A review of genetic variation underlying chicken phenotypic diversity

Janet E Fulton; Amy M McCarron; Abigail Mullen; Lowdan Ali; Katy J Tarrant

doi:10.1016/j.psj.2025.105761

. 2025 Sep 1;104(11):105761. doi: 10.1016/j.psj.2025.105761

A review of genetic variation underlying chicken phenotypic diversity

Janet E Fulton ^a, Amy M McCarron ^a, Abigail Mullen ^a, Lowdan Ali ^a, Katy J Tarrant ^b,^⁎

PMCID: PMC12683159 PMID: 40946656

Abstract

Chickens exhibit extensive phenotypic diversity, much of which is found within local landraces as well as historical and commercially utilized breeds across the globe. These breeds have preserved a wide array of observable and quantifiable traits, including differences in feather structure, pigmentation, comb morphology, and skeletal development. Progress in molecular genetics has identified the genetic variants underlying many of these traits, offering valuable insights into how individual genes, regulatory elements, and genetic pathways influence development and morphology. These discoveries also highlight the importance of chickens as a model organism for studying vertebrate embryogenesis, gene interactions, core cellular mechanisms, and as a distinctive animal model for rare human diseases. Much of the research published on the molecular genetic mechanisms of this phenotypic variability is scattered across diverse, often specialized scientific publications, making it difficult for interested individuals to easily access a consolidated view of known genotype-phenotype relationships in chickens. This review addresses that gap by assembling a summary of 46 chicken phenotypes for which the causative gene and underlying mutation have been identified. An additional 11 traits for which the associated chromosomal region is known but the precise causative variant remains unresolved are also included. Where available, photographic images of each phenotype are provided to support breed documentation efforts and serve as a visual reference for researchers and students. By compiling this information in a single, accessible source, the review aims to support a wide range of users while highlighting the unique contributions of chickens to functional genetics.

Keywords: Genetics, Phenotype, Rare breeds, Genetic variation

Introduction

Generations of selective breeding of multiple phenotypic variants in the chicken (Gallus gallus) have resulted in many diverse chicken breeds now known globally. The American Poultry Association Standard of Perfection classifies poultry breeds using multiple traits, which include features such as feather color, feather morphology, comb shape and size, body size, specific bone length, number of toes, and egg color (American Standard of Perfection, 1993). More than 50 unique chicken breeds exist, plus multiple variants within these breeds that differ by feather color, comb type, or other specific features. Furthermore, other unique breeds are known, both historical and indigenous, in European and Asian countries.

The chicken has long served as a valuable model organism for vertebrate research. The ease of embryonic accessibility in chickens, combined with precise developmental staging plus ease of embryonic manipulation, makes them uniquely suited for studying the consequences of specific mutations in vivo. Early studies of Mendelian inheritance in animals were reported by Bateson (1902) with multiple examples from chickens, including observations that traits, such as the Andalusian coloring, do not breed true due to heterozygosity of ‘dissimilar allelomorphs’. Additionally, the walnut comb trait was revealed to result from a combination of rose and pea comb alleles, identified as ‘dihybridism’ (Bateson, 1902; Bateson and Punnett, 1906).

