OMIA:000810-9031 : Polydactyly in Gallus gallus (chicken)

In other species: rock pigeon , turkey , dog , domestic cat , horse , pig , Arabian camel , guanaco , llama , Western roe deer , taurine cattle , goat , sheep , domestic guinea pig , alpaca , springbok

Categories: Skeleton phene (incl. short stature & teeth) , Limbs / fins / digit / tail phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 174500 (trait) , 605522 (gene) , 188740 (trait)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal dominant

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2010

Cross-species summary: Often called preaxial polydactyly (PPD)

Species-specific symbol: Po

History: This is one of the first five animal traits (all in chickens) to be described as Mendelian, by Bateson and Saunders (1902; pages 87-124). The other four traits are Rose-comb (OMIA 000884-9031), Pea-comb (OMIA 000782-9031), Dominant White (OMIA 000373-9031), and Yellow skin (OMIA 001449-9031).

Mapping: This disorder was originally mapped to linkage group E (Warren, 1949). Using bulked segregant analysis with microsatellite markers, Pitel et al. (2000) mapped it to chromosome GGA2p, a result confirmed by Yang et al. (2013). Dorshorst et al. (2010) refined the location to 4.8Mb on chromosome GGA2p. Using linkage analysis and GWAS in 367 members of an F2 of a cross between Beijing-You chickens and Cobb-Vantress commercial broilers, each genotyped with the Illumina 60K Chicken SNP Beadchip (yielding 42,585 informative SNPs), Sun et al. (2014) confirmed the SSH region on chromosome GGA2 as being the most important, but also obtained genome-wide significance for SNPs on chromosomes GGA20 and GGA26. Sheng et al. (2015) reported the strongest association with Polydactyly in a region on chromosome GGA2 that contains the BRAM1 gene. This paper was withdrawn in March 2016 (Sheng et al., 2016). Zhang et al. (2016) showed that the causal mutation for Polydactyly in European breeds maps to the same region of chromosome GGA2 as the mutation that is causal in Chinese breeds, but is not the same mutation.

Molecular basis: Polydactyly results from faults in the regulation of the developmental gene Sonic Hedgehog (SHH), which is expressed only at the border of the posterior limb bud, in a region called the zone of polarizing activity (ZPA). The faults in regulation result from mutations in an enhancer located in intron 5 of the LMBR1 gene, located about 1 MB upstream of SHH. The enhancer is called the ZPA regulatory sequence (ZRS). Thus polydactyly results from mutations in ZRS, which affect expression of SHH in the developing limb bud. The first report of the causal mutation (a SNP in the SHH enhancer) was by Dorshorst et al. (2010). This discovery was confirmed by Maas et al. (2011). Zhang et al. (2016) showed that this mutation is causal in 24 indigenous Chinese breeds, but is not causal for Polydactyly in the Houdan breed, from France. He et al. (2017): "a highly purebred BF [Beijing fatty] line with 100% penetrance of Po was obtained and served as an ideal model for the study of Po in fowls. By observing the process of pure breeding and cross breeding, we provided evidence that chicken polydactyly was a complete dominant trait [in this line]. With the help of an integrated strategy of RAD-seq [restriction-site-associated DNA sequencing] and resequencing, we further confirmed that this dominant trait was highly associated with the genotype of rs80659072 [(Gallus_gallus-5.0) GGA2:8500245C>T (in an intron of LMBR1)] in the BF line." Chu et al. (2017): "The plausible mutation rs80659072 in the zone of polarizing activity regulatory sequence (ZRS) in chickens was an essential but not sufficient condition for polydactyly and polyphalangy in Beijing You chickens."

Clinical features: "Homozygous (Po/Po) and heterozygous (Po/+) mutants may have an additional preaxial digit on one or both feet and/or wings; or affected individuals may display a longer than normal first digit on one or both feet" (Robb et al., 2011)

Breeds: Beijing You, China (Chicken) (VBO_0006660), Silkie (Chicken) (VBO_0000619).
Breeds in which the phene has been documented. (If a likely causal variant has been documented for the phene, see the variant table breeds in which the variant has been reported).

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
SHH sonic hedgehog Gallus gallus 2 NC_052533.1 (8097333..8087761) SHH 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
836 Polydactyly SHH regulatory Naturally occurring variant GRCg6a 2 g.8553470G>T published as "single SNP in a highly conserved cis-regulatory region of Sonic Hedgehog was significantly associated with polydactyly" rs80659072 2010 20064842

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2022). OMIA:000810-9031: 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.

