OMIA:001259-9031 : Feather colour, chocolate in Gallus gallus (chicken) |
Categories: Pigmentation phene
Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 115501 (gene) , 612271 (trait)
Links to MONDO diseases: No links.
Mendelian trait/disorder: yes
Mode of inheritance: Z-linked
Considered a defect: no
Key variant known: yes
Year key variant first reported: 2018
Species-specific symbol: choc
Inheritance: Carefoot (1996) showed that this trait is Z-linked recessive. This was confirmed independently by Li et al. (2018).
Mapping: Li et al. (2019) linkage-mapped the choc trait to "a 3.57‐Mb region defined by rs16106682 (28.27 Mb) and rs14778077 (31.84 Mb) on chromosome Z" that includes the TYRP1 gene.
Molecular basis: Li et al. (2019) sequenced the positional (Z-linked) candidate gene TYRP1 and discovered that "The only unique sequence polymorphism found in chocolate animals was a missense variation with a G to T change at position 30,830,367 bp (c.640C > A for TYRP1 coding sequence) leading to a His214Asn change in TYRP1. . . . Genotyping this SNP (ChrZ:30,830,367 bp) in the entire VT mapping population, in the 77 BC1 females from INRA (41 chocolate feathered and 36 black feathered), and in 428 non‐chocolate chickens from 118 different stocks or populations of experimental lines . . . , showed its complete association with choc, consistent with the hypothesis that it is the causal mutation for the chocolate phenotype."
Genetic engineering:
Unknown
Have human generated variants been created, e.g. through genetic engineering and gene editing
Breed:
Orpington (Chicken) (VBO_0000588).
Breeds in which the phene has been documented. For breeds in which a likely causal variant has been documented, see the variant table below
Associated gene:
| Symbol | Description | Species | Chr | Location | OMIA gene details page | Other Links |
|---|---|---|---|---|---|---|
| TYRP1 | tyrosinase-related protein 1 | Gallus gallus | Z | NC_052572.1 (31227860..31238589) | TYRP1 | Homologene, Ensembl , NCBI gene |
Variants
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1057 | Orpington (Chicken) Wyandotte (Chicken) | Chocolate feathered | TYRP1 | missense | Naturally occurring variant | GRCg6a | Z | g.30830300G>T | c.640C>A | p.(H214N) | 2019 | 30457703 |
Cite this entry
Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2023). OMIA:001259-9031: Online Mendelian Inheritance in Animals (OMIA) [dataset]. https://omia.org/. https://doi.org/10.25910/2AMR-PV70
References
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.
| 2020 | Andersson, L., Bed’hom, B., Chuong, CM., Inaba, M.Inaba, M., Okimoto, R.Okimoto, R., Tixier-Boichard, M. : |
| The genetic basis for pigmentation phenotypes in poultry In S. E. Aggrey, H. Zhou, M. Tixier-Boichard, & D. D. Rhoads (Eds.), Advances in Poultry Genetics and Genomics. Cambridge, UK: Burleigh Dodds Science Publishing. , 2020. | |
| 2019 | Li, J., Bed'hom, B., Marthey, S., Valade, M., Dureux, A., Moroldo, M., Péchoux, C., Coville, J.L., Gourichon, D., Vieaud, A., Dorshorst, B., Andersson, L., Tixier-Boichard, M., Li, J., Bed'hom, B., Marthey, S., Valade, M., Dureux, A., Moroldo, M., Péchoux, C., Coville, J.L., Gourichon, D., Vieaud, A., Dorshorst, B., Andersson, L., Tixier-Boichard, M., Li, J., Bed'hom, B., Marthey, S., Valade, M., Dureux, A., Moroldo, M., Péchoux, C., Coville, J.L., Gourichon, D., Vieaud, A., Dorshorst, B., Andersson, L., Tixier-Boichard, M., Li, J., Bed'hom, B., Marthey, S., Valade, M., Dureux, A., Moroldo, M., Péchoux, C., Coville, J.L., Gourichon, D., Vieaud, A., Dorshorst, B., Andersson, L., Tixier-Boichard, M. : |
| A missense mutation in TYRP1 causes the chocolate plumage color in chicken and alters melanosome structure. Pigment Cell Melanoma Res 32:381-390, 2019. Pubmed reference: 30457703. DOI: 10.1111/pcmr.12753. | |
| 1996 | Carefoot, W.C. : |
| Chocolate - a sex-linked recessive plumage colour mutant of the domestic fowl British Poultry Science 37:867-868, 1996. Pubmed reference: 8894230. DOI: 10.1080/00071669608417915. |
Edit History
- Created by Frank Nicholas on 06 Sep 2005
- Changed by Frank Nicholas on 26 Mar 2019
- Changed by Frank Nicholas on 27 Mar 2019
- Changed by Frank Nicholas on 30 May 2019
- Changed by Imke Tammen2 on 10 Nov 2023