The identification of blood groups in the chicken by Landsteiner and co-workers solidified the value of the chicken as a biomedical animal model for human diseases (Landsteiner and Miller, 1924). Within the US, the number of university departments with a focus on poultry research increased from 2 in 1910 to 44 in 1950 (Thaxton et al, 2003). Many of the chicken genetic variants discussed within this manuscript were originally reported in the 1950s-1960s, likely due to the large number of poultry science departments with available resources and scientific expertise. Elwood Briles initiated the intense study of chicken blood groups in the early 1950s, and along with Doug Gilmour, identified the 13 currently identified chicken blood systems (Briles et al., 1950a; Briles, 1962; Briles, 1984; Gilmour, 1959). Early mapping studies attempted to determine genomic relationships between the genes responsible for the visible chicken genotypic variants, including blood systems and various enzyme polymorphisms. Classical linkage groups were developed based on segregation ratios occurring in progeny of crosses utilizing specific parental phenotypes and chromosomal rearrangement breakpoints (where applicable), and 8 linkage groups were described by Bitgood and Somes (1990). An integrated genetic and physical map of the chicken genome was described by Burt and co-workers (1995) which combined information from two chicken reference populations East Lansing, US and Wageningen, NL) and utilized multiple genetic markers including microsatellites, ev gene loci, and chicken repeat elements (CR1) with a total of 461 markers, resulting in the identification of 33 linkage groups. With the subsequent development of additional DNA markers, more detailed maps were produced with 1889 loci identifying 50 linkage groups (Groenen et al., 2000). Gene expression microarrays provided critical information on tissue expression, defined level of transcription, and variation within genes, all of which aided in gene identification in conjunction with genomic sequencing (Burnside et al., 2005).

One hundred years after the seminal work of Bateson and Punnett, the chicken became the first agricultural animal to have its genome sequenced. The genome, obtained from an inbred Red Jungle Fowl at the University of California, Davis, was published in 2004 (Hillier et al., 2004). Simultaneously, 2.8 million single nucleotide polymorphisms (SNP) were identified within three different chicken breeds: an inbred White Leghorn layer line, commercial broiler samples, and the Silkie breed (Wong et al., 2004). Arrays are now available that can rapidly provide genotypes for up to 600,000 SNP from one DNA sample, and the cost of genome sequencing has decreased to less than $200 per genome.

These resources have provided a foundation for genetic studies, which were further enhanced by developing various genomic analysis tool sets. Such tools enabled access to genomic sequences, gene identification, and annotation. Researchers were then able to perform comparative genomic studies across multiple species, significantly advancing the field of avian genetics. The application of genome-based tools has facilitated the identification of genes associated with novel phenotypes and, in many cases, the specific genetic variants responsible for these traits. This has allowed researchers to connect phenotype (observable characteristics) with genotype (gene information) at a much deeper level. The term "phenomics" has recently been introduced to describe the systematic study of these connections, highlighting the growing importance of integrating genomic and phenotypic data in research.

This manuscript has two objectives. The first objective is to summarize 46 variants in the chicken for which the gene or causative mutation is now known. The genetic basis behind these variants is published in multiple journals. A recent book chapter provides an excellent summary of those variants with their responsible genes that impact color in chickens in both feather and skin (Andersson et al., 2020). This manuscript was inspired by that specific reference, with the goal of providing a single source as an easy reference to genetic information underlying the numerous phenotypic variants found in the chicken breeds of today. Each trait is briefly described, followed by the currently known molecular genetic information. These are not meant to be exhaustive descriptions but rather provide a general introduction to the phenotype with identified gene and responsible genetic variation mechanisms. The second objective was to indicate the relevance or application of this information to other sectors of biology and genetics (where possible). Each mutation provides insights into fundamental biological processes related to development, embryonic patterning, gene interactions, and/or gene functions. Several of these variants also serve as valuable animal models for specific human diseases.

The locations provided herein of each gene are based on the chicken genome build 6 (GRCg6a/galGal6), an improved version of the original inbred Red Jungle fowl line from the University of California, Davis (Hillier et al., 2004). Recently, two new genomes, one from a broiler (GRCg7b) and one from a White Leghorn (GRCg7w), have been sequenced with improved annotation, accuracy, and variation detection (Warren et al., 2023). Specific base pair locations of the genes and their relevant variants have not been indicated, as these can change depending on which genome build and which genetic resource is providing the genome location information. For example, KRT75 is reported at chr33:5,241,761-5,245,597 (UCSC: GRCg6a/galGal6) vs chr34:2,056,921-2,060,738 (Ensembl: bGalGal1.mat.broiler.GRCg7b) and Sox5 (Pea comb) is located at chr1:66,093,644-66,566,305 (Ensembl; bGalGal1.pat.whiteleghornlayer.GRCg7w) vs chr1:65,772,453-66,226,631 (Ensembl: bGalGal1.mat.broiler.GRCg7b). This information can be obtained from any public domain genome database, including UCSC, NCBI, and Ensembl.