2017 Chu, Q., Yan, Z., Zhang, J., Usman, T., Zhang, Y., Liu, H., Wang, H., Geng, A., Liu, H. :
Association of SNP rs80659072 in the ZRS with polydactyly in Beijing You chickens. PLoS One 12:e0185953, 2017. Pubmed reference: 29016641. DOI: 10.1371/journal.pone.0185953.
He, C., Chen, Y., Yang, K., Zhai, Z., Zhao, W., Liu, S., Ding, J., Dai, R., Yang, L., Xu, K., Zhou, Z., Gu, C., Huang, Q., Meng, H. :
Genetic pattern and gene localization of polydactyly in Beijing fatty chicken. PLoS One 12:e0176113, 2017. Pubmed reference: 28489934. DOI: 10.1371/journal.pone.0176113.
2016 Sheng, X., Chen, Y., Jia, Y., Qi, X., Feng, Y., Huang, Z., Guo, Y. :
Retraction notice to "The identification of loci for polydactyly in chickens using a genome-wide association study" [GENE 568/2 (2015) 176-180]. Gene 584:195, 2016. Pubmed reference: 27049671. DOI: 10.1016/j.gene.2016.03.040.
Zhang, Z., Nie, C., Jia, Y., Jiang, R., Xia, H., Lv, X., Chen, Y., Li, J., Li, X., Ning, Z., Xu, G., Chen, J., Yang, N., Qu, L. :
Parallel evolution of polydactyly traits in Chinese and European chickens. PLoS One 11:e0149010, 2016. Pubmed reference: 26859147. DOI: 10.1371/journal.pone.0149010.
2015 Sheng, X., Chen, Y., Jia, Y., Qi, X., Feng, Y., Huang, Z., Guo, Y. :
The identification of loci for polydactyly in chickens using a genome-wide association study. Gene 568:176-80, 2015. Pubmed reference: 26003297. DOI: 10.1016/j.gene.2015.05.049.
2014 Sun, Y., Liu, R., Zhao, G., Zheng, M., Sun, Y., Yu, X., Li, P., Wen, J. :
Genome-wide linkage analysis and association study identifies loci for polydactyly in chickens. G3 (Bethesda) 4:1167-72, 2014. Pubmed reference: 24752238. DOI: 10.1534/g3.114.011338.
2013 Yang, K., Chen, Y., Gu, C., Zhou, Z., He, C., Tang, L., Li, S., Zhao, L., Meng, H., Huang, Q. :
Polydactyly mutation is linked with chromosome 2p region in Beijing fatty chicken. Anim Genet 44:118-9, 2013. Pubmed reference: 22582748. DOI: 10.1111/j.1365-2052.2012.02369.x.
2012 Robb, E.A., Delany, M.E. :
The expression of preaxial polydactyly is influenced by modifying genetic elements and is not maintained by chromosomal inversion in an avian biomedical model. Cytogenet Genome Res 136:50-68, 2012. Pubmed reference: 22286052. DOI: 10.1159/000335005.
2011 Dunn, IC., Paton, IR., Clelland, AK., Sebastian, S., Johnson, EJ., McTeir, L., Windsor, D., Sherman, A., Sang, H., Burt, DW., Tickle, C., Davey, MG. :
The chicken polydactyly (Po) locus causes allelic imbalance and ectopic expression of Shh during limb development. Dev Dyn 240:1163-72, 2011. Pubmed reference: 21465618. DOI: 10.1002/dvdy.22623.
Maas, S.A., Suzuki, T., Fallon, J.F. :
Identification of spontaneous mutations within the long-range limb-specific Sonic hedgehog enhancer (ZRS) that alter Sonic hedgehog expression in the chicken limb mutants oligozeugodactyly and silkie breed. Dev Dyn 240:1212-22, 2011. Pubmed reference: 21509895. DOI: 10.1002/dvdy.22634.
Robb, EA., Gitter, CL., Cheng, HH., Delany, ME. :
Chromosomal mapping and candidate gene discovery of chicken developmental mutants and genome-wide variation analysis of MHC congenics. J Hered 102:141-56, 2011. Pubmed reference: 21273214. DOI: 10.1093/jhered/esq122.
2010 Dorshorst, B., Okimoto, R., Ashwell, C. :
Genomic regions associated with dermal hyperpigmentation, polydactyly and other morphological traits in the Silkie chicken. J Hered 101:339-50, 2010. Pubmed reference: 20064842. DOI: 10.1093/jhered/esp120.
2009 Bouldin, CM., Harfe, BD. :
Aberrant FGF signaling, independent of ectopic hedgehog signaling, initiates preaxial polydactyly in Dorking chickens. Dev Biol 334:133-41, 2009. Pubmed reference: 19616534. DOI: 10.1016/j.ydbio.2009.07.009.
2006 Huang, YQ., Deng, XM., Du, ZQ., Qiu, X., Du, X., Chen, W., Morisson, M., Leroux, S., Ponce de Leon, FA., Da, Y., Li, N. :
Single nucleotide polymorphisms in the chicken Lmbr1 gene are associated with chicken polydactyly. Gene 374:10-8, 2006. Pubmed reference: 16650944. DOI: 10.1016/j.gene.2005.07.047.
2005 Vargas, AO., Fallon, JF. :
Birds have dinosaur wings: The molecular evidence. J Exp Zoolog B Mol Dev Evol 304:86-90, 2005. Pubmed reference: 15880773. DOI: 10.1002/jez.b.21042.
