OMIA:001199-9823 : Coat colour, extension in Sus scrofa

In other species: cattle , dog , horse , red fox , sheep , jaguar , jaguarundi , American black bear , woolly mammoth , domestic cat , rabbit , domestic guinea pig , goat , Arctic fox , rock pocket mouse , oldfield mouse , gray squirrel , lesser earless lizard , little striped whiptail , water buffalo , domestic yak , alpaca , , coyote , reindeer , Geoffroy's cat , Colocolo , ass , Arabian camel , Mongolian gerbil , raccoon dog , fallow deer , zebu , lorises , antarctic fur seal

Categories: Pigmentation phene

Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 266300 (trait) , 155555 (gene)

Links to MONDO diseases: No links.

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal

Considered a defect: no

Key variant known: yes

Year key variant first reported: 1998

Cross-species summary: The extension locus encodes the melanocyte-stimulating hormone receptor (MSHR; now known as MC1R). This receptor controls the level of tyrosinase within melanocytes. Tyrosinase is the limiting enzyme involved in synthesis of melanins: high levels of tyrosinase result in the production of eumelanin (dark colour, e.g. brown or black), while low levels result in the production of phaeomelanin (light colour, e.g. red or yellow). When melanocyte-stimulating hormone (MSH) binds to its receptor, the level of tyrosinase is increased, leading to production of eumelanin. The wild-type allele at the extension locus corresponds to a functional MSHR, and hence to dark pigmentation in the presence of MSH. As explained by Schneider et al. (PLoS Genet 10(2): e1004892; 2015), "The most common causes of melanism (black coat) mutations are gain-of-function alterations in MC1R, or loss-of function alterations in ASIP, which encodes Agouti signaling protein, a paracrine signaling molecule that inhibits MC1R signaling". Mutations in MC1R have been associated with white colouring in several species.

Molecular basis: By cloning and sequencing a very likely comparative candidate gene (based on recent discoveries of the molecular basis of the Extension coat-colour locus in cattle, horses, foxes and chickens), Kijas et al. (1998) identified five different missense mutations in the porcine MC1R gene, and showed their correspondence with documented alleles at the porcine Extension (E) locus:

G274A + T296C; p.Val92Met + p.Leu99Pro: dominant black in Asian pigs (E^D1)

G361A; p.Asp121Asn: dominant black in European pigs (E^D2)

C491T + G727A; p.Ala164Val + Ala243Thr: red (e)

Kijas et al. (2001) added another allele: nt67insCC (Codon 23): black spotting on red or white background (E^P)

Since then, many other alleles have been documented.

(from Table 4 of Switonski et al., 2013)

Linderholm et al. (2016) reported a new haplotype (0601) for black.

Wu et al. (2017) "found 2 haplotypes, E^QY and E^qy, from 13 closely linked mutations of MC1R" and "E^qy presented a recessive inheritance mode in black spotted Qingyu pigs"

Jia et al. (2017) reported a likely causal variant for recessive white in Bama miniature pigs: "A 2-bp CC insertion mutation (c.67_68insCC) was identified and co-segregated with the mutant phenotype completely . . . . This CC insertion at codon 23 results in a frameshift mutation (p.Arg23ProfsTer33) that produces a prematurely terminated, nonfunctional receptor."

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
MC1R melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) Sus scrofa 6 NC_010448.4 (182187..181225) MC1R 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.

