OMIA:002416-8932 : Eye colour, SLC2A11B-related in Columba livia
Categories: Pigmentation phene
Links to MONDO diseases: No links.
Mendelian trait/disorder: yes
Mode of inheritance: Autosomal recessive
Considered a defect: no
Key variant known: yes
Year key variant first reported: 2021
Species-specific name: pear-eye
Species-specific symbol: tr
Species-specific description: Andrade et al. (2021): "Eye color arises from the deposition of pigments in the pigmented epithelium of the iris. ... Pigeons typically have eyes exhibiting a range of yellow and red hues, which arise from the deposition of pterin pigments in the anterior surface of the iris combined with strong vascularization [Oliphant, 1987]. In addition to the wild-type eye color phenotype, mutant phenotypes such as the pearl-eye arose during domestication [Hollander and Owen, 1939]. Electron microscopy imaging shows that pigment cells in the iris of pearl-eye pigeons are structurally identical to pigment cells in wild-type birds, but lack yellow pterin pigments (the red coloration in both eye color types is due to blood vessels) [Oliphant, 1987]."
Inheritance: Andrade et al. (2021): "Classical genetic studies indicate an autosomal recessive mode of inheritance for pearl-eye [Hollander and Owen, 1939], as presumably birds carrying two copies of the mutant allele (tr/tr) are impaired in their capacity to synthesize or deposit pterins in the iris compared to wild-type birds (Tr/Tr or Tr/tr)."
Mapping: Andrade et al. (2021): "Using a combination of genome-wide association analysis and linkage information in pedigrees, we mapped variation in eye coloration in pigeons to a small genomic region of ~8.5kb. This interval contained a single gene, SLC2A11B, which has been previously implicated in skin pigmentation and chromatophore differentiation in fish."
Molecular basis: Andrade et al. (2021) "used a combination of genetic, genomic and gene expression analyses to reveal the molecular mechanism underlying eye color variation in the domestic pigeon. ... Loss of yellow pigmentation is likely caused by a point mutation [AKCR02000030.1:1,895,934G>A] that introduces a premature STOP codon and leads to lower expression of SLC2A11B through nonsense-mediated mRNA decay."
Si et al. (2021) have identified the same variant in a different study: "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."
Maclary et al. (2021) identified the same nonsense variant in exon 3 of SLC2A11B which was previously reported by Andrade et al. (2021) and Si et al.; 2021) as likely causal variant for pearl iris colour in several pigeon breeds.
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|SLC2A11B||Columba livia||-||no genomic information (-..-)||SLC2A11B||Ensembl|
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WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.
Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.
|OMIA Variant ID||Breed(s)||Variant Phenotype||Gene||Allele||Type of Variant||Source of Genetic Variant||Reference Sequence||Chr.||g. or m.||c. or n.||p.||Verbal Description||EVA ID||Inferred EVA rsID||Year Published||PubMed ID(s)||Acknowledgements|
|1298||Pearl-eye||SLC2A11B||tr||nonsense (stop-gain)||Naturally occurring variant||AKCR02000030.1||g.1895934G>A||p.(W49X)||Andrade et al. (2021): "This mutation creates a premature STOP codon in exon 3 of the likely canonical SLC2A11B transcript."||2021||33621224|
Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.
|2021||Andrade, P., Gazda, M.A., Araújo, P.M., Afonso, S., Rasmussen, J.A., Marques, C.I., Lopes, R.J., Gilbert, M.T.P., Carneiro, M. :|
|Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates. PLoS Genet 17:e1009404, 2021. Pubmed reference: 33621224 . DOI: 10.1371/journal.pgen.1009404.|
|Andrade, P., Carneiro, M. :|
|Pterin-based pigmentation in animals. Biol Lett 17:20210221, 2021. Pubmed reference: 34403644 . DOI: 10.1098/rsbl.2021.0221.|
|Maclary, E.T., Phillips, B., Wauer, R., Boer, E.F., Bruders, R., Gilvarry, T., Holt, C., Yandell, M., Shapiro, M.D. :|
|Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia). Mol Biol Evol 38:5376-5390, 2021. Pubmed reference: 34459920 . DOI: 10.1093/molbev/msab260.|
|Si, S., Xu, X., Zhuang, Y., Gao, X., Zhang, H., Zou, Z., Luo, S.J. :|
|The genetics and evolution of eye color in domestic pigeons (Columba livia). PLoS Genet 17:e1009770, 2021. Pubmed reference: 34460822 . DOI: 10.1371/journal.pgen.1009770.|
|1987||Oliphant, L.W. :|
|Observations on the pigmentation of the pigeon iris. Pigment Cell Res 1:202-8, 1987. Pubmed reference: 3508278 . DOI: 10.1111/j.1600-0749.1987.tb00414.x.|
|1939||Hollander, WF, Owen, RD :|
|Iris pigmentation in domestic pigeons Genetica 21:408-419, 1939.|
- Created by Imke Tammen2 on 03 Sep 2021