OMIA:001654-8932 : Feather colour, almond in Columba livia (rock pigeon)

Categories: Pigmentation phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 605513 (gene)

Mendelian trait/disorder: yes

Mode of inheritance: Z-linked incomplete dominant

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2020

Species-specific symbol: St

Species-specific description: Bruders et al. (2020): "The classical pigmentation pattern in C. livia known as Almond is caused by a semi-dominant mutation (St allele) at the sex-linked Stipper (St) locus [Wriedt and Christie, 1925] . . . . Unlike most other pigmentation pattern traits in pigeons, the variegated or sprinkled patchwork of plumage colors in Almond is apparently random within and among individuals . . . Furthermore, the color pattern changes in an unpredictable manner with each molt [Hollander and Cole, 1950; Hollander, 1942; Quinn, 1971]. The number of pigmented feathers in Almond pigeons also increases with each successive molt, and this effect is more pronounced in males . . . . Notably, this phenomenon is the opposite of what is typically observed with pigmentation traits that change throughout the lifespan of an individual, such as vitiligo and graying, which result in a decrease in pigment over time . . . . In addition to Almond, at least six other alleles at St lead to varying degrees of depigmentation in pigeons, suggesting that the St locus might be a mutational hotspot".

Inheritance: Bruders et al. (2020): "Almond is a sex-linked, semi-dominant trait controlled by the classical Stipper (St) locus. Heterozygous males (ZStZ+ sex chromosomes) and hemizygous Almond females (ZStW) are favored by breeders for their attractive plumage. In contrast, homozygous Almond males (ZStZSt) develop severe eye defects and often lack plumage pigmentation, suggesting that higher dosage of the mutant allele is deleterious."

Molecular basis: Bruders et al. (2020) "found a copy number variant (CNV) within the differentiated region that captures complete or partial coding sequences of four genes, including the melanosome maturation gene Mlana. We did not find fixed coding changes in genes within the CNV, but all genes are misexpressed in regenerating feather bud collar cells of Almond birds. Notably, six other alleles at the St locus are associated with depigmentation phenotypes, and all exhibit expansion of the same CNV."

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
MLANA melan-A Columba livia Z NC_088642.1 (60017050..60023754) MLANA Homologene, Ensembl , NCBI gene


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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
1209 Almond MLANA st repeat variation Naturally occurring variant "The CNV captures a 77-kb segment of the reference genome (ScoHet5_227: 5,181,467–5,259,256), with an additional increase in coverage in a nested 25-kb segment (ScoHet5_227: 5,201,091–5,226,635). Read-depth analysis confirmed 7 copies of the outer 77-kb segment and 14 copies of the inner 25-kb segment in the genomes of female (ZStW) Almond pigeons, which have an St locus on only one chromosome. We used PCR to amplify across the outer and inner CNV breakpoints of Almond pigeons and determined that the CNV consists of tandem repeats of the 77-kb and nested 25-kb segments (Fig 3)." (Bruders et al., 2020) 2020 32433666

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2020). OMIA:001654-8932: 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.

2020 Bruders, R., Van Hollebeke, H., Osborne, E.J., Kronenberg, Z., Maclary, E., Yandell, M., Shapiro, M.D. :
A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia). PLoS Genet 16:e1008274, 2020. Pubmed reference: 32433666. DOI: 10.1371/journal.pgen.1008274.
1971 Quinn, J.W. :
The Pigeon Breeders Notebook An Introduction to Pigeon Science. Published by Author, Atwater, Ohio. , 1971.
1942 Hollander, W.F. :
Auto-sexing in the domestic pigeon Journal of Heredity 33:135-140, 1942.
Hollander, W.F. :
Auto-sexing in the domestic pigeon. Journal of Heredity 33:135-140, 1942.
1940 Hollander, W.F., Cole, L.J. :
Somatic Mosaics in the Domestic Pigeon. Genetics 25:16-40, 1940. Pubmed reference: 17246956.
1925 Wriedt, C., Christie, W. :
Zur Genetik der gesprenkelten Haustaube Induktive Abstammungs- und Vererbungslehre 38:271-306, 1925.

Edit History

  • Created by Frank Nicholas on 24 Oct 2011
  • Changed by Frank Nicholas on 03 Jun 2020