- phenotypes


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Gallus gallus, chicken

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Lavender phenotype in chicken

Vaez M, Follett SA, Bed'hom B, Gourichon D, Tixier-Boichard M, Burke T. A single point-mutation within the melanophilin gene causes the lavender plumage colour dilution phenotype in the chicken. BMC Genet. 2008 Jan 15;9:7.

The lavender phenotype in the chicken causes the dilution of both black (eumelanin) and red/brown (phaeomelanin) pigments. Defects in three genes involved in intracellular melanosomal transport, previously described in mammals, give rise to similar diluted pigmentation phenotypes as those seen in lavender chickens.

Lavender phenotype in chicken

The lavender phenotype. Chickens expressing (a) wild type (LAV*N/LAV*N), and (b) lavender (LAV*L/LAV*L), phenotypes on an extended black (E*E) background.

Lavender chicken

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Pea-comb phenotype in chicken

Wright D, Boije H, Meadows JR, Bed'hom B, Gourichon D, Vieaud A, Tixier-Boichard M, Rubin CJ, Imsland F, Hallböök F, Andersson L. Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens. PLoS Genet. 2009 Jun;5(6):e1000512.

The featherless comb and wattles are defining features of the chicken. Pea-comb is a dominant mutation in chickens that drastically reduces the size of the comb and wattles. It is an adaptive trait in cold climates as it reduces heat loss and makes the chicken less susceptible to frost lesions. Whilst the Pea-comb allele was known to show a dominant inheritance and drastically reduce the size of both comb and wattles, the genetics underlying the mutation remained elusive. Chicken comb is primarily composed of collagen and hyaluronan, which are produced by chondrocytes. These cells are formed through the condensation and differentiation of mesenchyme cells during the chondrogenesis pathway, the early stages of which are regulated by SOX transcription factors. In this work authors pinpoint a massive amplification of a duplicated sequence in the first intron of SOX5 as causing the Pea-comb phenotype.

Wild type and pea-comb chickens

Wild-type and Pea-comb chickens. (A) Wild-type male, (B) wild-type female, (C) Pea-comb male and (D) Pea-comb female (Photo by David Gourichon).

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Yellow feet phenotype in chicken

Eriksson J, Larson G, Gunnarsson U, Bed'hom B, Tixier-Boichard M, Strömstedt L, Wright D, Jungerius A, Vereijken A, Randi E, Jensen P, Andersson L. Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS Genet. 2008 Feb 29;4(2)

This study convincingly demonstrates that while domestic chickens inherited the mitochondrial, and most of their nuclear genome from red junglefowl, the yellow skin allele originates from a species of junglefowl other than the red junglefowl, most likely from the grey junglefowl.

Origin of yellow feet phenotype in chicken

A. Map of South Asia onto which the ranges of four species of junglefowl are drawn.
B. European domestic chicken with yellow legs. Red, grey, blue, and green regions represent the respective ranges of red, grey, Ceylon, and green junglefowls.
C. Red junglefowl. D. Grey junglefowl. E. Ceylon junglefowl. F. Green junglefowl.
(Photo: Figures 1B: Björn Jacobsson; 1C: Erik Bongcam-Rudloff; 1D: John Corder, World Pheasant Association; 1E: Jean Howman, World Pheasant Association; 1F: Kenneth W Fink, World Pheasant Association).


Naked neck phenotype in chicken

Mou C, Pitel F, Gourichon D, Vignoles F, Tzika A, Tato P, Yu L, Burt DW, Bed'hom B, Tixier-Boichard M, Painter KJ, Headon DJ. Cryptic patterning of avian skin confers a developmental facility for loss of neck feathering. PLoS Biol. 2011 Mar;9(3):e1001028.

