A 37-kb tandem duplication is associated with the Group 4 “baldhead” piebalding pattern.

(A) Plot of genotypes within the candidate region identified by pFST for Group 4 birds. Each row shows an individual bird, and each vertical line a SNP, colored by genotype relative to the reference genome. Approximate locations of genes are illustrated at top, and regions of interest delineated by brackets, below. (B) Plot of normalized whole genome sequencing read coverage for representative birds from seven different breeds. Three baldhead breeds show an increase in coverage. * marks a coverage drop that coincides with both a LINE element and a nearby stretch of “N” bases in the reference genome and is not associated with a piebalding phenotype. (C) Schematic of the predicted structure of the baldhead-associated duplication. The duplicated region includes the 5’ portion of VAMP7 and the entirety of both RPAC2 and EDNRB2. Black triangles below indicate primer pairs used to amplify across the central breakpoint (also see S8 Fig).