Genome-wide Association Study Reveals New Loci Associated With Pyrethroid Resistance in Aedes aegypti

Abstract

Genome-wide association studies (GWAS) use genetic polymorphism across the genomes of individuals with distinct characteristics to identify genotype-phenotype associations. In mosquitoes, complex traits such as vector competence and insecticide resistance could benefit from GWAS. We used the Aedes aegypti 50k SNP chip to genotype populations with different levels of pyrethroid resistance from Northern Brazil. Pyrethroids are widely used worldwide to control mosquitoes and agricultural pests, and their intensive use led to the selection of resistance phenotypes in many insects including mosquitoes. For Ae. aegypti, resistance phenotypes are mainly associated with several mutations in the voltage-gated sodium channel, known as knockdown resistance (kdr). We phenotyped those populations with the WHO insecticide bioassay using deltamethrin impregnated papers, genotyped the kdr alleles using qPCR, and determined allele frequencies across the genome using the SNP chip. We identified single-nucleotide polymorphisms (SNPs) directly associated with resistance and one epistatic SNP pair. We also observed that the novel SNPs correlated with the known kdr genotypes, although on different chromosomes or not in close physical proximity to the voltage gated sodium channel gene. In addition, pairwise comparison of resistance and susceptible mosquitoes from each population revealed differentiated genomic regions not associated with pyrethroid resistance. These new bi-allelic markers can be used to genotype other populations along with kdr alleles to understand their worldwide distribution. The functional roles of the genes near the newly discovered SNPs require new studies to determine if they act synergistically with kdr alleles or reduce the fitness cost of maintaining resistant alleles.

Strong positive selection in Aedes aegypti and the rapid evolution of insecticide resistance

“…If our hypothesis is correct, the frequency of the haplotype bearing these resistance mutations may continue to increase in the coming years under continuing selective pressure from insecticide use. Indeed, the Brazilian sample is from 2012, so allele frequencies at these loci may be very different in the present day, as the resistant alleles at V1016I and F1534C are common (Linss et al 2014, David et al 2018, Melo Costa et al 2020, Cosme et al 2022) and increasing in frequency (Linss et al 2014) in some parts of Brazil. This situation highlights the need for an increased use of temporal data in vector genomics.…”

Strong Positive Selection inAedes aegyptiand the Rapid Evolution of Insecticide Resistance

“…In Ae. aegypti , variation in ankyrin domain-containing genes has been associated with pyrethroid resistance ( Campbell et al 2019 ); in addition, the ankyrin repeat region-containing gene AAEL011338 was identified as harboring a locus associated with pyrethroid resistance in a Brazilian sample ( Cosme et al 2022 ).…”

“…If our hypothesis is correct, the frequency of the haplotype bearing these resistance mutations may continue to increase in the coming years under continuing selective pressure from insecticide use. Indeed, the Brazilian sample is from 2012, so allele frequencies at these loci may be very different in the present day, as the resistant alleles at V1016I and F1534C are common ( Linss et al 2014 ; David et al 2018 ; Melo Costa et al 2020 ; Cosme et al 2022 ) and increasing in frequency ( Linss et al 2014 ) in some parts of Brazil. This situation highlights the need for an increased use of temporal data in vector genomics.…”

Molecular signature of domestication in the arboviral vectorAedes aegypti

“…, Ir8) (29), the para sodium channel gene ( e.g. , kdr mutations) (23,30,31), and odorant receptors ( e.g. , AeOR4) (6).…”

“…Most efforts have been focused on identifying specific genes linked to hallmarks of domestication such as host-seeking behavior or insecticide resistance, the latter being a side effect of recurrent insecticidal interventions to control mosquito populations (22)(23)(24), based on the differential expression across Ae. aegypti populations (25)(26)(27)(28) and/or the presence of nonsynonymous variants within a few target loci, including genes encoding for detoxification enzymes (e.g., P450s) (23), neurotransmitter receptors (e.g., Ir8) (29), the para sodium channel gene (e.g., kdr mutations) (23,30,31), and odorant receptors (e.g., AeOR4) (6).…”