Vertebrate skin is characterized by its patterned array of appendages, whether feathers, hairs, or scales. In avian skin the distribution of feathers occurs on two distinct spatial levels. Grouping of feathers within discrete tracts, with bare skin lying between the tracts, is termed the macropattern, while the smaller scale periodic spacing between individual feathers is referred to as the micropattern. The degree of integration between the patterning mechanisms that operate on these two scales during development and the mechanisms underlying the remarkable evolvability of skin macropatterns are unknown. A striking example of macropattern variation is the convergent loss of neck feathering in multiple species, a trait associated with heat tolerance in both wild and domestic birds. In chicken, a mutation called Naked neck is characterized by a reduction of body feathering and completely bare neck. Here we perform genetic fine mapping of the causative region and identify a large insertion associated with the Naked neck trait. A strong candidate gene in the critical interval, BMP12/GDF7, displays markedly elevated expression in Naked neck embryonic skin due to a cis-regulatory effect of the causative mutation. BMP family members inhibit embryonic feather formation by acting in a reaction-diffusion mechanism, and we find that selective production of retinoic acid by neck skin potentiates BMP signaling, making neck skin more sensitive than body skin to suppression of feather development. This selective production of retinoic acid by neck skin constitutes a cryptic pattern as its effects on feathering are not revealed until gross BMP levels are altered. This developmental modularity of neck and body skin allows simple quantitative changes in BMP levels to produce a sparsely feathered or bare neck while maintaining robust feather patterning on the body.

Naked neck phenotype in chicken

The Naked neck phenotype is caused by a cis-regulatory mutation that results in elevated BMP12 expression.
(A) Adult Na/Na. Feathers are absent on the neck and head, excepting the crown.
(B) E8.5 embryos hybridized with a β-catenin probe to mark the patterning field and feather primordia. Punctate expression of β-catenin in feather placodes is seen on the body but not the neck of the mutant. WT, wild type; Na/Na, Naked neck.
(C) E12.5 embryos showing limited lateral tract expansion (arrows) in Na/Na, reducing body feather coverage.
(D) Quantitative RT-PCR determination of BMP12 expression in body and neck skin of E7.5 and E8.5 wild type and Na/Na embryos.
(E,F) In situ hybridization detecting BMP12 in wild type and Na/Na embryos at (E) E7.5 and (F) E8.5. Wild type and mutant embryos were hybridized and photographed together. Na/Na embryos have elevated and diffuse expression of BMP12 in the skin.
(G) Sequence traces of PCR products from E8.5 Na/+. Genomic DNA PCR products display double peaks following a TA indel polymorphism in the BMP12 3′UTR. RT-PCR products from neck and body skin show a single trace throughout, indicating predominant expression of the Naked neck BMP12 allele, while both alleles are detected in RT-PCR products from other tissues.
(H) Schematic showing insertion of chromosome 1 sequences into chromosome 3 at the Naked neck locus. Chromosome coordinates, the Naked neck identical by descent segment, gene names, exons, untranslated regions, and non-coding elements conserved between chicken and human genomes, based on the ENSEMBL genome viewer, are indicated.

Naked neck rooster

Feathered neck rooster

Different neck phenotype in one brood of chicken


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Recessive White (mow) and Mottled (mo) Plumage Phenotypes in the Chicken

Kinoshita K, Akiyama T, Mizutani M, Shinomiya A, Ishikawa A, Younis HH, Tsudzuki M, Namikawa T, Matsuda Y. Endothelin Receptor B2 (EDNRB2) Is Responsible for the Tyrosinase-Independent Recessive White (mow) and Mottled (mo) Plumage Phenotypes in the Chicken PLoS One. 2014; 9(1): e86361.

