GEPHE SUMMARY
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Gephebase Gene
Entry Status
Published
GepheID
GP00002367
Main curator
Santos
PHENOTYPIC CHANGE
Trait Category
Trait
Trait State in Taxon A
Orange iris color
Trait State in Taxon B
Pearl (white) iris color
Ancestral State
Taxon A
Taxonomic Status
Taxon A
Latin Name
Common Name
rock pigeon
Synonyms
Columba livia domestica; rock pigeon; carrier pigeon; domestic pigeon; rock dove; Columba livia Gmelin, JF, 1789
Rank
species
Lineage
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erygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba
Parent
NCBI Taxonomy ID
is Taxon A an Infraspecies?
Yes
Taxon A Description
orange-eyed Archangel domestic pigeon
Taxon B
Latin Name
Common Name
rock pigeon
Synonyms
Columba livia domestica; rock pigeon; carrier pigeon; domestic pigeon; rock dove; Columba livia Gmelin, JF, 1789
Rank
species
Lineage
Show more ...
erygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba
Parent
NCBI Taxonomy ID
is Taxon B an Infraspecies?
Yes
Taxon B Description
pearl-eyed Old Dutch Capuchin domestic pigeon
GENOTYPIC CHANGE
Generic Gene Name
slc2a11b
Synonyms
slc2a11b; SO:0001217
String
-
Sequence Similarities
-
GO - Molecular Function
GO - Biological Process
GO - Cellular Component
GO:0016020 : membrane
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UniProtKB
Danio rerio
Danio rerio
Presumptive Null
Molecular Type
Aberration Type
SNP Coding Change
Nonsense
Molecular Details of the Mutation
"The premature stop codon in pearl-eyed pigeons falls in exon 3 of SLC2A11B, and is predicted to severely truncate the resulting protein from 504 to 57 amino acids."
"Based on genotypes at the two coding SNPs in the pearl eye haplotype, we found that gene expression in embryo head samples only shows changes associated with the pearl eye haplotype in SLC2A11B, and not in any other genes within 15 kb of the pearl eye haplotype, further supporting SLC2A11B as the primary candidate for the pearl eye phenotype (supplementary fig. S3A, Supplementary Material online). Embryo heads homozygous for the pearl allele show a significant reduction in SLC2A11B expression (P = 3.94 × 10−6, two-tailed t-test; supplementary fig. S3B, Supplementary Material online). Analysis of read distribution within the SLC2A11B gene shows a decrease in spliced reads specifically within the first three annotated exons, suggesting that alternative splicing or nonsense-mediated decay may be occurring (supplementary fig. S3D, Supplementary Material online)."
"Based on genotypes at the two coding SNPs in the pearl eye haplotype, we found that gene expression in embryo head samples only shows changes associated with the pearl eye haplotype in SLC2A11B, and not in any other genes within 15 kb of the pearl eye haplotype, further supporting SLC2A11B as the primary candidate for the pearl eye phenotype (supplementary fig. S3A, Supplementary Material online). Embryo heads homozygous for the pearl allele show a significant reduction in SLC2A11B expression (P = 3.94 × 10−6, two-tailed t-test; supplementary fig. S3B, Supplementary Material online). Analysis of read distribution within the SLC2A11B gene shows a decrease in spliced reads specifically within the first three annotated exons, suggesting that alternative splicing or nonsense-mediated decay may be occurring (supplementary fig. S3D, Supplementary Material online)."
Experimental Evidence
| Taxon A | Taxon B | Position | |
|---|---|---|---|
| Codon | TGG | TGA | - |
| Amino-acid | Trp | STP | - |
Main Reference
Authors
Maclary ET; Phillips B; Wauer R; Boer EF; Bruders R; Gilvarry T; Holt C; Yandell M; et al.
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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.
© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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