Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae.

Seth N. Redmond (1) , Karin Eiglmeier (1) , Christian Mitri (1) , Kyriacos Markianos (2) , Wamdaogo Guelbéogo (3) , Awa Gneme (3) , Alison T. Isaacs (1) , Boubacar Coulibaly (4) , Emma Brito-Fravallo (1) , Gareth Maslen (5, 6) , Daniel Mead (5, 6) , Oumou Niare (4) , Sekou F. Traore (4) , N'Fale Sagnon (3) , Dominic Kwiatkowski (6, 5) , Michelle M. Riehle (7) , Kenneth D Vernick (1)

1 Génétique et Génomique des Insectes vecteurs
2 HMS - Harvard Medical School [Boston]
3 CNRFP - Centre National de Recherche et de Formation sur le Paludisme [Ouagadougou, Burkina Faso]
4 Malaria Research and Training Center [Bamako, Mali]
5 The Wellcome Trust Sanger Institute [Cambridge]
6 The Wellcome Trust Centre for Human Genetics [Oxford]
7 UMN - University of Minnesota [Twin Cities]

BACKGROUND: The genome-wide association study (GWAS) techniques that have been used for genetic mapping in other organisms have not been successfully applied to mosquitoes, which have genetic characteristics of high nucleotide diversity, low linkage disequilibrium, and complex population stratification that render population-based GWAS essentially unfeasible at realistic sample size and marker density. METHODS: We designed a novel mapping strategy for the mosquito system that combines the power of linkage mapping with the resolution afforded by genetic association. We established founder colonies from West Africa, controlled for diversity, linkage disequilibrium and population stratification. Colonies were challenged by feeding on the infectious stage of the human malaria parasite, Plasmodium falciparum, mosquitoes were phenotyped for parasite load, and DNA pools for phenotypically similar mosquitoes were Illumina sequenced. Phenotype-genotype mapping was carried out in two stages, coarse and fine. RESULTS: In the first mapping stage, pooled sequences were analysed genome-wide for intervals displaying relativereduction in diversity between phenotype pools, and candidate genomic loci were identified for influence upon parasite infection levels. In the second mapping stage, focused genotyping of SNPs from the first mapping stage was carried out in unpooled individual mosquitoes and replicates. The second stage confirmed significant SNPs in a locus encoding two Toll-family proteins. RNAi-mediated gene silencing and infection challenge revealed that TOLL 11 protects mosquitoes against P. falciparum infection. CONCLUSIONS: We present an efficient and cost-effective method for genetic mapping using natural variation segregating in defined recent Anopheles founder colonies, and demonstrate its applicability for mapping in a complex non-model genome. This approach is a practical and preferred alternative to population-based GWAS for first-pass mapping of phenotypes in Anopheles. This design should facilitate mapping of other traits involved in physiology, epidemiology, and behaviour.

Mots clés: Genotype; Insect; Genome; Chromosome Mapping; Anopheles/*genetics/parasitology; Malaria; Falciparum/*genetics/parasitology/transmission; Insect Vectors/genetics; Humans; *Genome-Wide Association Study; Animals; Host-Parasite Interactions/genetics; Phenotype; Plasmodium falciparum/*genetics/pathogenicity; Polymorphism; Single Nucleotide; Toll-Like Receptors/*genetics

Domaines: Parasitologie; Santé publique et épidémiologie; Zoologie des invertébrés

Seth N. Redmond, Karin Eiglmeier, Christian Mitri, Kyriacos Markianos, Wamdaogo Guelbéogo, et al.. Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae.. BMC Genomics, 2015, 16 (1), pp.779. ⟨10.1186/s12864-015-2009-z⟩. ⟨pasteur-02008320⟩