Fig 1.
Eye color in domestic pigeons (Columba livia).
Wild-type individuals exhibit a pigmented yellow iris, while pearl-eye mutants (controlled by a recessive allele) show unpigmented eyes. The yellow coloration of wild-type pigeons is due to the deposition of pterins in the pigmented epithelium of the iris. Photo credits: P. M. Araújo.
Fig 2.
Genetic mapping of the pearl-eye locus in domestic pigeons.
(A) −log10 transformation of Fisher’s exact test P-values under a recessive model of association. Each dot represents an individual SNP. The red solid line indicates the Bonferroni-corrected critical value (P = 1.13x10-8). (B) FST scan across the genome between wild-type and pearl-eye pigeons. Each dot represents FST averaged over 20 kb windows and iterated in steps of 4 kb across each scaffold. (C) Ratio of nucleotide diversity (π) in wild-type and pearl-eye pigeons. Each dot represents the ratio averaged over 20 Kb windows and iterated in steps of 4 kb across each scaffold. In all three panels, the different scaffolds are presented on the x-axis in the same order as they appear in the rock pigeon reference genome assembly.
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.
Fig 4.
Gene expression in wild-type and pearl-eye pigeons.
(A) Volcano plot with results from differential expression analysis of iris of the two phenotypes, comparing log-fold changes in expression with FDR-adjusted P-values. Significant results are highlighted in blue and SLC2A11B is indicated. (B) Differences in expression of SLC2A11B in the iris of both phenotypes as measured by RT-qPCR. Expression levels are normalized to the expression of beta-actin (ACTB). (C) Allele imbalance for the candidate causal mutation (AKCR02000030.1:1,895,934bp) in three pigeons heterozygous for the wild-type (G) and pearl-eye (A) alleles. The bars indicate for each individual the proportion of reads supporting each allele.