OMIA:001745-9823 : Coat colour, white belt, KIT-related 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 dominant
Considered a defect: no
Key variant known: yes
Year key variant first reported: 2012
Species-specific symbol: I^Be
History: This trait was first studied by Spillman (1907).
Inheritance: Spillman (1907) postulated that the belt phenotype required a dominant allele at each of two autosomal loci. By the early 1980s, the trait was regarded as single-locus autosomal dominant (Ollivier and Sellier, 1982). The results of Rubin et al. (2012) indicate four alleles at this locus, namely Wild-type, Dominant white (OMIA 000209-9825), Patch (OMIA 001743-9825) and Belt (this entry). (with thanks to Leif Andersson)
Mapping: From a genome scan with 65 microsatellite markers on 67 backcross offspring from matings between non-belted sires and F1 (belted x non-belted) dams, Giuffra et al. (1999) linkage-mapped the belt locus to the centromeric region of chromosome SSC8, which contains two potential candidate genes, namely KIT and EDNRA. They then showed complete co-segregation of the belt phenotype with a SNP at position 2678 of exon 19 of the KIT gene, which strongly suggested that belt is an allele at the KIT locus. This study established for the first time that Belt is an allele to the Dominant white allele (see OMIA 000209-9825). Before this study Belt and Dominant white were considered to be two independent loci in the pig. (with thanks to Leif Andersson)
Molecular basis: Utilising extensive genome sequence data from tens of pigs, Rubin et al. (2012) showed that Hampshire pigs (belted phenotype) have "a 4.3-kb duplication (DUP2) located ∼100 kb upstream of KIT and a 23-kb duplication (DUP3) ∼100 kb downstream of KIT, which in turn contained a fourth ∼4.3-kb duplication (DUP4) not present on wild-type chromosomes". Across four breeds, belted pigs always had DUP2 and DUP4, but some lacked DUP3. The authors "conclude that DUP2–4 is strongly associated with the presence of the Belt and propose that one or more of these duplications are required for manifestation of the Belt phenotype . . . DUP2 is the strongest causative candidate because it overlaps with one of the most well-conserved noncoding regions located upstream of KIT".
Fontanesi et al. (2016) identified a "SNP (g.43597545C>T; position on porcine chromosome 8 in the Sscrofa10.2 genome assembly)". The authors reprted that "Allele T was almost fixed in [the belted] Cinta Senese [breed] (95.9%) and absent in many breeds and was considered the tag SNP of the belted allele".
By genotyping "the SNP rs328592739 in Krškopolje, Cinta Senese and Swäbisch-Hall belted pigs" and by studying whole-genome sequence data from a wide variety of breeds, Ogorevc et al. (2017) showed that this SNP "is not associated with white belt phenotype across different [other than Cinta Senese and Hampshire] pig breeds".
Breeds: Cinta Senese, Italy (Pig) (VBO_0013055), Essex, United Kingdom of Great Britain and Northern Ireland (Pig) (VBO_0016873), Hampshire Down (Sheep) (VBO_0001431), Schwäbisch Hällisches Schwein, Germany (Pig) (VBO_0012910), Wessex Saddleback (Pig) (VBO_0001211).
|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|
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
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|
|743||Essex, United Kingdom of Great Britain and Northern Ireland (Pig) Hampshire Down (Sheep) Schwäbisch Hällisches Schwein, Germany (Pig) Wessex Saddleback (Pig)||White belt||KIT||complex rearrangement||Naturally occurring variant||8||Hampshire pigs (belted phenotype) have "a 4.3-kb duplication (DUP2) located ~¼100 kb upstream of KIT and a 23-kb duplication (DUP3) ~100 kb downstream of KIT, which in turn contained a fourth ~4.3-kb duplication (DUP4) not present on wild-type chromosomes". Across four breeds, belted pigs always had DUP2 and DUP4, but some lacked DUP3.||2012||23151514|
|1135||Cinta Senese, Italy (Pig)||White belt||KIT||not known||Naturally occurring variant||Sscrofa11.1||8||g.41488472C>T||c.2499C>T||p.(P833P)||ENSSSCT00000009679.4:c.2499C>T ENSSSCP00000009430.3:p.Pro833= ENSSSCT00000062378.2:c.*1559C>T Sscrofa10.2 g.43,597,545C>T; Ensembl VEP analysis suggests that this can be a synonymous or 3_prime_UTR_variant depending on the transcript analysed||rs328592739||rs328592739||2016||Reference not in PubMed; see OMIA 001745-9823 for reference details||Ogorevc et al. (2017) reported the EVA ID of this variant as rs328592739|
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.
|2017||Ogorevc, J., Zorc, M., Škrlep, M., Bozzi, R., Petig, M., Fontanesi, L., Čandek-Potokar, M., Dovc, P. :|
|Is KIT Locus Polymorphism rs328592739 Related to White Belt Phenotype in Krškopolje Pig? Agriculturae Conspectus Scientificus 82:155-161, 2017.|
|2016||Fontanesi, L., Scotti, E., Gallo, M., Nanni Costa, L., Dall'Olio, S. :|
|Authentication of “mono-breed” pork products: Identification of a coat colour gene marker in Cinta Senese pigs useful to this purpose Livestock Science 184:71-77, 2016. DOI: 10.1016/j.livsci.2015.12.007.|
|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.|
|2006||Xu, GL., Ren, J., Ding, NS., Ai, HS., Guo, YM., Chen, CY., Huang, LS. :|
|Genetic analysis of the KIT and MC1R genes in Chinese indigenous pigs with belt-like coat color phenotypes. Anim Genet 37:518-9, 2006. Pubmed reference: 16978185 .|
|1999||Giuffra, E., Evans, G., Tornsten, A., Wales, R., Day, A., Looft, H., Plastow, G., Andersson, L. :|
|The Belt mutation in pigs is an allele at the Dominant white (I/KIT) locus Mammalian Genome 10:1132-1136, 1999. Pubmed reference: 10594235 .|
|1982||Ollivier, L., Sellier, P. :|
|Pig genetics: a review Annales de Genetique et de Selection Animale 14:481-544, 1982.|
|1970||Ten Cate, C.L. :|
|[White-belted pigs in the middle ages.] Zeitschrift fur Tierzuchtung und Zuchtungsbiologie 87:220-229, 1970.|
|1954||Gamba, F.N. :|
|L'allevamento della razza suini Cinta senese nella tenuta di Arceno [Breeding the Sienese Belted on the Arceno estate] Rivista di Zootecnia 27:262-265, 1954.|
|1943||Bushnell, R.J. :|
|Linked color factors in Hampshire swine. Linkage of black and the basic white of the belt pattern Journal of Heredity 34:302-307, 1943.|
|1921||Durham, G.B. :|
|Inheritance of belting spotting in cattle and swine. American Naturalist 55:476-477, 1921.|
|1907||Spillman, W.J. :|
|Inheritance of the belt in Hampshire swine. Science 25:541-3, 1907. Pubmed reference: 17734524 . DOI: 10.1126/science.25.640.541.|
- Created by Frank Nicholas on 25 Nov 2012
- Changed by Frank Nicholas on 25 Nov 2012
- Changed by Frank Nicholas on 25 Nov 2019
- Changed by Frank Nicholas on 26 Nov 2019
- Changed by Imke Tammen2 on 24 Feb 2021