title: A Multipurpose, High-Throughput Single-Nucleotide Polymorphism Chip for the Dengue and Yellow Fever Mosquito, Aedes aegypti.
abstract: The dengue and yellow fever mosquito, Aedes aegypti, contributes significantly to global disease burden. Genetic study of Aedes aegypti is essential to understanding its evolutionary history, competence as a disease vector, and the effects and efficacy of vector control methods. The prevalence of repeats and transposable elements in the Aedes aegypti genome complicates marker development and makes genome-wide genetic study challenging. To overcome these challenges, we developed a high-throughput genotyping chip, Axiom_aegypti1. This chip screens for 50,000 single-nucleotide polymorphisms present in Aedes aegypti populations from around the world. The array currently used genotypes 96 samples simultaneously. To ensure that these markers satisfy assumptions commonly made in many genetic analyses, we tested for Mendelian inheritance and linkage disequilibrium in laboratory crosses and a wild population, respectively. We have validated more than 25,000 of these markers to date, and expect this number to increase with more sampling. We also present evidence of the chip's efficacy in distinguishing populations throughout the world. The markers on this chip are ideal for applications ranging from population genetics to genome-wide association studies. This tool makes rapid, cost-effective, and comparable genotype data attainable to diverse sets of Aedes aegypti researchers, from those interested in potential range shifts due to climate change to those characterizing the genetic underpinnings of its competence to transmit disease.
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511 b.evans@yale.edu.
authors.forename: Benjamin R
authors.initials: BR
authors.lastname: Evans
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511.
authors.forename: Andrea
authors.initials: A
authors.lastname: Gloria-Soria
authors.affiliation: Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut 06520.
authors.forename: Lin
authors.initials: L
authors.lastname: Hou
authors.affiliation: Princeton Neuroscience Institute and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08540.
authors.forename: Carolyn
authors.initials: C
authors.lastname: McBride
authors.affiliation: Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California 92697.
authors.forename: Mariangela
authors.initials: M
authors.lastname: Bonizzoni
authors.affiliation: Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut 06520.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Zhao
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511.
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Powell
mesh_terms: D000330:Aedes / Q000235:genetics*; D000818:Animals; D003715:Dengue / Q000635:transmission; D014644:Genetic Variation; D005828:Genetics, Population; D049750:Genome, Insect; D023281:Genomics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D040582:Inheritance Patterns; D007303:Insect Vectors / Q000235:genetics*; D015810:Linkage Disequilibrium; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D015004:Yellow Fever / Q000635:transmission
keywords: Aedes aegypti; SNP; genomics; population genetics; vector biology