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Improving the population genetics toolbox for the study of the African malaria vector Anopheles nili: microsatellite mapping to chromosomes

Ashley Peery1, Maria V Sharakhova1, Christophe Antonio-Nkondjio2, Cyrille Ndo2, Mylene Weill3, Frederic Simard45 and Igor V Sharakhov1*

Author Affiliations

1 Department of Entomology, Virginia Polytechnic and State University, West Campus Drive, Blacksburg, VA 24061, USA

2 Malaria Research Laboratory, Organisation de Coordination pour la lutte contre les Endémies en Afrique Centrale (OCEAC), Yaounde, BP 288, Cameroon

3 Institut des Sciences de l'Evolution, Université Montpellier 2, Centre National de la Recherche Scientifique, Place Eugène Bataillon, C.C. 065, 34095 Montpellier, France

4 Unité Mixte de Recherche 224 'Maladies Infectieuses et Vecteurs: Ecologie, Genetique, Evolution et Controle (MIVEGEC)', Team 'Biology, Ecology and Evolution of vector Systems (BEES)', Institut de Recherche pour le Developpement (IRD), BP 64501, Montpellier 34394, France

5 Institut de Recherche en Sciences de la Santé (IRSS), 399 Avenue de la Liberte, Bobo Dioulasso, 01BP171, Burkina Faso

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Parasites & Vectors 2011, 4:202  doi:10.1186/1756-3305-4-202

Published: 19 October 2011



Anopheles nili 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.


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 An. nili using fluorescent in situ 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 An. nili genome assembly generated on an Illumina platform. Two additional loci were assigned to specific chromosome arms of An. nili based on in silico sequence similarity and chromosome synteny with Anopheles gambiae. Three microsatellites were mapped inside or in the vicinity of the polymorphic chromosomal inversions 2Rb and 2Rc. A statistically significant departure from Hardy-Weinberg equilibrium, due to a deficit in heterozygotes at the 2Rb inversion, and highly significant linkage disequilibrium between the two inversions, were detected in natural An. nili populations collected from Burkina Faso.


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 An. nili 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 An. nili.

Chromosome inversions; genome sequence; malaria vector; microsatellite markers; population structure