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
170 Duroc (Pig) Red MC1R e missense Naturally occurring variant Sscrofa11.1 6 g.181461C>T c.727G>A p.(A243T) Variant is called p.(A240T) in original paper (Kijas et al., 1998). Two substitutions were found in recessive red (e/e) animals p.(A161V) and p.(A240T) - the p.(A240T) was considered as causative (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2 rs321432333 1998 9799269
171 Duroc (Pig) Red MC1R e missense Naturally occurring variant Sscrofa11.1 6 g.181697G>A c.491C>T p.(A164V) Variant is called p.(A161V) in original paper (Kijas et al., 1998). Two substitutions were found in recessive red (e/e) animals p.(A161V) and p.(A240T) - the p.(A240T) was considered as causative (Kijas et al., 1998). cDNA and protein location based in this table are based on transcript ENSSSCT00000022534.2 rs45435032 1998 9799269
169 Hampshire Down (Sheep) Dominant black MC1R E^D2 missense Naturally occurring variant Sscrofa11.1 6 g.181818C>T c.370G>A p.(D124N) Variant is called p.(D121N) in original paper (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2. rs326921593 rs326921593 2016 27703696 9799269
168 Large Black (Pig) Meishan (Pig) Dominant black MC1R E^D1 missense Naturally occurring variant Sscrofa11.1 6 g.181883A>G c.305T>C p.(L102P) Variant is called p.(L99P) in original paper (Kijas et al., 1998). Two silent (p.(A240A), p.(N118N)) and two missense substitutions p.(V92M) and p.(L99P) were found in dominant black Asian pigs (E^D1/E^D1) (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2. rs45434630 rs45434630 1998 9799269
1290 Large Black (Pig) Meishan (Pig) Dominant black MC1R E^D1 missense Naturally occurring variant Sscrofa11.1 6 g.181905C>T c.283G>A p.(V95M) Variant is called p.(V92M) in original paper (Kijas et al., 1998). Two silent (p.(A240A), p.(N118N)) and two missense substitutions p.(V92M) and p.(L99P) were found in dominant black Asian pigs (E^D1/E^D1) (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2. rs45434629 rs45434629 1998 9799269
597 Bama Xiang Zhu, China (Pig) Pietrain (Pig) Coat colour, black spotting on red or white background MC1R E^P, E^qy insertion, small (<=20) Naturally occurring variant Sscrofa11.1 6 g.182126_182127insGG c.67_68insCC p.(R23Pfs*33) Variant was published as nt67insCC (Kijas et al., 2001), g.462-463CC (Wu et al., 2017), c.67_68insCC (Jia et al. 2017) rs1113295336 rs1113295336 2017 28002929 28411032 11404341


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.

