The genetics and evolution of eye color in domestic pigeons (Columba livia)

Author summary Birds exhibit striking eye color variations, providing a unique angle for understanding avian evolution. Here we identified the genetic basis of the pearl (white) iris color in domestic pigeons (Columba livia) to a nonsense mutation W49X in SLC2A11B via whole genome sequencing and genome-wide association study (GWAS) approaches. SLC2A11B is a gene with known roles in fish pigment cells differentiation and transcriptome analysis indicated that SLC2A11B loss of function may downregulate the xanthophore-differentiation gene CSF1R and the key pteridine biosynthesis gene GCH1, resulting in the pigeon's pearl iris phenotype. The SLC2A11B variant was estimated to have originated at approximately 5,400 years ago coinciding with the onset of pigeon domestication and was then under positive selection likely associated with artificial breeding. Potentially impaired SLC2A11B was also found in six species from six distinct avian lineages. Analysis of vertebrate SLC2A11B orthologs revealed relaxed selection in the avian clade, consistent with the scenario that the SLC2A11B-involved development of dermal pigment cells likely degenerated in the presence of feather coverage. Our study sheds new light on the largely unknown genetic mechanism underlying the evolution of avian iris color variations. The eye color of birds, generally referring to the color of the iris, results from both pigmentation and structural coloration. Avian iris colors exhibit striking interspecific and intraspecific variations that correspond to unique evolutionary and ecological histories. Here, we identified the genetic basis of pearl (white) iris color in domestic pigeons (Columba livia) to explore the largely unknown genetic mechanism underlying the evolution of avian iris coloration. Using a genome-wide association study (GWAS) in 92 pigeons, we mapped the pearl iris trait to a 9 kb region containing the facilitative glucose transporter gene SLC2A11B. A nonsense mutation (W49X) leading to a premature stop codon in SLC2A11B was identified as the causal variant. Transcriptome analysis suggested that SLC2A11B loss of function may downregulate the xanthophore-differentiation gene CSF1R and the key pteridine biosynthesis gene GCH1, thus resulting in the pearl iris phenotype. Coalescence and phylogenetic analyses indicated that the mutation originated approximately 5,400 years ago, coinciding with the onset of pigeon domestication, while positive selection was likely associated with artificial breeding. Within Aves, potentially impaired SLC2A11B was found in six species from six distinct lineages, four of which associated with their signature brown or blue eyes. Analysis of vertebrate SLC2A11B orthologs revealed relaxed selection in the avian clade, consistent with the scenario that during and after avian divergence from the reptilian ancestor, the SLC2A11B-involved development of dermal chromatophores likely degenerated in the presence of feather coverage. Our findings provide new insight into the mechanism of avian iris color variations and the evolution of pigmentation in vertebrates.