title: A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster.
abstract: Various approaches can be applied to uncover the genetic basis of natural phenotypic variation, each with their specific strengths and limitations. Here, we use a replicated genome-wide association approach (Pool-GWAS) to fine-scale map genomic regions contributing to natural variation in female abdominal pigmentation in Drosophila melanogaster, a trait that is highly variable in natural populations and highly heritable in the laboratory. We examined abdominal pigmentation phenotypes in approximately 8000 female European D. melanogaster, isolating 1000 individuals with extreme phenotypes. We then used whole-genome Illumina sequencing to identify single nucleotide polymorphisms (SNPs) segregating in our sample, and tested these for associations with pigmentation by contrasting allele frequencies between replicate pools of light and dark individuals. We identify two small regions near the pigmentation genes tan and bric-à-brac 1, both corresponding to known cis-regulatory regions, which contain SNPs showing significant associations with pigmentation variation. While the Pool-GWAS approach suffers some limitations, its cost advantage facilitates replication and it can be applied to any non-model system with an available reference genome.
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria.
authors.forename: Héloïse
authors.initials: H
authors.lastname: Bastide
authors.forename: Andrea
authors.initials: A
authors.lastname: Betancourt
authors.forename: Viola
authors.initials: V
authors.lastname: Nolte
authors.forename: Raymond
authors.initials: R
authors.lastname: Tobler
authors.forename: Petra
authors.initials: P
authors.lastname: Stöbe
authors.forename: Andreas
authors.initials: A
authors.lastname: Futschik
authors.forename: Christian
authors.initials: C
authors.lastname: Schlötterer
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D004331:Drosophila melanogaster / Q000235:genetics*; D005260:Female; D005828:Genetics, Population; D049750:Genome, Insect; D055106:Genome-Wide Association Study; D010641:Phenotype; D010858:Pigmentation / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*