Only those variants for which the specific gene and, in many cases, the causative mutation are included in this review. There are multiple additional phenotypic variants in the chicken for which the gene is not known, though for some, at least a chromosomal region has been defined. Unfortunately, many of these variants are no longer available for study as poultry genetic stocks have rapidly been eliminated over the past five decades (Pisenti et al., 2001; Fulton and Delany, 2003; Miller, 2004).

Within this review, the phenotypic variants are grouped by the central region or tissue affected, acknowledging that many of these variants impact multiple areas or tissues. Table 1 provides a summary of the described variant phenotypes. To assist with historical identification, the original assigned gene name is included. For variants associated with specific breeds, examples of relevant breeds are provided. The table also includes the responsible gene and the genetic variant identified as the causative mutation. A brief description of DNA variant type is also provided to illustrate the wide range of genetic mutations that cause the phenotypes. The most common genetic variation identified is the SNP (single nucleotide polymorphism), a single base pair change in the DNA sequence. This single change can have many consequences depending on the specific change and its location within a gene. This can include a change in the amino acid sequence of the final protein product, a deletion of an internal portion of a protein, truncation of a large segment of the final transcribed product, failure to produce the gene product, or misexpression of the gene product. Copy number variants (CNV) may reflect a short duplication of a specific genomic region or a larger duplicated portion of the genome. These CNVs may influence a regulatory element, interrupt gene transcription, or cause aberrant gene expression. A deletion (DEL) can remove a segment of or an entire gene. The term INS indicates an insertion of a genomic DNA sequence into a novel location, while the term EV indicates an insertion of either a complete or partial sequence of avian endogenous retroviral DNA into the chicken genome. Duplication (DUP) describes the duplication and subsequent insertion of this duplicated DNA near the original location, and Inversion (INV) indicates a large piece of chromosomal DNA has been moved, or flipped in its chromosomal location, thus potentially impacting multiple genes, both within the affected chromosomal segment and nearby to the insertion sites. Details on the specific mutation type involved can be found in the text's more detailed descriptions. It should also be noted that some of the phenotypic variations found may result from a combination of several genetic mechanisms. Fig. 1 serves as a companion to Table 1, providing an approximate visual reference for the relative chromosome positions of genes associated with the described phenotypic traits. Only phenotypes with known chromosome locations are shown, offering context for how these genes are positioned in relation to one another within the chicken genome.

Table 1.

Summary of genetic information for the phenotypic variants.