2022 Ji, R.L., Tao, Y.X. :
Melanocortin-1 receptor mutations and pigmentation: Insights from large animals. Prog Mol Biol Transl Sci 189:179-213, 2022. Pubmed reference: 35595349 . DOI: 10.1016/bs.pmbts.2022.03.001.
Lan, J., Wang, M., Qin, K., Liu, X., Shi, X., Sun, G., Liu, X., Chen, Y., He, Z. :
Functional characterization of cAMP signaling of variant porcine MC1R alleles in PK15 cells. Anim Genet 53:317-326, 2022. Pubmed reference: 35292981 . DOI: 10.1111/age.13189.
Li, Y., Yuan, R., Gong, Z., Zou, Q., Wang, Y., Tang, G., Zhu, L., Li, X., Jiang, Y. :
Evaluation of coat color inheritance and production performance for crossbreed from Chinese indigenous Chenghua pig crossbred with Berkshire. Anim Biosci 35:1479-1488, 2022. Pubmed reference: 35240015 . DOI: 10.5713/ab.21.0574.
2019 Frantz, L.A.F., Haile, J., Lin, A.T., Scheu, A., Geörg, C., Benecke, N., Alexander, M., Linderholm, A., Mullin, V.E., Daly, K.G., Battista, V.M., Price, M., Gron, K.J., Alexandri, P., Arbogast, R.M., Arbuckle, B., Bӑlӑşescu, A., Barnett, R., Bartosiewicz, L., Baryshnikov, G., Bonsall, C., Borić, D., Boroneanţ, A., Bulatović, J., Çakirlar, C., Carretero, J.M., Chapman, J., Church, M., Crooijmans, R., De Cupere, B., Detry, C., Dimitrijevic, V., Dumitraşcu, V., du Plessis, L., Edwards, C.J., Erek, C.M., Erim-Özdoğan, A., Ervynck, A., Fulgione, D., Gligor, M., Götherström, A., Gourichon, L., Groenen, M.A.M., Helmer, D., Hongo, H., Horwitz, L.K., Irving-Pease, E.K., Lebrasseur, O., Lesur, J., Malone, C., Manaseryan, N., Marciniak, A., Martlew, H., Mashkour, M., Matthews, R., Matuzeviciute, G.M., Maziar, S., Meijaard, E., McGovern, T., Megens, H.J., Miller, R., Mohaseb, A.F., Orschiedt, J., Orton, D., Papathanasiou, A., Pearson, M.P., Pinhasi, R., Radmanović, D., Ricaut, F.X., Richards, M., Sabin, R., Sarti, L., Schier, W., Sheikhi, S., Stephan, E., Stewart, J.R., Stoddart, S., Tagliacozzo, A., Tasić, N., Trantalidou, K., Tresset, A., Valdiosera, C., van den Hurk, Y., Van Poucke, S., Vigne, J.D., Yanevich, A., Zeeb-Lanz, A., Triantafyllidis, A., Gilbert, M.T.P., Schibler, J., Rowley-Conwy, P., Zeder, M., Peters, J., Cucchi, T., Bradley, D.G., Dobney, K., Burger, J., Evin, A., Girdland-Flink, L., Larson, G. :
Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe. Proc Natl Acad Sci U S A 116:17231-17238, 2019. Pubmed reference: 31405970 . DOI: 10.1073/pnas.1901169116.
Ribani, A., Utzeri, V.J., Geraci, C., Tinarelli, S., Djan, M., Veličković, N., Doneva, R., Dall'Olio, S., Nanni Costa, L., Schiavo, G., Bovo, S., Usai, G., Gallo, M., Radović, Č., Savić, R., Karolyi, D., Salajpal, K., Gvozdanović, K., Djurkin-Kušec, I., Škrlep, M., Čandek-Potokar, M., Ovilo, C., Fontanesi, L. :
Signatures of de-domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution. Anim Genet 50:166-171, 2019. Pubmed reference: 30741434 . DOI: 10.1111/age.12771.
2017 Jia, Q., Cao, C., Tang, H., Zhang, Y., Zheng, Q., Wang, X., Zhang, R., Wang, X., Luo, A., Wei, H., Meng, A., Zhou, Q., Wang, H., Zhao, J. :
A 2-bp insertion (c.67_68insCC) in MC1R causes recessive white coat color in Bama miniature pigs. J Genet Genomics 44:215-217, 2017. Pubmed reference: 28411032 . DOI: 10.1016/j.jgg.2017.02.003.
Wu, X., Tan, Z., Shen, L., Yang, Q., Cheng, X., Liao, K., Bai, L., Shuai, S., Li, M., Li, X., Zhang, S., Zhu, L. :
Coat colour phenotype of Qingyu pig is associated with polymorphisms of melanocortin receptor 1 gene. Asian-Australas J Anim Sci 30:938-943, 2017. Pubmed reference: 28002929 . DOI: 10.5713/ajas.16.0376.
2016 Linderholm, A., Spencer, D., Battista, V., Frantz, L., Barnett, R., Fleischer, R.C., James, H.F., Duffy, D., Sparks, J.P., Clements, D.R., Andersson, L., Dobney, K., Leonard, J.A., Larson, G. :
A novel MC1R allele for black coat colour reveals the Polynesian ancestry and hybridization patterns of Hawaiian feral pigs. R Soc Open Sci 3:160304, 2016. Pubmed reference: 27703696 . DOI: 10.1098/rsos.160304.
