| Summary: | <p>Abstract</p> <p>Background</p> <p><it>Anopheles nili </it>is a major vector of malaria in the humid savannas and forested areas of sub-Saharan Africa. Understanding the population genetic structure and evolutionary dynamics of this species is important for the development of an adequate and targeted malaria control strategy in Africa. Chromosomal inversions and microsatellite markers are commonly used for studying the population structure of malaria mosquitoes. Physical mapping of these markers onto the chromosomes further improves the toolbox, and allows inference on the demographic and evolutionary history of the target species.</p> <p>Results</p> <p>Availability of polytene chromosomes allowed us to develop a map of microsatellite markers and to study polymorphism of chromosomal inversions. Nine microsatellite markers were mapped to unique locations on all five chromosomal arms of <it>An. nili </it>using fluorescent <it>in situ </it>hybridization (FISH). Probes were obtained from 300-483 bp-long inserts of plasmid clones and from 506-559 bp-long fragments amplified with primers designed using the <it>An. nili </it>genome assembly generated on an Illumina platform. Two additional loci were assigned to specific chromosome arms of <it>An. nili </it>based on <it>in silico </it>sequence similarity and chromosome synteny with <it>Anopheles gambiae</it>. Three microsatellites were mapped inside or in the vicinity of the polymorphic chromosomal inversions <it>2Rb </it>and <it>2Rc</it>. A statistically significant departure from Hardy-Weinberg equilibrium, due to a deficit in heterozygotes at the <it>2Rb </it>inversion, and highly significant linkage disequilibrium between the two inversions, were detected in natural <it>An. nili </it>populations collected from Burkina Faso.</p> <p>Conclusions</p> <p>Our study demonstrated that next-generation sequencing can be used to improve FISH for microsatellite mapping in species with no reference genome sequence. Physical mapping of microsatellite markers in <it>An. nili </it>showed that their cytological locations spanned the entire five-arm complement, allowing genome-wide inferences. The knowledge about polymorphic inversions and chromosomal locations of microsatellite markers has been useful for explaining differences in genetic variability across loci and significant differentiation observed among natural populations of <it>An. nili</it>.</p>
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