	Phenotype	Original Gene Name	Common Breed sources	Chr	New Gene Name	Human Model	Variant Type	Fig. #
Integument
	Pea Comb	P	Brahma, Buckeye, Araucana	1	SOX5	-	CNV	1
	Rose-comb	R	Hamburg, Wyandotte	7	CCDC108, MNR2	sperm motility disorders	INV	2, 15
	Walnut Comb	P and R	Wyandotte	1, 7				3
	Duplex Comb	D; DC and DV alleles	Sicillian Buttercup, Crevecoeur	2	CMC1, EOMES	-	DUP	4, 5
Feather
	Crest	Cr	Crevecoeur, Polish	33	HOXC10	-	DUP	6, 7, 25
	Ear tuft	Et	Araucana	15	TXNRD2	DiGeorge syndrome	DEL	8
	Fast/Slow feathering	K	White Leghorn	Z	PRLR	-	DEL, DUP	9, 10
	Feathered shanks	Pti1 and Pti2	Silkie, Langshan, Cochin	13, 15	PITX1, TBX5	-	DEL, SNP	11, 12, 13
	Frizzle	F	-	33 (34)	KRT75 or KRT75L4	-	DEL	14
	Henny Feathering	Hf	Sebright, Campine	10	CYP19A1 (aromatase)	-	EV	15
	Muff and Beard	Mb	Crevecoeur, Houdan, Faverolles	27	HOXB8	-	DUP	16
	Naked Neck	Na	Naked Neck, Turken	3	BMP12 (GDF7)	-	INS	17
	Scaleless	sc	-	4	FGF20	-	SNP	18
	Silky	h (hookless)	Silkie	3	PDSS2	-	SNP	19
Skeletal
	Cleft Palate	cpp (cleft primary palate)	-	11	ESRP2	-	DEL	-
	Creeper	Cp (Creeper)	Japanese Bantam, Scots Dumpy	7	IHH, NHEJ1	-	DEL	20
	Dwarfism, Autosomal	adw	-	1	TMEM263	-	SNP	21
	Dwarfism, Sex-linked	SLD (sex-linked dwarfism)	-	Z	GHR	Laron syndrome	DEL; SNP	21
	Limbless	ll	-	2	Sp8 (candidate)	limb development	Unk	22
	Nanomelia	nm (nanomelia)	-	10	ACAN	aggrecan associated diseases	SNP	-
	Polydactyly	Po (polydactyly)	Dorking, Houdan, Silkie	2	Shh, possible others	preaxial polydactyly	SNP	23, 24
	Rumpless, dominant	RP (rumplessness)	Araucana	2	Irx1, Irx2, others	-	SNP	25
	Rumplessness, sex-linked		Hongshan	Z	possible pseudogene	-		-
	Talpid 2	ta2	-	1	C2CD3	oral-facial-digital syndrome	DEL	-
	Talpid 3	ta3	-	5	KIAA0586	Joubert syndrome	INS	-
	wingless2	wg-2	-	12	RAF1	RASopathy	SNP	-
	wingless, sex-linked	ws	-	Z	-	-	-	-
Cellular
	Blood type A	Ea-A	-	26	C4BPM	-	SNP	-
	Blood type B	Ea-B	-	16	MHC region	-	SNP	-
	Blood type D	Ea-D	-	1	CD99	-	SNP	-
	Blood type E	Ea-E	-	26	FCAMR	-	SNP	-
	Blood type I	Ea-I	-	23	RHCE	-	SNP	-
	Hypolipedemia	y (recessive yellow)	-	Z	ABCA1	Tangier Disease	SNP	-
	Tumor virus resistance-A	tva	-	28	CD320	-	DEL, SNP	-
	Tumor virus resistance-B	tvb	-	22	TNFRSF10B	-	SNP	-
	Tumor virus resistance-C	tvc	-	28	BTN1A1	-	SNP	-
	Tumor virus resistance-J	tvj	-	23	NHE1	-	SNP	-
	Ev genes1	ev; erv	-	multiple locations		-	EV	-
	Fishy taint	FT	-	8	FMO3	trimethylaminuria	SNP	-
Soft tissue
Eye	Blindness rc	rc (rods and cones); rd (retinal degeneration)	-	1	GUCY2D	Leber’s congenital amaurosis	DEL	-
	Blindness Rdd	Rdd (retinal dysplasia and degeneration)	-	Z	MPDZ	retinitis pigmentosa	SNP	-
	Blindness rge	rge (retinopathy globe enlarged)	-	1	GNB3	Night blindness	DEL	-
Muscle	Muscular Dystrophy	AM (abnormal muscling)	-	2	WWP1	-	SNP	-
Ovary	Restricted ovulator	ro (restricted ovulator)	-	Z	VLDLR	-	SNP	-
Other
	Blue Shell	O (oocyanin)	Araucana	1	SLC01B3	-	EV	26
	Epilepsy	epi, Fepi	-	25	SV2A	Photosensitive epilepsy	SNP	-

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Fig 1 — Visual representation of the approximate location of genes known to impact phenotypic traits in the chicken. Ev genes are not included as they are too numerous and found in multiple genomic locations. Chicken phenotypic variants for which a chromosome and specific region have been defined, but the actual causative gene or variant is unknown, are indicated by †.

