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

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

Categories: Pigmentation phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 266300 (trait) , 155555 (gene)

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."
Li et al. (2024) "created a melanocortin 1 receptor (MC1R)-edited pig model through somatic cell nuclear transfer (SCNT) by using porcine kidney cells modified by the CRISPR-Cas9 system. We then carried out whole-genome sequencing of two MC1R-edited pigs and two cloned wild-type siblings, together with the donor cells, to assess the genome-wide presence of single-nucleotide variants and small insertions and deletions (indels) and found only one candidate off-target indel in both MC1R-edited pigs." This study involves genetically modified organisms (GMO).


Genetic engineering: Yes - in addition to the occurrence of natural variants, variants have been created artificially, e.g. by genetic engineering or gene editing
Have human generated variants been created, e.g. through genetic engineering and gene editing

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 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 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 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 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 2017 28002929 28411032 11404341

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2024). OMIA:001199-9823: Online Mendelian Inheritance in Animals (OMIA) [dataset].


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.

2024 Li, Z., Lan, J., Shi, X., Lu, T., Hu, X., Liu, X., Chen, Y., He, Z. :
Whole-genome sequencing reveals rare off-target mutations in MC1R-edited pigs generated by using CRISPR-Cas9 and somatic cell nuclear transfer. CRISPR J 7:29-40, 2024. Pubmed reference: 38353621. DOI: 10.1089/crispr.2023.0034.
2023 Giovannini, S., Strillacci, M.G., Bagnato, A., Albertini, E., Sarti, F.M. :
Genetic and phenotypic characteristics of belted pig reeds: A review. Animals (Basel) 13:3072, 2023. Pubmed reference: 37835678. DOI: 10.3390/ani13193072.
Ribani, A., Taurisano, V., Karatosidi, D., Schiavo, G., Bovo, S., Bertolini, F., Fontanesi, L. :
Signatures of admixture and genetic uniqueness in the autochthonous Greek black pig breed deduced from gene polymorphisms affecting domestication-derived traits. Animals (Basel) 13:1763, 2023. Pubmed reference: 37889646. DOI: 10.3390/ani13111763.
Zheng, H., Xiong, S.Y., Xiao, S.J., Zhang, Z.K., Tu, J.M., Cui, D.S., Yu, N.B., Huang, Z.Y., Li, L.Y., Guo, Y.M. :
Association between MC1R gene and coat color segregation in Shanxia long black pig and Lulai black pig. BMC Genom Data 24:74, 2023. Pubmed reference: 38036989. DOI: 10.1186/s12863-023-01161-2.
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 (Edinb) 105:274-81, 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
  • Changed by Imke Tammen2 on 28 Feb 2024