OMIA:000782-9031 : Pea comb in Gallus gallus (chicken)

Categories: Craniofacial phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 604975 (gene) , 616803 (trait)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal dominant

Considered a defect: no

Key variant known: yes

Year key variant first reported: 2009

Cross-species summary: This phenotype comprises a comb that is greatly reduced in size. The wattles are also usually reduced in size.

Species-specific symbol: P

History: This trait was one of the five first animal traits (all in chickens) whose Mendelian inheritance was documented (by Bateson and Saunders, 1902; pages 87-124) after the rediscovery of Mendel's result. The other four traits are Rose-comb (OMIA 000884-9031), Polydactyly (OMIA 000810-9031), Dominant White (OMIA 000373-9031), and Yellow skin (OMIA 001449-9031).

Inheritance: As noted above, Bateson and Saunders (1902; pages 87-124) provided convincing evidence of Mendelian inheritance (autosomal dominance) of this trait. Heterozygotes tend to have slightly larger combs than homozygotes.

Mapping: The first evidence of linkage involving the pea-comb locus was obtained by Hertweg (1933), who showed pea comb is linked to "marbling" down pattern. Bruckner and Hutt (1939) extended this linkage group to include blue egg. Warren (1949) provided additional data for this linkage group. Several decades later, this linkage group was shown by Bitgood et al. (1980) to correspond to chromosome GGA1. Using a set of SNPs chosen specifically for this purpose, Wright et al. (2009) fine-mapped the locus to the region 67,831,796-68,456,921 bp of GGA1, which contains just one gene, namely SOX5.

Molecular basis: In a striking piece of detective work, Wright et al. (2009) showed that the gene for pea-comb is SOX5, an important transcription factor. The wild-type allele at this locus (which results in normal combs and wattles) has a duplication of approximately 2.5kb of sequence near an evolutionarily conserved region in intron 1. The pea comb mutant phenotype results from large-scale amplification of this duplication: pea comb alleles typically have 20-40 copies of the duplicated sequence, which must be sufficient to interfere with transcription. Thus the pea comb mutation is a regulatory mutation.

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
SOX5 SRY (sex determining region Y)-box 5 Gallus gallus 1 NC_052532.1 (65588747..66230345) SOX5 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
758 Japanese Game Bantam (Chicken) Pea comb SOX5 repeat variation Naturally occurring variant 1 "Pea-comb is caused by a massive amplification of a duplicated sequence located near evolutionary conserved non-coding sequences in intron 1 of the gene encoding the SOX5 transcription factor." The pea-comb mutant phenotype results from large-scale amplification of this duplication: pea comb alleles typically have 20-40 copies of the duplicated sequence, which must be sufficient to interfere with transcription. 2009 19521496

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2022). OMIA:000782-9031: 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.

