OMIA:001743-9823 : Coat colour, patch in Sus scrofa
Categories: Pigmentation phene
Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 172800 (trait) , 164920 (gene)
Links to MONDO diseases: No links.
Mendelian trait/disorder: yes
Mode of inheritance: Autosomal co-dominant
Considered a defect: no
Key variant known: yes
Year key variant first reported: 1998
Species-specific symbol: I^p
Species-specific description: This trait is characterised by "white patches and fully colored patches separated by sharp borders . . . Patch animals were white but with fully wild-colored patches, that is, both skin and all hairs were colored; the proportion of colored coat was variable and covered between 10% and 90% of the body" (Marklund et al., 1998)
History: This trait was first reported by Johansson et al. (1992) in the Swedish gene-mapping reference pedigree, i.e. in the F2 offspring from crosses between European wild boars and Swedish Yorkshire sows. In these offspring "There was a varying expression of patch, ranging from almost fully colored individuals with only a white belly to almost completely white animals with only a small patch of wild-colored coat." (Johansson et al., 1992)
Inheritance: Segregation analysis in the Swedish gene-mapping reference pedigree suggested to Johansson et al. (1992) "that patch is controlled by a variant allele [at the dominant white locus], tentatively denoted I^p, which is recessive to I [dominant white] but dominant to i [wild type]." The results of Rubin et al. (2012) indicate four alleles at this locus, namely Wild-type, Dominant white (OMIA 000209-9825), Patch (this entry) and Belt (OMIA 001745-9825). (with thanks to Leif Andersson)
Mapping: Using RFLPs for two comparative (from mouse) candidate genes, namely ALB and PDGFRA, Johansson et al. (1992) reported that the dominant white/patch locus is very tightly linked to both ALB and PDGFRA (theta=0), which are on chromosome SSC8. A third comparative candidate gene, closely linked to ALB and PDGFRA in mice, could not be mapped in pig because no RFLP could be detected. However, given its close linkage to ALB and PDGFRA in mice and in humans, KIT was also a very strong comparative positional candidate gene for porcine dominant white/patch.
Molecular basis: Marklund et al. (1998) showed that, like the dominant white allele, the patch allele is a duplication of KIT. The difference between the two alleles is that the dominant white allele also has a "G to A substitution in the first nucleotide of intron 17 disrupting the highly conserved GT pair at the 5′ splice site" resulting in the skipping of exon 17, whereas the patch allele does not have this substitution. From the results of genome sequencing of tens of pigs, Rubin et al. (2012) confirmed that the patch allele comprises a 450kb duplication that includes KIT (roughly in the middle).
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|KIT||v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog||Sus scrofa||8||NC_010450.4 (41402334..41492306)||KIT||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|
|715||Coat colour, patch||KIT||duplication||Naturally occurring variant||8||the patch allele comprises a 450kb duplication that includes KIT (roughly in the middle)||1998||9724328|
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.
|2012||Rubin, C.J., Megens, H.J., Barrio, A.M., Maqbool, K., Sayyab, S., Schwochow, D., Wang, C., Carlborg, O., Jern, P., Jørgensen, C.B., Archibald, A.L., Fredholm, M., Groenen, M.A., Andersson, L. :|
|Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci U S A :, 2012. Pubmed reference: 23151514 . DOI: 10.1073/pnas.1217149109.|
|1998||Marklund, S., Kijas, J., Rodriguezmartinez, H., Ronnstrand, L., Funa, K., Moller, M., Lange, D., Edforslilja, I., Andersson, L. :|
|Molecular basis for the dominant white phenotype in the domestic pig Genome Research 8:826-833, 1998. Pubmed reference: 9724328 .|
- Changed by Frank Nicholas on 24 Nov 2012
- Created by Frank Nicholas on 24 Nov 2012
- Changed by Frank Nicholas on 25 Nov 2012