OMIA:001216-9615 : Coat colour, roan in Canis lupus familiaris
In other species: cattle , horse , pig , goat , sheep , alpaca
Categories: Pigmentation phene
Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 184745 (gene) , 611664 (trait)
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 description: see also: OMIA 002264-9615 : Coat colour, ticked in Canis lupus familiaris
Mapping: Brancalion et al. (2021) "applied genome-wide association to compare English Cocker Spaniels [ECS] of roan phenotype (N = 34) with parti-color (non-roan) English Cocker Spaniels (N = 9) .... An interval of genome‐wide significant association with roan coat color spans CFA38:10 268 280–11 341,635 (canfam3.1). ... Association over the denser marker set revealed the strongest association at CFA38:11 069 051G>A (Praw = 8.0 × 10−8) for roan vs. parti‐color in ECSs. ... Among ESSs [English Springer Spaniel], two markers demonstrated indicative association with ticked vs. clear: CFA38:11 122 467G>T (Praw = 1.7 × 10−5) and CFA38 11 124 294A>C (Praw = 1.7 × 10−5). ... In Spaniels, the haplotypes work as an allelic series including alleles (t, recessive clear; T, dominant ticked/parti‐color; and TR, incomplete dominant roan) to control the appearance of pigmented spots or flecks in otherwise white areas of the canine coat."
Kawakami et al. (2021) identified the same "genomic region on chromosome 38 that is strongly associated with a mottled coat pattern (roaning) by genome-wide association study" in Wirehaired Pointing Griffons and Australian Cattle Dogs.
Molecular basis: Brancalion et al. (2021): "The roan (TR) haplotype is diverged from the reference/clear haplotype at four putative functional sites. Two are missense variants CFA38:g.11 085 443G>A and CFA38:g.11 111 286C>T ... . By analysis of regional coverage in representative individuals, we identified a duplicated DNA segment (11 398 bp) lying within the 67th intron of USH2A and spanning CFA38:11 131 841–11 143 239 (canfam3.1), which is unique to the TR [roan] haplotype ... . Subsequent testing for the presence of the PCR product capturing the junction between the duplicated segments identified the product in roan ECSs [English Cocker Spaniel], all Dalmatians (typically described as evenly spotted), German Short‐haired Pointer (typically roan) and Australian Cattle Dogs (typically roan). ... DBVC coverage data (Fig. S1) show the presence of a VNTR mutation at CFA38:11 112 907–11 113 501. This variant lies close to an intron–exon boundary (ENSCAFG00000010731.4 exon 62/71) and it may affect the phenotypic expression of the USH2A gene."
Kawakami et al. (2021) identified the same duplication in Wirehaired Pointing Griffons and Australian Cattle Dogs: a "putative causal variant in this region, an 11-kb tandem duplication (11,131,835–11,143,237) characterized by sequence read coverage and discordant reads of whole-genome sequence data, microarray probe intensity data, and a duplication-specific PCR assay. The tandem duplication is in an intronic region of usherin gene (USH2A), which was perfectly associated with roaning but absent in non-roaned dogs. ... Surprisingly, all Dalmatians (N = 262) carried the duplication embedded in identical or similar haplotypes with roaned dogs, indicating this region as a shared target of selection during the breed’s formation. We propose that the Dalmatian’s unique spots were a derived coat pattern by establishing a novel epistatic interaction between roaning “R-locus” on chromosome 38 and an uncharacterized modifier locus."
Breeds: Australian Cattle Dog, English Cocker Spaniel, German Shorthaired Pointer, Wirehaired Griffon.
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|USH2A||Usher syndrome 2A (autosomal recessive, mild)||Canis lupus familiaris||38||NC_051842.1 (11776697..11089431)||USH2A||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|
|1300||Australian Cattle Dog Dalmatian English Cocker Spaniel German Shorthaired Pointer Wirehaired Griffon||Roan||USH2A||T^R||duplication||Naturally occurring variant||CanFam3.1||38||Brancalion et al. (2021) "identified a duplicated DNA segment (11 398 bp) lying within the 67th intron of USH2A and spanning CFA38:11131841–11143239 (canfam3.1)". Kawakami et al. (2021) identified the same duplication: "an 11-kb tandem duplication (11,131,835–11,143,237)"||2021||33539602 33755696|
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.
|2022||[No authors listed] :|
|Canine coat pigmentation genetics: a review. Anim Genet 53:474-475, 2022. Pubmed reference: 35510419 . DOI: 10.1111/age.13185.|
|Brancalion, L., Haase, B., Wade, C.M. :|
|Canine coat pigmentation genetics: a review. Anim Genet 53:33-34, 2022. Pubmed reference: 34751460 . DOI: 10.1111/age.13154.|
|2021||Brancalion, L., Haase, B., Mazrier, H., Willet, C.E., Lindblad-Toh, K., Lingaas, F., Wade, C.M. :|
|Roan, ticked and clear coat patterns in the canine are associated with three haplotypes near usherin on CFA38. Anim Genet 52:198-207, 2021. Pubmed reference: 33539602 . DOI: 10.1111/age.13040.|
|Kawakami, T., Jensen, M.K., Slavney, A., Deane, P.E., Milano, A., Raghavan, V., Ford, B., Chu, E.T., Sams, A.J., Boyko, A.R. :|
|R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting. PLoS One 16:e0248233, 2021. Pubmed reference: 33755696 . DOI: 10.1371/journal.pone.0248233.|
|2010||Bunbury-Cruikshank, L., Lantz, C., Perloski, M., Våge, J., Willet, C., Young, A., Andersson, L., Bannasch, DL., Distl, O., Lingaas, F., Linblad-Toh, K., Wade, C. :|
|Ticking and roan in the canine are controlled by the same novel region. Fifth International Conference on Advances in Canine and Feline Genomics and Inherited Disease 23-25 Sept. Baltimore :, 2010.|
|1957||Little, C.C. :|
|The Inheritance of Coat Color in Dogs Comstock Publishing Associates, Cornell University Press, Ithaca, NY :, 1957.|
- Created by Imke Tammen2 on 25 Feb 2021
- Changed by Imke Tammen2 on 06 Apr 2021
- Changed by Imke Tammen2 on 08 Apr 2021