A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster.

Bastide, Héloïse, Betancourt, Andrea ORCID: 0000-0001-9351-1413, Nolte, Viola, Tobler, Raymond ORCID: 0000-0002-4603-1473, Stöbe, Petra, Futschik, Andreas ORCID: 0000-0002-7980-0304 and Schlötterer, Christian
(2013) A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster. PLoS genetics, 9 (6). e1003534-.

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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.

Item Type: Article
Uncontrolled Keywords: Animals, Drosophila melanogaster, Pigmentation, Chromosome Mapping, Genetics, Population, Regulatory Sequences, Nucleic Acid, Phenotype, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Female, Genome, Insect, Genome-Wide Association Study
Depositing User: Symplectic Admin
Date Deposited: 31 Oct 2016 09:43
Last Modified: 07 Feb 2024 11:44
DOI: 10.1371/journal.pgen.1003534
Open Access URL: http://journals.plos.org/plosgenetics/article?id=1...
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URI: https://livrepository.liverpool.ac.uk/id/eprint/3004204