OMIA 000214-9913 : Coat colour, white spotting in Bos taurus
Hofstetter et al. (2019) "hypothesize[d] that rs722765315 [variant g.31908435G>A in MITF] represents the most likely causative variant for the white-spotting phenotype observed in Brown Swiss cattle. Presence of the mutant allele in a heterozygous or homozygous state supports a dominant mode of inheritance with incomplete penetrance and results in a variable extent of coat colour depigmentation."
From "the largest GWAS of white spotting to date", conducted on New Zealand cattle (Jersey, Holstein-Friesian and their cross), Jivinji et a. (2019) "extend[ed] those [results] of previous studies that reported KIT as a likely causal gene for white spotting, and report novel associations between candidate causal mutations in both the MITF and PAX3 genes."Breeds: Brown Swiss, Holstein, Holstein-Friesian, Jersey, Simmental. Associated genes:
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|MITF||microphthalmia-associated transcription factor||Bos taurus||22||NC_037349.1 (31843514..31614654)||MITF||Homologene, Ensembl, NCBI gene|
|PAX3||paired box 3||Bos taurus||2||NC_037329.1 (110471285..110369553)||PAX3||Homologene, Ensembl, NCBI gene|
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 headers.
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.
|Breed(s)||Variant Phenotype||Gene||Allele||Type of Variant||Reference Sequence||Chr.||g. or m.||c. or n.||p.||Verbal Description||EVA ID||Inferred EVA rsID||Year Published||PubMed ID(s)||Acknowledgements|
|Holstein Simmental||White spotting||MITF||regulatory||ARS-UCD1.2||22||g.31650821T>A||c.33+112A>T||UMD3.1 position is g.31769189||rs210634530||2012||22486495||Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.|
|Brown Swiss||White spotting||MITF||regulatory||ARS-UCD1.2||22||g.31790063G>A||c.104+53185C>T||FN 190425: The Ensembl entry for rs722765315 lists two transcripts: ENSBTAT00000067269.1:c.104+53185C>T and ENSBTAT00000076082.1:c.-53+31498C>T||rs722765315||2019||30506810||The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.|
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.
|2019||Hofstetter, S., Seefried, F., Häfliger, I.M., Jagannathan, V., Leeb, T., Drögemüller, C., Hofstetter, S., Seefried, F., Häfliger, I.M., Jagannathan, V., Leeb, T., Drögemüller, C. :|
|A non-coding regulatory variant in the 5'-region of the MITF gene is associated with white-spotted coat in Brown Swiss cattle. Anim Genet 50:27-32, 2019. Pubmed reference: 30506810. DOI: 10.1111/age.12751.|
|Jivanji, S., Worth, G., Lopdell, T.J., Yeates, A., Couldrey, C., Reynolds, E., Tiplady, K., McNaughton, L., Johnson, T.J.J., Davis, S.R., Harris, B., Spelman, R., Snell, R.G., Garrick, D., Littlejohn, M.D. :|
|Genome-wide association analysis reveals QTL and candidate mutations involved in white spotting in cattle. Genet Sel Evol 51:62, 2019. Pubmed reference: 31703548. DOI: 10.1186/s12711-019-0506-2.|
|2013||Jansen, S., Aigner, B., Pausch, H., Wysocki, M., Eck, S., Benet-Pagès, A., Graf, E., Wieland, T., Strom, T.M., Meitinger, T., Fries, R. :|
|Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage. BMC Genomics 14:446, 2013. Pubmed reference: 23826801. DOI: 10.1186/1471-2164-14-446.|
|2012||Fontanesi, L., Scotti, E., Russo, V. :|
|Haplotype variability in the bovine MITF gene and association with piebaldism in Holstein and Simmental cattle breeds. Anim Genet 43:250-6, 2012. Pubmed reference: 22486495. DOI: 10.1111/j.1365-2052.2011.02242.x.|
|2010||Hayes, B.J., Pryce, J., Chamberlain, A.J., Bowman, P.J., Goddard, M.E. :|
|Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits. PLoS Genet 6:e1001139, 2010. Pubmed reference: 20927186. DOI: 10.1371/journal.pgen.1001139.|
|2009||Liu, L., Harris, B., Keehan, M., Zhang, Y. :|
|Genome scan for the degree of white spotting in dairy cattle. Anim Genet 40:975-7, 2009. Pubmed reference: 19531114. DOI: 10.1111/j.1365-2052.2009.01936.x.|
|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.|
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