Every effort was taken to include images that reflect the actual phenotype, as shown in Table 1. The Livestock Conservancy was instrumental in providing many beautiful photographs of the breeds exhibiting these variants. There are many additional phenotypic variants that have been described over the past century or more. For some of these, a specific chromosome or gene region is identified, but no specific gene or causative mutation is known (see Table 2). The improvements in the development of molecular biology tools, including greatly decreased genomic sequencing costs, chicken pan-genome sequences, and GWAS (Genome-wide association studies), could be applied to these mutant stocks to identify the responsible gene, if the genetic stocks still exist.

Table 2.

Chicken phenotypic variants for which a chromosomal and/or specific region has been defined, but the causative gene or genetic defect is unknown.

Trait	Gene Symbol	Chromosome^*	Description	Reference
Coloboma	co	Z (0.176Mb)	eye, craniofacial defects, polydactyly	Robb et al., 2013
Congenital Loco	lo	12 (1.1Mb region)	RIR, dorsal backward bending of neck	Okumura et al., 2013
Congenital Loco	lo	Z (3.3Mb region)	Silkie (lack of muscle control in neck)	Shiina and Kobayashi, 2024
Diplopodia-1	dp-1	1 (0.586Mb)	polydactyly	O'Hare et al., 2019
Diplopodia-3	dp-3	24 (0.95Mb)	polydactyly	Robb et al., 2011
Diplopodia-4	dp-5	Z (2.67Mb)	polydactyly	Robb et al., 2011
Eudiplopodia	eu	5 (1.07Mb)	5-9 extra digits on feet	Robb et al., 2011
Scleroderma	sc	2, 12 and 14	ischemic lesions of comb	Ek et al., 2012
Stunted tail	none assigned	Z (0.2Mb)	Honshan (abnormal feather development)	Wang et al., 2017
Vulture hocks	V	13 (2.2Mb)	flight-type feathers on tibia	Dorshorst et al., 2010
Stumpy	stu	10 (1.8Mb)	conical leg buds, nonvascularized allantois	Robb et al., 2011

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^⁎

Identified chromosome associated and estimated size of region of interest (within parentheses)

Mutant phenotypes

Integument–combs

The comb is a fleshy growth on the top of the head. This organ, unique to the chicken, is important for body temperature regulation, as well as serving as an indicator of sexual maturity and general health. There are multiple variations of the chicken comb, with the single comb found in the wild Jungle Fowl ancestors of the domestic fowl. This single comb is a thin, vertical, and flat tissue with several distinct peaks on the top. It may be upright or fall over to one side of the head. There are eight distinct comb types described, which include buttercup, cushion, pea, rose, single, strawberry, V-shaped (duplex), and walnut, present in different chicken breeds (American Standard of Perfection, 1993). The underlying genetic cause of these variants has been reported for pea, rose, walnut, and duplex comb. Images of the wild-type single comb are shown in later figures (e.g., Fig. 13).

Fig 13 — Mille fleur d’Uccle Bantam male with feathered shanks (moderate). Also has a single comb, muff, and beard. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

Pea Comb. The pea-comb mutation (Fig. 2) was one of the four traits in chickens used as examples of Mendelian inheritance in animals over 100 years ago (Bateson, 1902). The pea comb shape and size are greatly modified from the wild-type. The homozygote has three longitudinal rows of papilla, whilst the heterozygotes have one primary central blade with less conspicuous lateral ridges. The comb and wattles are greatly reduced in size compared to the wild-type. Fig. 2 shows a pea comb in a young pullet of the Buckeye breed, where the three ridges can be seen. Fig. 9 also shows a pea comb of an older Araucana male, with less obvious definitive ridges. The pea comb is also associated with a thickened ridge of skin running over the length of the keel bone (Crawford, 1960). The phenotypic differences between homozygotes and heterozygotes indicate that pea comb is due to an autosomal gene with incomplete dominance (Hutt, 1949). The pea comb phenotype is considered to provide adaptive advantages in cold habitats as the greatly diminished size of the comb and wattles results in less heat loss and frostbite (Wright et al., 2009).

