OMIA 000209-9823 : Coat colour, dominant white in Sus scrofa |
Following analysis of whole-genome resequencing data from tens of pigs from a wide range of breeds, Rubin et al. (2012) have enhanced our understanding of this intriguing locus: the Dominant white allele (I) carries at least three causal polymorphisms, namely a 450 kb duplication (also present in Patch - see OMIA 001743-9825), the splice mutation mentioned above (unique to Dominant white) and smaller duplication(s) (that occur within the 450kb duplication) causing Belt (see OMIA 001745-9825).(with thanks to Leif Andersson)
Genetic testing: Li et al. (2018) reported "a simple, rapid method, with high specificity and stability, for the detection of the KIT genotype in pigs was established using TaqMan MGB probe real-time quantitative PCR." Associated gene: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 |
Variants
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.
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
979 | Dominant white | KIT | I | complex rearrangement | Naturally occurring variant | 8 | This dominant white allele carries at least three causal polymorphisms, namely a 450 kb duplication (originally reported by Johansson Moller (1996); also present in Patch - see OMIA 001743-9825), the splice mutation reported by Marklund et al. (1998) (unique to Dominant white) and smaller duplication(s) (that occur within the 450kb duplication) causing Belt (see OMIA 001745-9825).(with thanks to Leif Andersson). To emphasise the original discovery of the duplication, the ref cited here is Johansson Moller (1996) | 1996 | 8875890 |
References
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 | Huang, M., Zhang, H., Wu, Z.P., Wang, X.P., Li, D.S., Liu, S.J., Zheng, S.M., Yang, L.J., Liu, B.B., Li, G.X., Jiang, Y.C., Chen, H., Ren, J. : | |
Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs. Animal 15:100354, 2021. Pubmed reference: 34543995. DOI: 10.1016/j.animal.2021.100354. | ||
2020 | Sun, G., Liang, X., Qin, K., Qin, Y., Shi, X., Cong, P., Mo, D., Liu, X., Chen, Y., He, Z. : | |
Functional analysis of KIT gene structural mutations causing the porcine dominant white phenotype using genome edited mouse models. Front Genet 11:138, 2020. Pubmed reference: 32194624. DOI: 10.3389/fgene.2020.00138. | ||
Xu, J., Fu, Y., Hu, Y., Yin, L., Tang, Z., Yin, D., Zhu, M., Yu, M., Li, X., Zhou, Y., Zhao, S., Liu, X. : | ||
Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features. J Anim Sci Biotechnol 11:115, 2020. Pubmed reference: 33292532. DOI: 10.1186/s40104-020-00520-8. | ||
2019 | Qin, K., Liang, X., Sun, G., Shi, X., Wang, M., Liu, H., Chen, Y., Liu, X., He, Z. : | |
Highly efficient correction of structural mutations of 450 kb KIT locus in kidney cells of Yorkshire pig by CRISPR/Cas9. BMC Mol Cell Biol 20:4, 2019. Pubmed reference: 31041890. DOI: 10.1186/s12860-019-0184-5. | ||
Wu, Z., Deng, Z., Huang, M., Hou, Y., Zhang, H., Chen, H., Ren, J. : | ||
Whole-Genome Resequencing Identifies <i>KIT</i> New Alleles That Affect Coat Color Phenotypes in Pigs. Front Genet 10:218, 2019. Pubmed reference: 30949195. DOI: 10.3389/fgene.2019.00218. | ||
2018 | Li, X., Li, X., Luo, R., Wang, W., Wang, T., Tang, H. : | |
Detection of KIT Genotype in Pigs by TaqMan MGB Real-Time Quantitative PCR. DNA Cell Biol :, 2018. Pubmed reference: 29485917. DOI: 10.1089/dna.2017.4070. | ||
Niu, L., Shi, K., Xie, J.J., Liu, S., Zhong, T. : | ||
KIT Gene in European and Asian Domestic Pig Breeds. Biomed Res Int 2018:8932945, 2018. Pubmed reference: 30211229. DOI: 10.1155/2018/8932945. | ||
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. | ||
2009 | Andersson, L. : | |
Studying phenotypic evolution in domestic animals: a walk in the footsteps of Charles Darwin. Cold Spring Harb Symp Quant Biol 74:319-25, 2009. Pubmed reference: 20375320. DOI: 10.1101/sqb.2009.74.039. | ||
2007 | Lai, F., Ren, J., Ai, H., Ding, N., Ma, J., Zeng, D., Chen, C., Guo, Y., Huang, L. : | |
Chinese White Rongchang Pig Does Not Have the Dominant White Allele of KIT but Has the Dominant Black Allele of MC1R. J Hered 98:84-87, 2007. Pubmed reference: 17150979. DOI: 10.1093/jhered/esl053. | ||
Pielberg, G., Andersson, L. : | ||
Gene copy number detection in animal studies. Methods Mol Biol 373:147-56, 2007. Pubmed reference: 17185764. | ||
Seo, BY., Park, EW., Ahn, SJ., Lee, SH., Kim, JH., Im, HT., Lee, JH., Cho, IC., Kong, IK., Jeon, JT. : | ||
An accurate method for quantifying and analyzing copy number variation in porcine KIT by an oligonucleotide ligation assay. BMC Genet 8:81, 2007. Pubmed reference: 18036219. DOI: 10.1186/1471-2156-8-81. | ||
