Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia)

Abstract

The iris of the eye shows striking color variation across vertebrate species, and may play important roles in crypsis and communication. The domestic pigeon (Columba livia) has three common iris colors, orange, pearl (white), and bull (dark brown), segregating in a single species, thereby providing a unique opportunity to identify the genetic basis of iris coloration. We used comparative genomics and genetic mapping in laboratory crosses to identify two candidate genes that control variation in iris color in domestic pigeons. We identified a nonsense mutation in the solute carrier SLC2A11B that is shared among all pigeons with pearl eye color, and a locus associated with bull eye color that includes EDNRB2, a gene involved in neural crest migration and pigment development. However, bull eye is likely controlled by a heterogeneous collection of alleles across pigeon breeds. We also found that the EDNRB2 region is associated with regionalized plumage depigmentation (piebalding). Our study identifies two candidate genes for eye colors variation, and establishes a genetic link between iris and plumage color, two traits that vary widely in the evolution of birds and other vertebrates.

Keywords: QTL mapping; comparative genomics; iris color; pigeon; pigment.

Fig. 1.

A single genomic locus is associated with pearl iris color in domestic pigeons. (A) Domestic pigeons typically have one of three major iris colors: the wild-type orange, pearl, or bull. (B) Genome-wide QTL scan for pearl eye in the Archangel x Old Dutch Capuchin cross. Red line indicates 5% genome-wide significance threshold. Insets: Archangel (left) and Capuchin (right) founders. (C) Eye color phenotypes of F₂ progeny with different genotypes at the QTL peak marker. Arc, allele from the Archangel founder. Cap, allele from the Capuchin founder. (D) Whole-genome pF_ST comparisons of orange-eyed and pearl-eyed pigeons. Gray dots represent SNPs, with different shades indicating different genomic scaffolds. Dashed red line indicates genome-wide significance threshold. (E) Genomic context of the pearl eye candidate region. Gene models for the region are shown in gray. SNPs in coding regions are shown in red, SNPs in noncoding regions are shown in blue. The minimal candidate interval, bounded on the left by the end of the haplotype identified by pF_ST and on the right by F₂ recombinants (see supplementary fig. S1, Supplementary Material online) is defined by gray shading. (F) Alignment of DNA (top) and predicted protein (bottom) sequences of SLC2A11B for pearl-eyed and orange-eyed pigeons. The start codon is highlighted in green. The DNA polymorphism at position ScoHet5_1307:1895934 is marked in red (pearl allele) or blue (orange allele); the resulting stop codon in the pearl allele is highlighted in red.

Fig. 2.

A single genomic locus is associated with bull eye color in two F₂ intercrosses. (A) F₂ offspring from an intercross between a Pomeranian Pouter and a Scandaroon have either bull (left two images) or orange (right two images) eyes. (B) F₂ offspring from an intercross between an Archangel and an Old Dutch Capuchin have orange (left), pearl (center), or bull (right) eyes. (C) Genome-wide QTL scan of the Pomeranian Pouter x Scandaroon cross for bull eye. Red line indicates 5% genome-wide significance threshold. (D) Iris color phenotype counts for each genotype at the bull eye peak marker from the Pomeranian Pouter x Scandaroon cross. Pom, allele from Pomeranian Pouter founder. Scan, allele from Scandaroon founder. (E) Genome-wide QTL scan of the Archangel x Old Dutch Capuchin cross for bull eye. Red line indicates 5% genome-wide significance threshold. (F) Iris color phenotype counts for each genotype at the bull eye peak marker from the Archangel x Capuchin cross. Arc, allele from the Archangel founder. Cap, allele from the Capuchin founder. (G) Whole-genome pF_ST comparisons of bull-eyed birds to birds with nonbull (orange or pearl) eyes. Dashed red line indicates 5% threshold for genome-wide significance.

Fig. 3.

Bull eye color is associated with white plumage in an F₂ intercross. (A) Examples of standard plumage patterning for the Pomeranian Pouter (left) and Scandaroon (right) breeds. Photos by Layne Gardner, used with permission. (B) Examples of variable piebald plumage patterning in Pomeranian Pouter x Scandaroon F₂ offspring. (C–E) Boxplots of association between eye color and proportion of white plumage on the (C) lateral right head, (D) dorsal right wing, and (E) lateral right neck of F₂ birds. **, P ≤ 0.0001; *, 0.0001 < P ≤ 0.01; n.s., P > 0.01. Boxes span from the first to third quartile of each data set, with lines indicating the median. Whiskers span up to 1.5× the interquartile range. (F–H) QTL scans for proportion of white plumage (left side of the panel) and proportion of white plumage by genotype at the peak marker (right) for (F) lateral right head, (G) dorsal right wing, and (H) lateral right neck. Red line, 5% genome-wide significance threshold.