2023 Ren, X., Guan, Z., Zhao, X., Zhang, X., Wen, J., Cheng, H., Zhang, Y., Cheng, X., Liu, Y., Ning, Z., Qu, L. :
Systematic selection signature analysis of Chinese gamecocks based on genomic and transcriptomic data. Int J Mol Sci 24:5868, 2023. Pubmed reference: 36982941. DOI: 10.3390/ijms24065868.
2019 Noorai, R.E., Shankar, V., Freese, N.H., Gregorski, C.M., Chapman, S.C. :
Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken. PLoS One 14:e0225834, 2019. Pubmed reference: 31821332. DOI: 10.1371/journal.pone.0225834.
2015 Moro, C., Cornette, R., Vieaud, A., Bruneau, N., Gourichon, D., Bed'hom, B., Tixier-Boichard, M. :
Quantitative effect of a CNV on a morphological trait in chickens. PLoS One 10:e0118706, 2015. Pubmed reference: 25768125. DOI: 10.1371/journal.pone.0118706.
2012 Boije, H., Harun-Or-Rashid, M., Lee, Y.J., Imsland, F., Bruneau, N., Vieaud, A., Gourichon, D., Tixier-Boichard, M., Bed'hom, B., Andersson, L., Hallböök, F. :
Sonic hedgehog-signalling patterns the developing chicken comb as revealed by exploration of the pea-comb mutation. PLoS One 7:e50890, 2012. Pubmed reference: 23227218. DOI: 10.1371/journal.pone.0050890.
Imsland, F., Feng, C., Boije, H., Bed'hom, B., Fillon, V., Dorshorst, B., Rubin, C-J., Liu, R., Gao, Y., Gu, X., Wang, Y., Gourichon, D., Zody, M.C., Zecchin, W., Vieaud, A., Tixier-Boichard, M., Hu, X., Hallböök, F., Li, N., Andersson, L. :
The rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb morphology and defective sperm motility. PLoS Genetics 8(6):e1002775, 2012. Pubmed reference: 22761584. DOI: 10.1371/journal.pgen.1002775.
2010 Sato, S., Sato, S., Otake, T., Suzuki, C., Uemoto, Y., Saburi, J., Hashimoto, H., Kobayashi, E. :
Sequence analysis of a pea comb locus on chicken chromosome 1. Anim Genet 41:659-61, 2010. Pubmed reference: 20412124. DOI: 10.1111/j.1365-2052.2010.02048.x.
2009 Wright, D., Boije, H., Meadows, J.R., Bed'hom, B., Gourichon, D., Vieaud, A., Tixier-Boichard, M., Rubin, C.J., Imsland, F., Hallböök, F., Andersson, L. :
Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens. PLoS Genet 5:e1000512, 2009. Pubmed reference: 19521496. DOI: 10.1371/journal.pgen.1000512.
2007 Halima, H., Neser, FW., van Marle-Koster, E., de Kock, A. :
Phenotypic variation of native chicken populations in northwest Ethiopia. Trop Anim Health Prod 39:507-13, 2007. Pubmed reference: 17969713.
2001 Carefoot, WC. :
Inheritance of the black hackle of the Indian Game bantam. Br Poult Sci 42:274-5, 2001. Pubmed reference: 11421339. DOI: 10.1080/00071660120048555.
2000 Bitgood, JJ., Briles, RW., Briles, WE. :
Further tests for genetic linkages of three morphological traits, three blood groups, and break points of two chromosome translocations on chromosome one in the chicken. Poult Sci 79:293-5, 2000. Pubmed reference: 10735192.
1996 Bartlett, J.R., Jones, C.P., Smith, E.J. :
Linkage analysis of endogenous viral element 1, blue eggshell, and pea comb loci in chickens Journal of Heredity 87:67-70, 1996. DOI: 10.1093/oxfordjournals.jhered.a022957.
1995 Smith, E., Mutayoba, S., Nahashon, S., Bartlett, J. :
Nutritional homeostatic capacity of a three-breed cross in poultry and associated effects of genotypes at the pea comb and endogenous viral element 1 loci. Poult Sci 74:1577-85, 1995. Pubmed reference: 8559720.
1993 Carefoot, WC. :
Further studies of linkage and mappings of the loci of genes in group 3 on chromosome 1 of the domestic fowl. Br Poult Sci 34:205-9, 1993. Pubmed reference: 8467400. DOI: 10.1080/00071669308417576.
Shoffner, R.N., Otis, J.S., Garwood, V.A. :
Association of dominant marker traits and metric traits in chickens. Poultry Science 72:1405-1410, 1993. Pubmed reference: 8378215.