2006 | Fésüs, L., Sarlós, P., Osváth, Z., Zsolnai, A., Komlósi, I., Rátky, J. : | |
Influence of the dominant white/KIT genotypes on the reproductive organs of pigs. J Reprod Dev 52:707-13, 2006. Pubmed reference: 16960427. | ||
Shi, KR., Wang, AG., Yuan, XF., Deng, XM., Li, N. : | ||
Analysis of the MC1R, KIT and ASIP loci in Chinese and European pigs. Anim Genet 37:300-2, 2006. Pubmed reference: 16734703. DOI: 10.1111/j.1365-2052.2006.01446.x. | ||
2005 | Johansson, A., Pielberg, G., Andersson, L., Edfors-Lilja, I. : | |
Polymorphism at the porcine Dominant white/KIT locus influence coat colour and peripheral blood cell measures. Anim Genet 36:288-96, 2005. Pubmed reference: 16026338. DOI: 10.1111/j.1365-2052.2005.01320.x. | ||
2003 | Pielberg, G., Day, AE., Plastow, GS., Andersson, L. : | |
A sensitive method for detecting variation in copy numbers of duplicated genes. Genome Res 13:2171-7, 2003. Pubmed reference: 12952884. DOI: 10.1101/gr.1188203. | ||
2002 | Giuffra, E., Tornsten, A., Marklund, S., Bongcam-Rudloff, E., Chardon, P., Kijas, J.M.H., Anderson, S.I., Archibald, A.L., Andersson, L. : | |
A large duplication associated with dominant white color in pigs originated by homologous recombination between LINE elements flanking KIT Mammalian Genome 13:569-577, 2002. Pubmed reference: 12420135. DOI: 10.1007/s00335-002-2184-5. | ||
Pielberg, G., Olsson, C., Syvanen, A.C., Andersson, L. : | ||
Unexpectedly high allelic diversity at the KIT locus causing dominant white color in the domestic pig Genetics 160:305-311, 2002. Pubmed reference: 11805065. | ||
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. | ||
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. | ||
1996 | Inoue, K., Tanaka, S., Kashiwazaki, N., Nakao, H., Nakatsuji, N., Sakaki, N., Tojo, H., Tachi, C. : | |
Quantitative analysis of striped coat-color patterns in large white-]duroc chimeric pigs with special reference to the genetic control mechanisms of the dominant black-eyed white phenotype Pigment Cell Research 9:289-297, 1996. Pubmed reference: 9125752. | ||
Johansson Moller, M., Chaudhary, R., Hellmén, E., Höyheim, B., Chowdhary, B., Andersson, L. : | ||
Pigs with the dominant white coat color phenotype carry a duplication of the KIT gene encoding the mast/stem cell growth factor receptor. Mamm Genome 7:822-30, 1996. Pubmed reference: 8875890. | ||
Sakurai, M., Zhou, J.H., Ohtaki, M., Itoh, T., Murakami, Y., Yasue, H. : | ||
Assignment of c-kit gene to swine chromosome 8P12-P21 by fluorescence in situ hybridization Mammalian Genome 7:397, 1996. Pubmed reference: 8661742. | ||
1992 | Johansson, M., Ellegren, H., Marklund, L., Gustavsson, U., Ringmarcederberg, E., Andersson, K., Edfors-Lilja, I., Andersson, L. : | |
The Gene for Dominant White Color in the Pig Is Closely Linked to ALB and PDGFRA on Chromosome-8 Genomics 14:965-969, 1992. Pubmed reference: 1362182. | ||
1979 | Lauvergne, J.J., Canope, I. : | |
Study of some colour variants of Creole pigs from Guadeloupe [French] Annales de Genetique Selection Animale 11:381-390, 1979. | ||
1948 | Hetzer, H.O. : | |
Inheritance of coat colour in swine. VII. Results of Landrace by Hampshire crosses. J Hered 39:122-8, 1948. Pubmed reference: 18865775. | ||
1946 | Hetzer, H.O. : | |
Inheritance of coat colour in swine. V. Results of Landrace by Duroc-Jersey crosses J Hered 37:217-24, 1946. Pubmed reference: 20281701. | ||
1945 | Hetzer, H.O. : | |
Inheritance of coat colour in swine. II. Results of Landrace by Poland China crosses Journal of Heredity 36:187-192, 1945. | ||
Hetzer, H.O. : | ||
Inheritance of coat colour in swine. III. Results of Landrace by Berkshire crosses Journal of Heredity 36:255-256, 1945. | ||
Hetzer, H.O. : | ||
Inheritance of coat colour in swine. IV. Analysis of hybrids of Landrace and Large Black Journal of Heredity 36:309-312, 1945. | ||
1923 | Wentworth, E.N., Lush, J.L. : | |
Inheritance in swine Journal of Agricultural Research 23:557-582, 1923. | ||
1906 | Spillman, W.J. : | |
Inheritance of color coat in swine. Science 24:441-3, 1906. Pubmed reference: 17801430. DOI: 10.1126/science.24.614.441. |
Edit History
- Created by Frank Nicholas on 20 Sep 2008
- Changed by Frank Nicholas on 08 Oct 2011
- Changed by Frank Nicholas on 09 Dec 2011
- Changed by Frank Nicholas on 03 Sep 2012
- Changed by Frank Nicholas on 25 Nov 2012
- Changed by Frank Nicholas on 26 Mar 2018
- Changed by Frank Nicholas on 08 Apr 2019
- Changed by Frank Nicholas on 26 Mar 2020