Mottled plumage phenotypes in chicken

Wild-type and mottled plumage phenotypes with two different extended black (E) backgrounds in Cochin bantam (CB) and Ehime-jidori (EJ).
(A) The wild-type (Mo+/−) (A-1) and mottled plumage (mo/mo) (A-2) in adult CB females with an E/E genetic background. (B) The wild-type (Mo+/−) (B-1) and mottled plumage (mo/mo) (B-2) in adult EJ females with an e+/e+ genetic background. (C-1) Feathers of the saddle from the wild-type CB female (Mo+/−) (left) and the mottled CB female (mo/mo) (right). (C-2) Feathers of the saddle from the wild-type EJ female (Mo+/−) (left) and the mottled EJ female (mo/mo) (right). (D) Down colour of newly hatched chicks of the wild type (Mo+/−) (D-1, left) and the mottled type (mo/mo) (D-1, right) in CB, and the wild type (Mo+/−) (D-2, left) and the mottled type (mo/mo) in EJ (D-2, right). These mottled-type chicks (mo/mo) have white yellowish down with pigmented spots on the head.

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Scaleless Phenotype in the Chicken

Wells KL, Hadad Y, Ben-Avraham D, Hillel J, Cahaner A, Headon DJ. Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of featherless chickens. BMC Genomics. 2012; 13: 257.

Scaleless phenotype in chicken

The scaleless phenotype.
Gross appearance of a sc/sc chicken. The majority of feathers and all scales are absent.

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The Crest Phenotype in Chicken

Wells KL, Hadad Y, Ben-Avraham D, Hillel J, Cahaner A, Headon DJ. The Crest Phenotype in Chicken Is Associated with Ectopic Expression of HOXC8 in Cranial Skin. PLoS One. 2012; 7(4): e34012.

Crested and wild type chickens

Crested and wild type chickens.
(A–D) Crest phenotype; (E–H) wild-type phenotype; (A and E) Silkie male; (B and F) Silkie female; (C) Chinese fatty chicken male; (D) Chinese fatty chicken female; (G) Chahua chicken male; (H) Chahua chicken female. (I) Overview of cranial feathers with gender indicated, sampled from 44 weeks old Silkie chickens. (a) Crested male; (b) Crested female; (c) Wild-type male; (d) Wild-type female. (J) There was a statistically significant difference in feather length between phenotypes. The number of feathers in each group obtained from three individuals were as follows: Crested male: 47; Crested female: 44; wild-type male: 100; wild-type female: 100 (**, P<0.01).

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Recessive white mutation in chickens

Chang CM, Coville JL, Coquerelle G, Gourichon D, Oulmouden A, Tixier-Boichard M. Complete association between a retroviral insertion in the tyrosinase gene and the recessive white mutation in chickens. BMC Genomics. 2006; 7: 19.

Comparison of plumage color in full sib chickens differing for their genotype at the C locus.

Comparison of plumage color in full sib chickens differing for their genotype at the C locus.
On the left, a chicken carrying the wild type allele at the C locus exhibits a colored plumage as determined by other feather color loci. Here the animal carries the wild type allele at the Extension locus, the wild type allele at the Columbian locus and the silver allele at the Silver locus. On the right, a recessive white chicken, full sib from the previous one, exhibits full white plumage.

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Pea-comb mutation in chickens

Boije H, Harun-Or-Rashid M, Lee YJ, 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. 2012; 7(12): e50890.

Comparison of Pea- and single-comb with respect to comb morphology, Alcian blue cartilage staining and SOX5 expression.

Comparison of Pea- and single-comb with respect to comb morphology, Alcian blue cartilage staining and SOX5 expression.
(A–D) Morphology of E12 and E18, Pea- and single-combs. (E–H) Alcian blue stained cross section of E12 and E18 Pea- and single-combs to visualize cartilaginous structures. Note that in spite of the differences in Pea- and single-comb morphology the underlying cartilage structures are normal. The sections are not exactly on the same level. (I) Bar graph with qRT-PCR results and fluorescence micrographs of immunohistological analysis of SOX5 mRNA levels. Bar graph data are normalized to the b-actin mRNA levels and is related to the b-actin mRNA level. (J–S) Photographs of Pea- (K, L, N–Q) and single combed (J, M, R, S) chicken of the sex and ages as indicated in the figure. E; embryonic day, pc; Pea-comb, sc; single-comb, w; weeks. Scale bars are 250 µm.

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