OMIA 000214-9615 : Coat colour, white spotting in Canis lupus familiaris
Using a linkage analysis of "5 families with heterozygous parents and offspring that included 11 white, 6 brown, and 19 spotted dogs", each genotyped for 1500 SNPs having a genome-wide coverage (with an average spacing of 1.6Mb), Leegwater et al. (2007) mapped this locus to a region of chromosome CFA20 which contains a very likely comparative candidate gene, namely MITF.
In a landmark study, Karlsson et al. (2007) mapped the white-spotting locus to less than 1 Mb on CFA20 via one of the first Genome-Wide Association Studies (GWAS) using 27,000 SNPs on just a few (approx 20) dogs. Subsequent fine mapping implicated the positional candidate gene MITF.
By conducting a proof-of-principle across-breed GWAS on "31 cases for white spotting from 11 breeds and 31 controls from 14 breeds", each genotyped with the Affymetrix Version 2 Custom Canine SNP (comprising 49,663 SNPs), Bannasch et al. (2010) confirmed the white-spotting locus to be MITF on CFA20.
Brancalion et al. (2021) describe “a common retrotransposed pseudogene of the canine MITF gene. Using a novel mapping strategy, the pseudogene was located on CFA19 and/or CFA32. We also describe an inverted assembly contig in Canfam3.1 … . These factors should be carefully considered when mapping genotype–phenotype correlations at this locus.”Molecular basis: In the words of Karlsson et al. (2007), "Complete sequencing of the white and solid haplotypes identifies candidate regulatory mutations in the melanocyte-specific promoter of MITF". As summarised by Körberg et al. (2014), Karlsson et al. (2007) identified "a short list of three candidate mutations within or in the vicinity of the MITF-M promoter, and one in the MITF-1B exon located upstream of MITF-M. The first of these is a canine-specific short interspersed nucleotide element (SINEC-Cf element), located about 3 kb upstream of the MITF-M transcription start site (TSS). The SINE insertion was only found in dogs presenting the extreme white (sw/sw) or piebald (sp/sp) phenotypes, and was absent in Irish-spotted (si/si) and solid (S/S) dogs. . . . The second candidate (SNP#21), a SNP located approximately 1.2 kb upstream of MITF-M TSS, occurs in a highly conserved region and the A allele at this locus is associated with white spotting alleles . . . . The third polymorphism is a variable length polymorphism (Lp) approximately 100 bp upstream of the MITF-M TSS. Long variants of the Lp (LpWhite) are associated with all three white-spotting alleles (sw, sp and si), whereas all solid dogs examined carried short Lp variants .. . , [from here on named LpSolid]. The fourth candidate mutation, a 12 bp deletion in exon 1B (Exon1B_del) also showed a very strong association with white spotting. It was found on all Extreme white and Piebald chromosomes tested, but it was also found in the heterozygous state in 4 out of 76 solid dogs."
Extensive sequence comparisons of MITF in wolves and dogs enabled Körberg et al. (2014) to conclude that "the simple repeat polymorphism [Lp above] has been a target for selection during dog domestication and breed formation", that it "affects promoter activity" by affecting "cooperativity between transcription factors binding on either flanking sides of the repeat"; and hence "the simple repeat polymorphism is a key regulator of white spotting in dogs".Associated gene:
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|MITF||microphthalmia-associated transcription factor||Canis lupus familiaris||20||NC_051824.1 (22101930..21883312)||MITF||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|
|424||Coat colour, white spotting||MITF||regulatory||Naturally occurring variant||CanFam3.1||20||g.21836232_21836427delinsN||This 198bp SINEC-Cf insertion is the first of three possible regulatory variants described by Karlsson et al. (2007).||2007||17906626||The genomic location was kindly provided by Professor Claire Wade in August 2018.|
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.
