DOI: 10.5061/dryad.d4d19
title: Data from: Complex patterns of cis-regulatory polymorphisms in ebony underlie standing pigmentation variation in Drosophila melanogaster

description: Pigmentation traits in adult Drosophila melanogaster were used in this
 study to investigate how phenotypic variations of continuous ecological
 traits can be maintained in a natural population. First, pigmentation
 variation in the adult female was measured at seven different body
 positions in 20 strains from the Drosophila melanogaster Genetic Reference
 Panel (DGRP) originating from a natural population in North Carolina.
 Next, to assess the contributions of cis-regulatory polymorphisms of the
 genes involved in the melanin biosynthesis pathway, allele-specific
 expression levels of four genes were quantified by amplicon sequencing
 using a 454 GS Junior. Among those genes, ebony was significantly
 associated with pigmentation intensity of the thoracic segment. Detailed
 sequence analysis of the gene regulatory regions of this gene indicated
 that many different functional cis-regulatory alleles are segregating in
 the population and that variations outside the core enhancer element could
 potentially play important roles in the regulation of gene expression. In
 addition, a slight enrichment of distantly associated SNP pairs was
 observed in the ~10 kb cis-regulatory region of ebony, which suggested the
 presence of interacting elements scattered across the region. In contrast,
 sequence analysis in the core cis-regulatory region of tan indicated that
 SNPs within the region are significantly associated with allele-specific
 expression level of this gene. Collectively, the data suggest that the
 underlying genetic differences in the cis-regulatory regions that control
 intraspecific pigmentation variation can be more complex than those of
 interspecific pigmentation trait differences, where causal genetic changes
 are typically confined to modular enhancer elements.
description: Female headless body
 images of Drosophila melanogaster_DGRP (RAL-208)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-303)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-324)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-335)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-357)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-358)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-360)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-365)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-380)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-399)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-517)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-555)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-705)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-707)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-732)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-774)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-786)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-799)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-820)Female headless body
 images of Drosophila melanogaster_DGRP (RAL-852)Miyagi et al_Appendix 1
 fileMiyagi
 et al_Appendix 1.xlsx