Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae

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, regionally-validated 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.

Mapping Trends in Insecticide Resistance Phenotypes in African Malaria Vectors

“…Such information would better inform models of predictive relationships between resistance and agricultural insecticide use. Further, more extensive data on the presence of resistance mechanisms, including a wider coverage of Vgsc allele frequencies, as well as metabolic resistance markers 40 , in field populations would potentially aid in predicting and interpreting resistance trends. The similarity in predicted spatiotemporal patterns in resistance across the four pyrethroids and DDT (e.g.…”

Associated patterns of insecticide resistance in field populations of malaria vectors across Africa

“…This result may reflect the lower power to detect associations for these classes because data volumes are lower ( SI Appendix , Table S1 ) and perhaps most importantly, variation in mortality was less, especially for the organophosphates to which resistance remains limited. In addition, while organophosphate insecticides were pooled for this analysis, cross-resistance between insecticides within this class has been found to be variable, which could cause variable cross-class interactions in field populations ( 30 – 32 ).…”

Effect of environmental variables and kdr resistance genotype on survival probability and infection rates in Anopheles gambiae (s.s.)

“…Temperature also affects the extent to which insecticides kill mosquitoes [ 25 , 26 ], possibly because mosquito immune responses [ 12 ], nervous-system sensitivity [ 62 ], and metabolic activity [ 63 ] are all temperature-dependent. Apart from its effect on mosquito survival in combination with ambient temperature [ 11 ], humidity was shown to have a strong impact on insecticide resistance phenotype [ 64 ].…”