Genome-Wide Selective Signature Analysis Revealed Insecticide Resistance Mechanisms in Cydia pomonella

SIMPLE SUMMARY: The codling moth, Cydia pomonella, is a quarantine pest that causes extensive damage to many important pome fruits. To control this pest, insecticides are frequently used, leading to the development of resistance. In this study, we analyzed resequencing data of two resistant and one susceptible strains of codling moth, detecting the positively selected genes under the insecticide selective pressure. Coupled with transcriptome data, we discussed the potential role in insecticide resistance of these positively selected genes. Our results identified eight genes including CYP6b2, CYP307a1, 5-hydroxytryptamine receptor, cuticle protein, and acetylcholinesterase, which are potentially involved in cross-resistance to azinphos-methyl and deltamethrin. Overall, our finding indicated that the insecticide resistance mechanism in C. pomonella is a complex physiological and biochemical process. ABSTRACT: The codling moth, Cydia pomonella L. (Lepidoptera, Tortricidae), is a serious invasive pest of pome fruits. Currently, C. pomonella management mainly relies on the application of insecticides, which have driven the development of resistance in the insect. Understanding the genetic mechanisms of insecticide resistance is of great significance for developing new pest resistance management techniques and formulating effective resistance management strategies. Using existing genome resequencing data, we performed selective sweep analysis by comparing two resistant strains and one susceptible strain of the insect pest and identified seven genes, among which, two (glycine receptor and glutamate receptor) were under strong insecticide selection, suggesting their functional importance in insecticide resistance. We also found that eight genes including CYP6B2, CYP307a1, 5-hydroxytryptamine receptor, cuticle protein, and acetylcholinesterase, are potentially involved in cross-resistance to azinphos-methyl and deltamethrin. Moreover, among several P450s identified as positively selected genes, CYP6B2, CYP4C1, and CYP4d2 showed the highest expression level in larva compared to other stages tested, and CYP6B2 also showed the highest expression level in midgut, supporting the roles they may play in insecticide metabolism. Our results provide several potential genes that can be studied further to advance understanding of complexity of insecticide resistance mechanisms in C. pomonella.