OMIA:001972-9793 : Coat colour, dun in Equus asinus
In other species: horse
Categories: Pigmentation phene
Possibly relevant human trait(s) and/or gene(s) (MIM number): 601621 (gene)
Links to MONDO diseases: No links.
Mendelian trait/disorder: yes
Mode of inheritance: Autosomal dominant
Considered a defect: no
Key variant known: yes
Year key variant first reported: 2020
History: Wang et al. (2020): "Coat color is one of the main traits that were selected during the domestication process. The base color of donkeys can be black or red (chestnut) [Sponenberg, 2009]. There is a dominant Dun allele causing strong dilution of the pigmentation, which becomes gray or light chestnut/rose Dun, in contrast to the recessive non-Dun allele (black or chestnut, as mentioned previously). The Dun coat is considered to be the ancestral wild type [Groves, 1986], while the non-Dun coat is found exclusively in domestic animals."
Mapping: Wang et al. (2020) "de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. ... Photos and records were used to determine the coat color of 44 donkeys, which were divided into two groups, i.e., Dun (23 gray donkeys) and non-Dun (21 black donkeys). In the two compared groups (Dun vs. non-Dun), we calculated π and Tajima’s D in the major selective sweep mapping to chromosome 8 (~ 42.6 Mb)."
Molecular basis: Wang et al. (2020) "found only one indel CT/C− located at chr8:42,742,556 (CT was the genotype of the reference genome), which segregated perfectly with the non-Dun phenotype. ... the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition. .... The alignment of sequences containing the non-Dun1 allele of horse with the donkey sequence that harbors the 1 bp deletion mentioned previously indicated that these sequences are homologous."
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|TBX3||T-box 3||Equus asinus||8||NC_052184.1 (42710482..42732232)||TBX3||Homologene, Ensembl , NCBI gene|
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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|
|1277||Non-dun||TBX3||deletion, small (<=20)||Naturally occurring variant||8||g.42742557delT||"This 1 bp deletion (chr8:g.42742556 CT>C−) is located ~18.6 kb downstream of the transcription start site of the TBX3 gene." (Wang et al., 2020)||2020||33293529|
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||Wang, C., Li, H., Guo, Y., Huang, J., Sun, Y., Min, J., Wang, J., Fang, X., Zhao, Z., Wang, S., Zhang, Y., Liu, Q., Jiang, Q., Wang, X., Guo, Y., Yang, C., Wang, Y., Tian, F., Zhuang, G., Fan, Y., Gao, Q., Li, Y., Ju, Z., Li, J., Li, R., Hou, M., Yang, G., Liu, G., Liu, W., Guo, J., Pan, S., Fan, G., Zhang, W., Zhang, R., Yu, J., Zhang, X., Yin, Q., Ji, C., Jin, Y., Yue, G., Liu, M., Xu, J., Liu, S., Jordana, J., Noce, A., Amills, M., Wu, D.D., Li, S., Zhou, X., Zhong, J. :|
|Donkey genomes provide new insights into domestication and selection for coat color. Nat Commun 11:6014, 2020. Pubmed reference: 33293529 . DOI: 10.1038/s41467-020-19813-7.|
|2009||Sponenberg, D. P. :|
|Equine Color Genetics, Wiley-Blackwell; 3rd edition :, 2009.|
|1986||Groves, C.P. :|
|The taxonomy, distribution and adaptations of recent equids. in 'Equids in the Ancient World' (R. H. Meadow and H. P. Uerpmann, eds.), Dr. Ludwig Reichert Verlag, Wiesbaden. :11-65, 1986.|
- Changed by Imke Tammen2 on 17 Dec 2020
- Created by Imke Tammen2 on 17 Dec 2020