2000 Pitel, F., Berge, R., Coquerelle, G., Crooijmans, R.P.M.A., Groenen, M.A.M., Vignal, A., Tixier-Boichard, M. :
Mapping the Naked Neck (NA) and Polydactyly (PO) mutants of the chicken with microsatellite molecular markers Genetics Selection Evolution 32:73-86, 2000. Pubmed reference: 14736408. DOI: 10.1051/gse:2000107.
1993 Shoffner, R.N., Otis, J.S., Garwood, V.A. :
Association of dominant marker traits and metric traits in chickens. Poult Sci 72:1405-10, 1993. Pubmed reference: 8378215. DOI: 10.3382/ps.0721405.
1992 Coelho, C.N.D., Upholt, W.B., Kosher, R.A. :
Role of the chicken homeobox-containing genes GHox-4.6 and GHox-8 in the specification of positional identities during the development of normal and polydactylous chick limb buds Development 115:629-37, 1992. Pubmed reference: 1358596. DOI: 10.1242/dev.115.2.629.
1989 Grewal, G.S., Brar, R.S. :
Three congenital anomalies of domestic fowl. Poult Sci 68:1019-20, 1989. Pubmed reference: 2780474. DOI: 10.3382/ps.0681019.
1974 Etches, RJ., Buckland, RB., Hawes, RO. :
The effect of the genes for rose comb and polydactyly on sperm transport in the hen's oviduct. Poult Sci 53:422-4, 1974. Pubmed reference: 4833050.
1971 Munro, S.S. :
Apparent transformation of polydactylism between two breeds of chickens via chemically extracted DNA. Poult Sci 50:1279-85, 1971. Pubmed reference: 5094377. DOI: 10.3382/ps.0501279.
1956 Zwilling, E., Hansborough, L.A. :
Interaction between limb bud ectoderm and mesoderm in the chick embryo. III. Experiments with polydactylous limbs. Journal of Experimental Zoology 132:219-239, 1956.
1954 Saeki, Y. :
Polydactyly in silky fowl Bulletin of the National Institute of Agricultural Science, Japan, Series G :49-55, 1954.
1949 Warren, DC. :
Linkage relations of autosomal factors in the fowl. Genetics 34:333-50, 1949. Pubmed reference: 17247319. DOI: 10.1093/genetics/34.3.333.
1948 Landauer, W. :
The phenotypic modification of hereditary polydactylism of fowl by selection and by insulin. Genetics 33:133-57, 1948. Pubmed reference: 17247274. DOI: 10.1093/genetics/33.2.133.
1944 Warren, D.C. :
Inheritance of polydactylism in the fowl. Genetics 29:217-31, 1944. Pubmed reference: 17247117. DOI: 10.1093/genetics/29.3.217.
1943 Hutt, F.B., Mueller, C.D. :
The linkage of polydactyly with multiple spurs and duplex comb in the fowl American Naturalist 77:70, 1943.
1941 Warren, D.C. :
New type of polydactylism in the fowl. Journal of Heredity 32:2-5, 1941.
1938 Warren, D.C. :
Mapping the genes of the fowl (abstract) Genetics 23:174 only, 1938. DOI: 10.1093/genetics/23.1.139.
1935 Fisher, R.A. :
Some results of an experiment or dominance in poultry, with special reference to polydactyly. Proceedings of the Linnean Society, London 147:71-88, 1935.
Fisher, R.A. :
Dominance in poultry. Philosophical Transactions of the Royal Society, Series B; Biological Sciences 225:197-226 , 1935. DOI: 10.1098/rstb.1935.0011.
1933 Warren, D.C. :
Nine independently inherited autosomal factors in the domestic fowl. Genetics 18:68-81, 1933. Pubmed reference: 17246678. DOI: 10.1093/genetics/18.1.68.
1902 Bateson, W., Saunders, E.R. :
Experimental studies in the physiology of heredity. Part III. The facts of heredity in the light of Mendel's discovery Reports to the Evolution Committee of the Royal Society 1:125-160, 1902.
Bateson, W., Saunders, E.R. :
Experimental studies in the physiology of heredity. Part II. Poultry Reports to the Evolution Committee of the Royal Society 1:87-124, 1902.

Edit History

  • Created by Frank Nicholas on 26 Feb 2011
  • Changed by Frank Nicholas on 30 Sep 2011
  • Changed by Frank Nicholas on 09 Dec 2011
  • Changed by Frank Nicholas on 04 Jan 2012
  • Changed by Frank Nicholas on 02 May 2012
  • Changed by Frank Nicholas on 05 Jul 2012
  • Changed by Frank Nicholas on 06 Jul 2012
  • Changed by Frank Nicholas on 25 Apr 2014
  • Changed by Frank Nicholas on 04 Apr 2016
  • Changed by Frank Nicholas on 11 Apr 2016
  • Changed by Frank Nicholas on 18 Sep 2017
  • Changed by Frank Nicholas on 10 Nov 2017
  • Changed by Frank Nicholas on 23 Feb 2022
  • Changed by Imke Tammen2 on 07 Mar 2022
  • Changed by Imke Tammen2 on 08 Apr 2022