title: Identification of field caught Anopheles gambiae s.s. and Anopheles arabiensis by TaqMan single nucleotide polymorphism genotyping.
abstract: BACKGROUND
  Identification of Anopheles gambiae s.s. and Anopheles arabiensis from field-collected Anopheles gambiae s.l. is often necessary in basic and applied research, and in operational control programmes. The currently accepted method involves use of standard polymerase chain reaction amplification of ribosomal DNA (rDNA) from the 3' 28S to 5' intergenic spacer region of the genome, and visual confirmation of amplicons of predicted size on agarose gels, after electrophoresis. This report describes development and evaluation of an automated, quantitative PCR method based upon TaqMan single nucleotide polymorphism (SNP) genotyping.
  
  
  METHODS
  Standard PCR, and TaqMan SNP genotyping with newly designed primers and fluorophore-labeled probes hybridizing to sequences of complementary rDNA specific for either An. gambiae s.s. or An. arabiensis, were conducted in three experiments involving field-collected An. gambiae s.l. from western Kenya, and defined laboratory strains. DNA extraction was from a single leg, sonicated for five minutes in buffer in wells of 96-well PCR plates.
  
  
  RESULTS
  TaqMan SNP genotyping showed a reaction success rate, sensitivity, and species specificity comparable to that of standard PCR. In an extensive field study, only 29 of 3,041 (0.95%) were determined to be hybrids by TaqMan (i.e., having rDNA sequences from both species), however, all but one were An. arabiensis by standard PCR, suggesting an acceptably low (ca. 1%) error rate for TaqMan genotyping in mistakenly identifying species hybrids.
  
  
  CONCLUSIONS
  TaqMan SNP genotyping proved to be a sensitive and rapid method for identification of An. gambiae s.l. and An. arabiensis, with a high success rate, specific results, and congruence with the standard PCR method.
authors.affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA. walker@msu.edu
authors.forename: Edward D
authors.initials: ED
authors.lastname: Walker
authors.forename: Alisha R
authors.initials: AR
authors.lastname: Thibault
authors.forename: Annette P
authors.initials: AP
authors.lastname: Thelen
authors.forename: Blair A
authors.initials: BA
authors.lastname: Bullard
authors.forename: Juan
authors.initials: J
authors.lastname: Huang
authors.forename: Maurice R
authors.initials: MR
authors.lastname: Odiere
authors.forename: Nabie M
authors.initials: NM
authors.lastname: Bayoh
authors.forename: Elizabeth E
authors.initials: EE
authors.lastname: Wilkins
authors.forename: John M
authors.initials: JM
authors.lastname: Vulule
mesh_terms: D000818:Animals; D000852:Anopheles / Q000145:classification* / Q000235:genetics*; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D005260:Female; D005838:Genotype; D007630:Kenya; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012680:Sensitivity and Specificity
chemical_list: D021903:DNA, Ribosomal Spacer