High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest

PLoS Genet. 2021 Jun 21;17(6):e1009422. doi: 10.1371/journal.pgen.1009422. eCollection 2021 Jun.

Abstract

Chemical control strategies are driving the evolution of pesticide resistance in pest populations. Understanding the genetic mechanisms of these evolutionary processes is of crucial importance to develop sustainable resistance management strategies. The acaricide pyflubumide is one of the most recently developed mitochondrial complex II inhibitors with a new mode of action that specifically targets spider mite pests. In this study, we characterize the molecular basis of pyflubumide resistance in a highly resistant population of the spider mite Tetranychus urticae. Classical genetic crosses indicated that pyflubumide resistance was incompletely recessive and controlled by more than one gene. To identify resistance loci, we crossed the resistant population to a highly susceptible T. urticae inbred strain and propagated resulting populations with and without pyflubumide exposure for multiple generations in an experimental evolution set-up. High-resolution genetic mapping by a bulked segregant analysis approach led to the identification of three quantitative trait loci (QTL) linked to pyflubumide resistance. Two QTLs were found on the first chromosome and centered on the cytochrome P450 CYP392A16 and a cluster of CYP392E6-8 genes. Comparative transcriptomics revealed a consistent overexpression of CYP392A16 and CYP392E8 in the experimental populations that were selected for pyflubumide resistance. We further corroborated the involvement of CYP392A16 in resistance by in vitro functional expression and metabolism studies. Collectively, these experiments uncovered that CYP392A16 N-demethylates the toxic carboxamide form of pyflubumide to a non-toxic compound. A third QTL coincided with cytochrome P450 reductase (CPR), a vital component of cytochrome P450 metabolism. We show here that the resistant population harbors three gene copies of CPR and that this copy number variation is associated with higher mRNA abundance. Together, we provide evidence for detoxification of pyflubumide by cytochrome P450s that is likely synergized by gene amplification of CPR.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acaricides / metabolism*
  • Animals
  • Chromosome Mapping / methods*
  • Cytochrome P-450 Enzyme System / metabolism*
  • DNA Copy Number Variations*
  • Inactivation, Metabolic*
  • Insecticide Resistance / genetics
  • Methylation
  • Quantitative Trait Loci
  • Tetranychidae / genetics*
  • Transcriptome

Substances

  • Acaricides
  • Cytochrome P-450 Enzyme System

Grants and funding

This work was supported by the Research Foundation - Flanders (FWO) [grant G009312N and grant G053815N to T.V.L.] and the Research Council (ERC) under the European Union's Horizon 2020 research and innovation program [grant 772026-POLYADAPT to T.V.L. and 773902–SUPERPEST to J.V. and T.V.L.], and by the USA National Science Foundation (award 1457346 to R.M.C). N.W. was supported by a Research Foundation - Flanders (FWO) and a BOF (Ghent University) post-doctoral fellowship (12T9818N and 01P03420, respectively). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.