Abstract:
Metabolic resistance to pyrethroid insecticides is widespread in Anopheles mosquitoes
and is a major threat to malaria control. DNA markers would aid predictive monitoring
of resistance, but few mutations have been discovered outside of insecticide-targeted
genes. Isofemale family pools from a wild Ugandan Anopheles gambiae population,
from an area where operational pyrethroid failure is suspected, were genotyped using a
candidate-gene enriched SNP array. Resistance-associated SNPs were detected in three
genes from detoxification superfamilies, in addition to the insecticide target site (the
Voltage Gated Sodium Channel gene, Vgsc). The putative associations were confirmed
for two of the marker SNPs, in the P450 Cyp4j5 and the esterase Coeae1d by
reproducible association with pyrethroid resistance in multiple field collections from
Uganda and Kenya, and together with the Vgsc-1014S (kdr) mutation these SNPs
explained around 20% of variation in resistance. Moreover, the >20 Mb 2La inversion
also showed evidence of association with resistance as did environmental humidity.
Sequencing of Cyp4j5 and Coeae1d detected no resistance-linked loss of diversity,
suggesting selection from standing variation. Our study provides novel, regionallyvalidated DNA assays for resistance to the most important insecticide class, and
establishes both 2La karyotype variation and humidity as common factors impacting the
resistance phenotype.