1992 Smyth, J.R., Deleon, F.A.P. :
Linkage relationship between the pea comb (P) and extended black (E) loci of the chicken Poultry Science 71:208-210, 1992.
1991 Bitgood, J.J., Kendall, R.L., Briles, R.W., Briles, W.E. :
Erythrocyte alloantigen loci Ea-D and Ea-I map to chromosome 1 in the chicken. Anim Genet 22:449-54, 1991. Pubmed reference: 1789498.
1990 Carefoot, W.C. :
Test for linkage between the eumelanin dilution blue (B1), the extended black (E) allele at the E-locus and the linked pea comb (P) and eumelanin extension (M1) genes in the domestic fowl. British Poultry Science 31:465-472, 1990. Pubmed reference: 2245344. DOI: 10.1080/00071669008417279.
1987 Carefoot, W.C. :
Relative positions of the loci of the peacomb (P), eumelanin restrictor (Db), eumelanin extension (Ml) and plumage pattern (Pg) genes of the domestic fowl British Poultry Science 28:347-350, 1987. Pubmed reference: 3607559. DOI: 10.1080/00071668708416968.
1983 Bitgood, J.J., Otis, J.S., Shoffner, R.N. :
Refined linkage value for comb and blue Egg: lack of effect of pea comb, blue egg, and naked on age at first egg in the domestic fowl. Poultry Science 62:235–238, 1983. DOI: 10.3382/ps.0620235.
1980 Bitgood, JJ., Shoffner, RN., Otis, JS., Briles, WE. :
Mapping of the genes for pea comb, blue egg, barring, silver, and blood groups A, E, H, and P in the domestic fowl. Poult Sci 59:1686-93, 1980. Pubmed reference: 7413575. DOI: 10.3382/ps.0591686.
1973 Zartman, DL. :
Location of the pea comb gene. Poult Sci 52:1455-62, 1973. Pubmed reference: 4773336.
1968 Buckland, RB., Hawes, RO. :
Comb type and reproduction in the male fowl segregation of the rose and pea comb genes. Can J Genet Cytol 10:395-400, 1968. Pubmed reference: 5699835.
1959 Kan, J., Manasco, B.D., Gyles, N.R., Smith, R.M. :
The effect of comb-type genotypes on six metric traits in a population of meat-type chickens Poultry Science 38:826-828, 1959.
1949 Warren, DC. :
Linkage relations of autosomal factors in the fowl. Genetics 34:333-50, 1949. Pubmed reference: 17247319.
1940 Munro, S.S., Kosin, I.L. :
Breast ridge in domestic fowl, a new dominant character linked with pea comb or another expression of the pea comb gene? American Naturalist 74:382-384, 1940.
1939 Bruckner, JH., Hutt, FB. :
Linkage of pea comb and blue egg in the fowl Science 90:88, 1939. Pubmed reference: 17798917. DOI: 10.1126/science.90.2326.88.
1938 Warren, D.C. :
Mapping the genes of the fowl (abstract) Genetics 23:174 only, 1938. DOI: 10.1093/genetics/23.1.139.
1933 Hertwig, P. :
Geschlechtsgebundene und autosomale Koppelungen bei Hühnern Verh. Deutsch. Zool. Ges . :112-118, 1933.
Warren, D.C. :
Nine independently inherited autosomal factors in the domestic fowl. Genetics 18:68-81, 1933. Pubmed reference: 17246678.
1908 Bateson, W., Punnett, R.C. :
Experimental studies in the physiology of heredity. Poultry Reports of the Evolution Committee of the Royal Society 4:18-35, 1908.
1905 Bateson, W., Punnett, R.C. :
Experimental studies in the physiology of heredity. Poultry. Reports to the Evolution Committee of the Royal Society 2:99-119, 1905.
Bateson, W., Punnett, R.C. :
A suggestion as to the nature of the "walnut"comb in fowls Proceedings of the Cambridge Philosophical Society 13:165-168, 1905.
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 16 Jun 2009
  • Changed by Frank Nicholas on 10 Sep 2011
  • Changed by Frank Nicholas on 09 Dec 2011
  • Changed by Frank Nicholas on 05 Jul 2012
  • Changed by Frank Nicholas on 07 Dec 2012
  • Changed by Frank Nicholas on 30 Jul 2013
  • Changed by Frank Nicholas on 16 Apr 2020
  • Changed by Frank Nicholas on 23 Feb 2022