OMIA:002200-9915 : Hyperpigmentation, ASIP-related in Bos indicus (indicine cattle (zebu))

In other species: chicken

Categories: Pigmentation phene

Possibly relevant human trait(s) and/or gene(s) (MIM number): 600201 (gene)

Links to MONDO diseases: No links.

Mendelian trait/disorder: yes

Considered a defect: no

Key variant known: yes

Year key variant first reported: 2021

Species-specific name: darkness of hair coat

Species-specific description: Trigo et al. (2021): "Our results indicate that the variant ASIP sequence causes darker coat pigmentation on specific parts of the body, most likely through a decreased expression of ASIP and consequently an increased production of eumelanin." Trigo et al. (2023) investigated "the extent of spread of ASIP-SV1 in different cattle populations. Of 216 sequences analyzed, 63 zebu (45.9%) and five taurine (6.3%) animals had at least one copy of ASIP-SV1. Four of the taurine animals presenting the SV were Romagnola cattle, a breed with history of zebu introgression. The remaining taurine animal was a Simmental, a breed frequently used in crossbreeding. These data provide evidence that ASIP-SV1 is commonly found in zebu populations, in addition to taurine animals with zebu admixture."

Mapping: Trigo et al. (2021) "performed a genome-wide association study (GWAS) for DHC [darkness of hair coat] using data from 432 Nellore bulls that were genotyped for more than 777 k single nucleotide polymorphism (SNP) markers. A single major association signal was detected in the vicinity of the agouti signaling protein gene (ASIP)."

Molecular basis: Trigo et al. (2021): "The analysis of whole-genome sequence (WGS) data from 21 bulls revealed functional variants that are associated with DHC, including a structural rearrangement involving ASIP (ASIP-SV1). We further characterized this structural variant using Oxford Nanopore sequencing data from 13 Australian Brahman heifers, which share ancestry with Nellore cattle; we found that this variant originates from a 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons."

Genetic engineering: Unknown
Have human generated variants been created, e.g. through genetic engineering and gene editing

Breeds: Brahman (Cattle) (VBO_0000159), Nelore (Cattle) (VBO_0000318).
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
ASIP Bos indicus - no genomic information (-..-) ASIP 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
1321 Brahman (Cattle) Nellore, India (Sheep) Darkness of hair coat ASIP delins, gross (>20) Naturally occurring variant 13 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons (Trigo et al.2021) 2021 33910501

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2023). OMIA:002200-9915: Online Mendelian Inheritance in Animals (OMIA) [dataset].


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.

2023 Trigo, B.B., Alves, N.F., Milanesi, M., Garcia, J.F., Terefe, E., Hanotte, O., Tijjani, A., Utsunomiya, Y.T. :
A structural variant at ASIP associated with the darkness of hair coat is found in multiple zebu cattle populations. Anim Genet , 2023. Pubmed reference: 37313778. DOI: 10.1111/age.13333.
2021 Trigo, B.B., Utsunomiya, A.T.H., Fortunato, A.A.A.D., Milanesi, M., Torrecilha, R.B.P., Lamb, H., Nguyen, L., Ross, E.M., Hayes, B., Padula, R.C.M., Sussai, T.S., Zavarez, L.B., Cipriano, R.S., Caminhas, M.M.T., Lopes, F.L., Pelle, C., Leeb, T., Bannasch, D., Bickhart, D., Smith, T.P.L., Sonstegard, T.S., Garcia, J.F., Utsunomiya, Y.T. :
Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genet Sel Evol 53:40, 2021. Pubmed reference: 33910501. DOI: 10.1186/s12711-021-00633-2.

Edit History

  • Created by Imke Tammen2 on 17 Jun 2021
  • Changed by Imke Tammen2 on 15 Jun 2023