Abstract
BackgroundSingle nucleotide polymorphisms (SNPs) are the most common source of genetic variation in eukaryotic species and have become an important marker for genetic studies. The mosquito Anopheles funestus is one of the major malaria vectors in Africa and yet, prior to this study, no SNPs have been described for this species. Here we report a genome-wide set of SNP markers for use in genetic studies on this important human disease vector.ResultsDNA fragments from 50 genes were amplified and sequenced from 21 specimens of An. funestus. A third of specimens were field collected in Malawi, a third from a colony of Mozambican origin and a third form a colony of Angolan origin. A total of 494 SNPs including 303 within the coding regions of genes and 5 indels were identified. The physical positions of these SNPs in the genome are known. There were on average 7 SNPs per kilobase similar to that observed in An. gambiae and Drosophila melanogaster. Transitions outnumbered transversions, at a ratio of 2:1. The increased frequency of transition substitutions in coding regions is likely due to the structure of the genetic code and selective constraints. Synonymous sites within coding regions showed a higher polymorphism rate than non-coding introns or 3' and 5'flanking DNA with most of the substitutions in coding regions being observed at the 3rd codon position. A positive correlation in the level of polymorphism was observed between coding and non-coding regions within a gene. By genotyping a subset of 30 SNPs, we confirmed the validity of the SNPs identified during this study.ConclusionThis set of SNP markers represents a useful tool for genetic studies in An. funestus, and will be useful in identifying candidate genes that affect diverse ranges of phenotypes that impact on vector control, such as resistance insecticide, mosquito behavior and vector competence.
Highlights
Single nucleotide polymorphisms (SNPs) are the most common source of genetic variation in eukaryotic species and have become an important marker for genetic studies
The average nucleotide diversity per gene in coding regions was 7.2 × 10-3 or around 1 SNP every 138 bp similar to that observed in An. gambiae (1 SNPs every 125 bp) [19]
The set of SNPs identified in this study provide a very useful tool for future genetic studies in An. funestus
Summary
Single nucleotide polymorphisms (SNPs) are the most common source of genetic variation in eukaryotic species and have become an important marker for genetic studies. The mosquito Anopheles funestus is one of the major malaria vectors in Africa and yet, prior to this study, no SNPs have been described for this species. The recent successful colonization of two strains of An. funestus [1] and the identification of a number of microsatellite markers [2,3] have facilitated more detailed studies of this species. An. funestus populations [4,5,6] and a subset of these microsatellite markers were used to build the first linkage map of this species [7]. Microsatellite markers (page number not for citation purposes) are not evenly distributed across the genome, and their low number so far is an obstacle to the development of high resolution linkage maps needed for QTL mapping or association studies in An. funestus.
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