Fig 9 — Araucana breed rooster with ear tufts and pea comb. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

The Pea-comb mutation is due to a tandem repeat of a duplicated sequence in intron 1 of the SOX5 gene (SRY box transcription factor 5) on chromosome 1 (Wright et al., 2009). Wild-type birds have two copies of the duplicated sequence, whereas all birds with the pea-comb mutation (from multiple breeds) have 20-40 copies, with smaller comb size correlated with increased copy number. The duplicated sequence is located between two Evolutionarily Conserved Non-Coding Sequences (ECNS), contains small CpG islands, as well as chicken repeat 1 elements (CR1), which may be involved in transcriptional regulation (Wright et al., 2009). The copy number variation (CNV) mutation causes an ectopic expression of SOX5 during morphogenesis of the comb (Moro et al., 2015). Due to the ectopic expression of SOX5, the mesenchyme response to SHH (sonic hedgehog) is changed, thereby altering comb morphogenesis. Experimental blocking of the SHH signaling resulted in a single-comb (wild-type) phenotype being transformed into a pea-comb-like appearance. This suggests that SHH regulation of comb development is distorted by the ectopic SOX5 expression (Boije, 2012).

Rose-Comb. The Rose-comb mutation results in a drastically altered comb phenotype as compared to the wild-type single-comb (see Fig. 3). The Rose-comb is flat, broad, and fleshy, terminating in a well-developed tapering spike (American Standard of Perfection, 1993). It is found in multiple breeds, with the general shape varying between breeds. Low fertility associated with the Rose-comb White Wyandotte breed was reported by Hutt (1940). Subsequent studies found that males homozygous for the Rose-comb allele had both reduced fertility and a shorter duration of fertility, while Rose-comb females had normal fertility (Crawford and Smyth, 1964a, 1964b). A similar study, utilizing the Rose-comb Silver Spangled Hamburg breed, confirmed the same negative impact of the Rose-comb phenotype on both fertility and duration of fertility in homozygous males (Crawford et al., 1971). The bantam Sebright rooster shown in Fig. 16 is an example of a Rose-comb with a typical spike. Fig. 3 shows a Dominique breed rooster with a Rose-comb.

Fig 16 — Faverolles breed, with muff and beard, and exhibiting a single comb. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

The Rose-comb phenotype is postulated to be caused by the disruption of the CCDC108 (coiled-coil domain containing 108) gene due to a structural rearrangement with an inversion breakpoint (Imsland et al., 2012). This large 7.4 Mb inversion moves the MNR2 (Multimerin 2) gene to a new location, causing misexpression of the gene during comb development. Gene products of CCDC108 and MNR2 are expressed in Rose-combed embryos, but not the wild-type embryos, suggesting that the rose-comb mutation is caused by ectopic expression of MNR2. The CCDC108 disruption is attributed to the 23.88 Mb breakpoint location of the inversion. CCDC108 protein is considered part of the sperm flagellum, as it is a major sperm protein and is expressed in the testis. Hence, the gene disruption leads to poor sperm motility (Imsland et al., 2012). Mutations in the CCDC108 gene (also called CFAP65) are associated with male infertility in humans and mice (Wang et al., 2019).

