Categories: Pigmentation phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 115501 (gene) , 612271 (trait)

Mendelian trait/disorder: yes

Mode of inheritance: Z-linked

Disease-related: 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."
Kinoshita et al. (2024) created TYRP1 knockout chicken using CRISPR/Cas9 technology. This study involves gene edited or genetically modified organisms (GMO).

Genetic engineering: Yes - in addition to the occurrence of natural variants, variants have been created artificially, e.g. by genetic engineering or gene editing
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. (If a likely causal variant has been documented for the phene, see the variant table breeds in which the variant has been reported).

Associated gene: