High-throughput genotyping of common chromosomal inversions in the afrotropical malaria mosquito Anopheles funestus

Simple Summary Chromosomal inversions occur when a segment of DNA breaks in two places, rotates 180 degrees, and reattaches. Inversions can protect sets of genetic variants, including those adapted to local conditions, from being split up in the random shuffling that occurs when genetic information is transmitted from one generation to the next. For this reason, inversions can play a role in local adaptation and range expansion. Like many malaria mosquitoes, Anopheles funestus, which plays a major role in transmitting malaria in sub-Saharan Africa, carries several common chromosomal inversions. Three of these inversions have been implicated in traits such as indoor resting behavior, which affects their rate of contact with both humans and insecticide-based interventions. Inversions therefore have relevance for malaria epidemiology and control. Inversions are traditionally identified by examining chromosomes under a microscope, but this method is difficult and time-consuming, and only applicable to a subset of female adult mosquitoes. To overcome this limitation, we developed high-throughput DNA-based diagnostic methods to predict the presence of inversions. The availability of these methods will allow scientists to more easily identify inversions in larger samples of mosquitoes, from all life stages and both sexes, which will help us determine how inversions are affecting malaria transmission. Polymorphic chromosomal inversions have been implicated in local adaptation. In anopheline mosquitoes, inversions also contribute to epidemiologically relevant phenotypes such as resting behavior. Progress in understanding these phenotypes and their mechanistic basis has been hindered because the only available method for inversion genotyping relies on traditional cytogenetic karyotyping, a rate-limiting and technically difficult approach that is possible only for the fraction of the adult female population at the correct gonotrophic stage. Here, we focus on an understudied malaria vector of major importance in sub-Saharan Africa, Anopheles funestus. We ascertain and validate tag single nucleotide polymorphisms (SNPs) using high throughput molecular assays that allow rapid inversion genotyping of the three most common An. funestus inversions at scale, overcoming the cytogenetic karyotyping barrier. These same inversions are the only available markers for distinguishing two An. funestus ecotypes that differ in indoor resting behavior, Folonzo and Kiribina. Our new inversion genotyping tools will facilitate studies of ecotypic differentiation in An. funestus and provide a means to improve our understanding of the roles of Folonzo and Kiribina in malaria transmission