Walnut Comb. The walnut comb is large, rounded, and flat, with grooves on the surface, resembling a walnut (Fig. 4). The phenotype results from the presence of the pea and Rose-comb genetic variants described previously (Hutt, 1949). Walnut comb is the first known example of gene interaction (in this case between the pea and Rose-comb variants) as described by Bateson (1902).

Duplex Comb. There are two different types of duplex combs. The Buttercup (genetic variant is called D*C), which is a cup-shaped comb with medium-sized points surrounding the cup (Fig. 5). The V-shaped comb (genetic variant is called D*V) has a greatly reduced comb mass with two points (V-shaped) in the anterior portion of the comb (Fig. 6; Somes, 1991; Dorshorst et al., 2015). The Duplex comb phenotypes are inherited in an incomplete dominant fashion. Crosses between breeds with different Duplex variants showed that the V-shaped comb is dominant over the Buttercup comb, whereas both are dominant over the normal single comb (Somes, 1991).

Fig 5 — Buttercup (breed) rooster with buttercup comb. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

Fig 6 — Crevecoeur (breed) rooster with a V-comb and exhibiting a crest, muff, and beard. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

The V-shape and Buttercup phenotypes are associated with a tandem duplication of ∼20Kb in an intron of the CMC1 (C-X9-C motif containing) gene (Dorshorst et al., 2015) on chromosome 2. This region includes putative cis-regulatory elements of the eomesodermin gene (EOMES), a T-box transcription factor gene. Expression of EOMES in the embryonic comb region of D*C and D*V embryos is elevated compared to the levels in a wild-type embryo (D*N). The V-shape and the Buttercup alleles have the identical 20 Kb duplication. The specific genetic variant that differs between the two alleles was not identified (Dorshorst et al., 2015).

Feathers

Feathers are a defining characteristic of birds. They are multi-purpose in providing essential functions such as insulation, flight, and protection (as reviewed in Lucas and Stettenheim, 1972; Pass, 1995; Stettenheim, 2000). Chickens’ feather structure differs depending on sex, location on the body, and genetics. Sexual dimorphism in feathering is well-known, with males having more elongated and decorative plumage, especially in the hackle, saddle, and tail areas. Conversely, females tend to have more consistent and compact feathers. Feather growth follows a highly organized pattern, originating from specific feather tracts, or pterylae, which are interspersed with featherless regions known as apteria (Yu et al., 2004). Variation in feather type and distribution across body regions is closely linked to function; for example, contour feathers provide aerodynamic efficiency, down feathers offer thermal insulation, and flight feathers contribute to locomotion and maneuverability. Beyond their biological importance, feathers have contributed to broader scientific understanding. They serve as a model system for studying morphogenesis, evolutionary development, and genetic inheritance in vertebrates (as in Sawyer and Knapp, 2003; Lin et al., 2006). The genetic mechanisms underlying feather phenotype in chickens ultimately provide valuable insight, serving as a model for developmental processes and the genetic basis of trait inheritance in avian species, while also contributing to our understanding of evolutionary adaptations.

Crest. The chicken crest is a phenotypic variant in which the feathers on the top of the head are elongated and point upwards, resulting in a tuft of feathers on top of the head. Crested chickens have ancient origins, being reported in both Roman (4th century) and European (16th century) archaeological sites (Brothwell, 1979; Gal et al., 2010). The Crest phenotype is found in multiple breeds exhibiting high variability in both size and degree of ‘spikeyness’. Larger-sized feather crests, such as those found in Polish and Sultan breeds, are also associated with cerebral hernia (Yoshimura et al., 2012). Feather morphology differs in males vs females, with males having pointed feathers and females having more rounded feathers. This is consistent with Crest being a homeotic mutation, in which the location of specific gene expression is altered, in this case, dorsal saddle feathers (pointed in males, rounded in females) expressed in the head region (Wang et al., 2012; Li et al., 2021). The differences in the female vs male crest feathers can be seen in Figs. 7 and 8, representing female and male examples, respectively.

