OMIA:002200-9915 : Hyperpigmentation, ASIP-related in Bos indicus
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."
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), Nellore, India (Sheep) (VBO_0016063).
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|ASIP||Bos indicus||-||no genomic information (-..-)||ASIP||Ensembl|
By default, variants are sorted chronologically by year of publication, to provide a historical perspective.
Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending
order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column
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|
|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.|
- Created by Imke Tammen2 on 17 Jun 2021