2013 Switonski, M., Mankowska, M., Salamon, S. :
Family of melanocortin receptor (MCR) genes in mammals-mutations, polymorphisms and phenotypic effects. J Appl Genet 54:461-72, 2013. Pubmed reference: 23996627 . DOI: 10.1007/s13353-013-0163-z.
2010 Li, J., Yang, H., Li, JR., Li, HP., Ning, T., Pan, XR., Shi, P., Zhang, YP. :
Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication. Heredity :, 2010. Pubmed reference: 20179735 . DOI: 10.1038/hdy.2009.191.
Mao, H., Ren, J., Ding, N., Xiao, S., Huang, L. :
Genetic variation within coat color genes of MC1R and ASIP in Chinese brownish red Tibetan pigs. Anim Sci J 81:630-4, 2010. Pubmed reference: 21108681 . DOI: 10.1111/j.1740-0929.2010.00789.x.
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.
Fang, M., Larson, G., Ribeiro, HS., Li, N., Andersson, L. :
Contrasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genet 5:e1000341, 2009. Pubmed reference: 19148282 . DOI: 10.1371/journal.pgen.1000341.
2007 D'Alessandro, E., Fontanesi, L., Liotta, L., Davoli, R., Chiofalo, V., Russo, V. :
Analysis of the MC1R gene in the Nero Siciliano pig breed and usefulness of this locus for breed traceability. Vet Res Commun 31 Suppl 1:389-92, 2007. Pubmed reference: 17682921 . DOI: 10.1007/s11259-007-0063-y.
Dun, G., Li, X., Cao, H., Zhou, R., Li, L. :
Variations of melanocortin receptor 1 (MC1R) gene in three pig breeds. J Genet Genomics 34:777-82, 2007. Pubmed reference: 17884687 . DOI: 10.1016/S1673-8527(07)60088-5.
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.
2006 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.
2004 Shi, K., Wang, A., Li, N., Deng, X. :
Single nucleotide polymorphism analysis on melanocortin receptor 1 (MC1R) of Chinese native pig. Sci China C Life Sci 47:287-92, 2004. Pubmed reference: 15524286 .
2003 Andersson, L. :
Melanocortin receptor variants with phenotypic effects in horse, pig, and chicken Annals of the New York Academy of Sciences 994:313-8, 2003. Pubmed reference: 12851331 .
Deng, SH., Gao, J., Ren, J., Chen, KF., Ding, NS., Ai, HS., Lin, WH., Wang, WJ., Liu, BS., Lai, FJ., Huang, LS. :
[Studies of the relationship of melanocortin receptor 1(MC1R) gene with coat color phenotype in pigs] Yi Chuan Xue Bao 30:949-54, 2003. Pubmed reference: 14669512 .
2001 Gustafsson, A.C., Kijas, J.M.H., Alderborn, A., Uhlen, M., Andersson, L., Lundeberg, J. :
Screening and scanning of single nucleotide polymorphisms in the pig melanocortin 1 receptor gene (MC1R) by pyrosequencing Animal Biotechnology 12:145-153, 2001. Pubmed reference: 11808630 . DOI: 10.1081/ABIO-100108341.
Kijas, J.M.H., Moller, M., Plastow, G., Andersson, L. :
A frameshift mutation in MC1R and a high frequency of somatic reversions cause black spotting in pigs Genetics 158:779-785, 2001. Pubmed reference: 11404341 .
1998 Kijas, J.M.H., Wales, R., Tornsten, A., Chardon, P., Moller, M., Andersson, L. :
Melanocortin receptor 1 (MC1R) mutations and coat color in pigs Genetics 150:1177-1185, 1998. Pubmed reference: 9799269 .
1996 Mariani, P., Moller, M.J., Hoyheim, B., Marklund, L., Davies, W., Ellegren, H., Andersson, L. :
The extension coat color locus and the loci for blood group O and tyrosine aminotransferase are on pig chromosome 6 Journal of Heredity 87:272-276, 1996. Pubmed reference: 8776875 .

Edit History

  • Created by Frank Nicholas on 01 Dec 2009
  • Changed by Frank Nicholas on 08 Oct 2011
  • Changed by Frank Nicholas on 09 Dec 2011
  • Changed by Frank Nicholas on 04 Sep 2012
  • Changed by Frank Nicholas on 17 Oct 2016
  • Changed by Frank Nicholas on 01 Sep 2017
  • Changed by Frank Nicholas on 02 Sep 2017
  • Changed by Imke Tammen2 on 25 Feb 2021
  • Changed by Imke Tammen2 on 11 Sep 2022
  • Changed by Imke Tammen2 on 16 Jan 2023