Data from: Complex patterns of cis-regulatory polymorphisms in ebony underlie standing pigmentation variation in Drosophila melanogaster

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.