|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.|
|Brancalion, L., Haase, B., Willet, C.E., Wade, C.M. :|
|Sequence variants of the canine melanocyte inducing transcription factor (MITF) locus reveal a common MITF-A processed pseudogene. Anim Genet 52:777-8, 2021. Pubmed reference: 34165209. DOI: 10.1111/age.13106.|
|Brancalion, L., Haase, B., Wade, C.M. :|
|Canine coat pigmentation genetics: a review. Anim Genet :, 2021. Pubmed reference: 34751460. DOI: 10.1111/age.13154.|
|Nord, M.E., Jensen, P. :|
|Genomic regions associated with variation in pigmentation loss in saddle tan Beagles. Genes (Basel) 12:316, 2021. Pubmed reference: 33672409. DOI: 10.3390/genes12020316.|
|2019||Dreger, D.L., Hooser, B.N., Hughes, A.M., Ganesan, B., Donner, J., Anderson, H., Holtvoigt, L., Ekenstedt, K.J. :|
|True Colors: Commercially-acquired morphological genotypes reveal hidden allele variation among dog breeds, informing both trait ancestry and breed potential. PLoS One 14:e0223995, 2019. Pubmed reference: 31658272. DOI: 10.1371/journal.pone.0223995.|
|2014||Baranowska Körberg, I., Sundström, E., Meadows, J.R., Rosengren Pielberg, G., Gustafson, U., Hedhammar, Å., Karlsson, E.K., Seddon, J., Söderberg, A., Vilà, C., Zhang, X., Åkesson, M., Lindblad-Toh, K., Andersson, G., Andersson, L. :|
|A simple repeat polymorphism in the MITF-M promoter is a key regulator of white spotting in dogs. PLoS One 9:e104363, 2014. Pubmed reference: 25116146. DOI: 10.1371/journal.pone.0104363.|
|2010||Bannasch, D., Young, A., Myers, J., Truvé, K., Dickinson, P., Gregg, J., Davis, R., Bongcam-Rudloff, E., Webster, M.T., Lindblad-Toh, K., Pedersen, N. :|
|Localization of canine brachycephaly using an across breed mapping approach. PLoS One 5:e9632, 2010. Pubmed reference: 20224736. DOI: 10.1371/journal.pone.0009632.|
|2009||Andersson, L. :|
|Genome-wide association analysis in domestic animals: a powerful approach for genetic dissection of trait loci. Genetica 136:341-9, 2009. Pubmed reference: 18704695. DOI: 10.1007/s10709-008-9312-4.|
|2007||Karlsson, E.K., Baranowska, I., Wade, C.M., Salmon Hillbertz, N.H., Zody, M.C., Anderson, N., Biagi, T.M., Patterson, N., Pielberg, G.R., Kulbokas, E.J., Comstock, K.E., Keller, E.T., Mesirov, J.P., von Euler, H., Kämpe, O., Hedhammar, A., Lander, E.S., Andersson, G., Andersson, L., Lindblad-Toh, K. :|
|Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet 39:1321-8, 2007. Pubmed reference: 17906626. DOI: 10.1038/ng.2007.10.|
|Leegwater, PA., van Hagen, MA., van Oost, BA. :|
|Localization of white spotting locus in Boxer dogs on CFA20 by genome-wide linkage analysis with 1500 SNPs. J Hered 98:549-52, 2007. Pubmed reference: 17548862. DOI: 10.1093/jhered/esm022.|
|2006||Rothschild, MF., Van Cleave, PS., Glenn, KL., Carlstrom, LP., Ellinwood, NM. :|
|Association of MITF with white spotting in Beagle crosses and Newfoundland dogs. Anim Genet 37:606-7, 2006. Pubmed reference: 17121617. DOI: 10.1111/j.1365-2052.2006.01534.x.|
|2004||van Hagen, MA., van der Kolk, J., Barendse, MA., Imholz, S., Leegwater, PA., Knol, BW., van Oost, BA. :|
|Analysis of the inheritance of white spotting and the evaluation of KIT and EDNRB as spotting loci in Dutch boxer dogs. J Hered 95:526-31, 2004. Pubmed reference: 15475400. DOI: 10.1093/jhered/esh083.|
|2000||Metallinos, D., Rine, J. :|
|Exclusion of EDNRB and KIT as the basis for white spotting in Border Collies. Genome Biol 1:research0004.1-4, 2000. Pubmed reference: 11178229.|
|1990||Pape, H. :|
|The Inheritance of the Piebald Spotting Pattern and Its Variation in Holstein-Friesian Cattle and in Landseer- Newfoundland Dogs Genetica 80:115-128, 1990. Pubmed reference: 2323567.|
|1957||Little, C.C. :|
|The Inheritance of Coat Color in Dogs Comstock Publishing Associates, Cornell University Press, Ithaca, NY :, 1957.|
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