title: No evidence for an association between common nonsynonymous polymorphisms in delta and bristle number variation in natural and laboratory populations of Drosophila melanogaster.
abstract: We test the hypothesis that naturally occurring nonsynonymous variants in the Delta ligand of the Notch signaling pathway contribute to standing variation in sternopleural and/or abdominal bristle number in Drosophila melanogaster, for both a large cohort of wild-caught flies and previously described laboratory lines. We sequenced the transcribed region of Delta for 16 naturally occurring chromosomes and 65 SNPs, including 7 nonsynonymous SNPs (nsSNPs), were observed. Identified nsSNPs and 6 additional common SNPs, all located in exon 6 and the 3' UTR, were genotyped in 2060 wild-caught flies using an OLA-based methodology and genotyped in 38 additional natural chromosomes via DNA sequencing. None of the genotyped nsSNPs were significantly associated with natural variation in bristle number as assessed by a permutation test. A 95% upper bound on the additive genetic variance attributable to each genotyped SNP in the large natural cohort is <2% of the total phenotypic variation. Results suggest that two previously detected genotype/phenotype associations between bristle number and variants in the introns of Delta cannot be explained by linkage disequilibrium between these variants and nearby nonsynonymous variants. Unidentified regulatory variants more parsimoniously explain previous observations.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697-2525, USA. anne.genissel@snv.jusseiu.fr
authors.forename: Anne
authors.initials: A
authors.lastname: Genissel
authors.forename: Tomi
authors.initials: T
authors.lastname: Pastinen
authors.forename: Andrea
authors.initials: A
authors.lastname: Dowell
authors.forename: Trudy F C
authors.initials: TF
authors.lastname: Mackay
authors.forename: Anthony D
authors.initials: AD
authors.lastname: Long
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D000830:Animals, Laboratory; D000835:Animals, Wild; D001483:Base Sequence; D004247:DNA / Q000235:genetics; D004331:Drosophila melanogaster / Q000033:anatomy & histology* / Q000235:genetics*; D005091:Exons; D005260:Female; D017344:Genes, Insect; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D047908:Intracellular Signaling Peptides and Proteins; D008297:Male; D008565:Membrane Proteins / Q000235:genetics*; D008969:Molecular Sequence Data; D010641:Phenotype; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D012689:Sequence Homology, Nucleic Acid
chemical_list: D020413:3' Untranslated Regions; D047908:Intracellular Signaling Peptides and Proteins; D008565:Membrane Proteins; C064045:delta protein; D004247:DNA