The western honey bee (Apis mellifera) is an essential pollinator that is facing global colony losses, caused by multiple factors, including pesticide exposure. Like other insects, honey bees rely on detoxification pathways to metabolize xenobiotics into less toxic or readily excretable forms. These pathways are central to insecticide resistance and are shaped by genetic variation. In honey bees, Cytochrome P450 monooxygenases (CYP) genes of clade 3 encode proteins are central to xenobiotic metabolism, but their allelic diversity across natural populations has never been systematically characterized.
We analyzed whole-genome sequencing data from 1,467 drones (haploid males) spanning 25 countries and 18 subspecies across all 4 major evolutionary lineages. Targeting all 28 CYP3 genes alongside 18 housekeeping controls, we identified 5247 single-nucleotide polymorphisms (SNPs) and calculated allele frequencies, haplotype diversity, and fixation index (FST). In addition, all variants were functionally annotated to evaluate their potential effects on protein function.
Our analysis revealed substantial heterogeneity in allelic diversity within the CYP3 clade. Genes implicated in xenobiotic detoxification—particularly CYP9Q3—displayed extensive allelic diversity, likely reflecting diversifying selection. Notably, we detected a previously reported CYP9Q3 haplotype conferring neonicotinoid sensitivity at low frequencies across Mediterranean populations, highlighting its potential utility for monitoring at-risk genotypes. Other genes mirrored the constrained mutational patterns of housekeeping genes, suggesting conserved physiological roles beyond detoxification. This functional specialization parallels observations in humans, where only a subset of CYPs bear the primary detoxification burden and are thus highly polymorphic.
Genetic diversity in A. mellifera is essential for colony resilience and adaptation. High CYP polymorphism likely enhances population-level tolerance to diverse environmental and dietary chemical exposures.
This work provides the first systematic assessment of CYP3 allelic diversity in A. mellifera, underscoring its fundamental importance for understanding pesticide responses and guiding protection efforts.
