We evaluated the hypothesis that the Drosophila melanogaster second chromosome gene scabrous
(sca), a candidate sensory bristle number quantitative trait locus (QTL), contributes to naturally
occurring variation in bristle number. Variation in abdominal and sternopleural bristle number
was quantified for wild-derived sca alleles in seven genetic backgrounds: as homozygous second
chromosomes (C2) in an isogenic background, homozygous lines in which approximately 20 cM
including the sca locus had been introgressed into the isogenic background (sca BC), as C2 and sca
BC heterozygotes and hemizygotes against a P element insertional sca allele and a P-induced sca
deficiency in the same isogenic background, and as sca BC heterozygotes against the wild-type sca
allele of isogenic strain. Molecular restriction map variation was determined for a 45 kb region
including the sca locus, and single-stranded conformational polymorphism (SSCP) was examined
for the third intron and parts of the third and fourth exons. Associations between each of the 27
molecular polymorphisms and bristle number were evaluated within each genotype and on the first
principal component score determined from all seven genotypes, separately for each sex and bristle
trait. Permutation tests were used to assess the empirical significance thresholds, accounting for
multiple, correlated tests, and correlated markers. Three sites in regulatory regions were associated
with female-specific variation in abdominal bristle number, one of which was an SSCP site in the
region of the gene associated with regulation of sca in embryonic abdominal segments.