OMIA 001259-9031 : Feather colour, chocolate in Gallus gallus

Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 115501 (gene) , 612271 (trait)

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."

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.

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
Orpington Wyandotte Chocolate feathered TYRP1 missense Naturally occurring variant GRCg6a Z g.30830300G>T c.640C>A p.(H214N) 2019 30457703

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