OMIA:002200-9915 : Hyperpigmentation, ASIP-related in Bos indicus (indicine cattle (zebu)) |
In other species: chicken
Categories: Pigmentation phene
Links to possible relevant human trait(s) and/or gene(s) in OMIM: 600201 (gene)
Mendelian trait/disorder: yes
Disease-related: 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."
Breeds:
Brahman (Cattle) (VBO_0000159),
Nelore (Cattle) (VBO_0000318).
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:
| Symbol | Description | Species | Chr | Location | OMIA gene details page | Other Links |
|---|---|---|---|---|---|---|
| ASIP | Bos indicus | - | no genomic information (-..-) | ASIP | Ensembl |
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 | 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]. 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.
| 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 54:544-548, 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