Fig 3. Fine mapping of the causal region for the pearl-eye phenotype.

(A) Genotyping across the candidate causal region. Each line corresponds to one individual, and each column to a single-nucleotide polymorphism. Color of each individual cell indicates the genotype, which can be either homozygous reference (red), heterozygous (orange) or homozygous alternative (yellow). We note that the reference genome contains the pearl eye haplotype. Pearl-eye pigeons are homozygous for a stretch of sequence of ~20kb. This interval can be further reduced by excluding a segment in which two wild-type individuals are homozygous, resulting in a ~8.5kb region. (B) Gene content along the candidate region. The 8.5kb interval identified in panel (A), here highlighted in red, contains a single protein coding gene: SLC2A11B. (C) Alignment of sequences of multiple avian species around the candidate causal mutation in SLC2A11B, indicating strong sequence conservation at the candidate position except for the pearl-eye haplotype. A scheme of the partial amino acid content at the 5’ end of exon 3 and the location of the premature STOP codon are shown. Additional bird species are represented in S1 Fig.