formulation of sustainable pest management strategies. However, I note that the cys-loop ligand-gated ion channel (cysLGIC) gene superfamily, encoding important target sites, such as nicotinic acetylcholine receptors (nAChRs) and γ-aminobutyric acid (GABA) receptors remain poorly characterized in CPB. In addition, previously suspected resistance-associated mutations have not been systematically surveyed across U.S. CPB populations. In the current research, leveraging the chromosome-level genome assembly of the Colorado potato beetle (CPB), I systematically characterized the cys-loop ligand-gated ion channel (cysLGIC) gene superfamily in the Colorado potato beetle. This work provides a foundational reference for the annotation of DNA and protein sequences of these receptors and can support future functional and comparative studies. In particular, I highlighted unique patterns observed in specific subunits, such as nAChR α4 and nAChR β1, and discussed their potential roles in mediating insecticide resistance. Furthermore, I conducted high-throughput genomic scanning of 31 resistance candidate genes using whole-genome sequencing data from 74 CPB samples, aiming to identify resistance-associated mutations. My results include the first detection of a super-kdr-like mutation (T929I in the voltage-sensitive sodium channel) conferring pyrethroid resistance in U.S. CPB populations, and the first identification of the A301S mutation in the Rdl gene, associated with resistance to both dieldrin and fiproles. Additionally, I provide evidence of selection acting on neonicotinoid resistance candidate genes and report novel genetic variants statistically associated with resistance phenotypes.