Fig 7 — Polish breed hen with a Crest. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

Fig 8 — Bearded buff laced Polish male with a Crest. This bird also has the muff and beard traits. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

The crest phenotype is inherited in a partially dominant manner, in which homozygous Crest birds (Cr/Cr) have a more pronounced phenotype than heterozygotes (Somes, 1990; Yoshimura et al, 2012). Early genetic mapping studies reported Crest as belonging to the linkage group consisting of Crest (Cr), dominant white (I), and Frizzling (F) (Warren and Hutt, 1936), which was subsequently defined as linkage group II (Bitgood and Somes, 1990).

Using GWAS analysis of a Silkie (crested) and White Plymouth Rock (non-crested) cross F₂ population, the genomic region responsible for the Crest phenotype was found on an unplaced scaffold (build GalGal3) identified as linkage group LGE22C19W28_E50C23 (Wang et al., 2012). This linkage group was not assigned a chromosomal location in the early chicken genome build, but was subsequently determined to be microchromosome 33 (Warren et al., 2017). Crest was mapped to the HomeoboxC (HOXC) gene cluster. The HOXC gene cluster in the chicken contains 10 HOXC genes, with homology to human HOXC genes that are important for cell position identity on the anterior-posterior axis. Ectopic expression of HOXC8 was found in the cranial region of birds with the Crest phenotype (Wang et al., 2012). With an updated chicken genome build (GalGal6), sequence was obtained from multiple breeds of Crested and non-crested birds for this HOXC region. All Crested samples contained a 197bp duplication within the intron of HOXC10 that was not present in non-crested birds, and it was proposed that this duplication involves an enhancer element that could impact expression of the HOXC gene cluster (Li et al., 2021).

The chicken microchromosome 33 also contains those genes now known to be responsible for Frizzle (KRT75; keratin 75) and Dominant White (PMEL17; premelanosome protein 17), thus confirming the early linkage studies showing that Crest, Frizzle, and Dominant White are in the same linkage group (Ng et al, 2012; Kerje et al., 2004).

Ear Tuft. Ear tufts are elongated feathers that protrude from the side of the chicken’s head near the ear (Fig. 9). They are feather-covered epidermal protrusions (peduncles) and are also associated with structural anomalies of the head, throat, and auditory canals (Somes and Pabilonia, 1981). The presence of ear tufts is a breed requirement for the Araucana breed (American Standard of Perfection, 1993). The gene was originally assigned the symbol Et for ear tuft and was determined to be inherited in a dominant manner with embryonic lethality of homozygotes occurring at 17-19 days of incubation (Somes, 1978; Somes and Pabilonia, 1981).

Using genome-wide association and haplotype analysis, a region on chromosome 15 was identified as containing the candidate gene for ear tufts (Noorai et al., 2012; Noorai et al., 2019). Ear tuft birds contained an 8.4 kb deletion on chromosome 15, encompassing an exon and intron of the gene TXNRD2 (thioredoxin reductase 2). This genome region is syntenic with human chromosome 22 and includes the genes TBX1 (T-box transcription factor 1), GNB1L (G protein subunit beta 1 like), and TXNRD2. DiGeorge syndrome is an autosomal dominant syndrome caused by microdeletions of human chromosome 22, resulting in haplodeficiency of TBX1 and affecting other genes in this syntenic region (Chieffo et al., 1997). TBX-1 is a transcription factor involved in the regulation of developmental processes. Physical anomalies associated with DiGeorge syndrome include abnormal embryonic development of the pharyngeal pouches, which ultimately impacts development of the middle and external ear, maxilla, mandible, and other neck and throat anomalies (Chieffo et al., 1997). The similarities in phenotype and candidate genes show that the ear tuft defect in chickens is an animal model for the human DiGeorge syndrome.

Fast/Slow Feathering. Fast or slow feathering rate refers to a phenotype observable in day-old chicks. Morphological differences between slow and fast feathering phenotypes are most identifiable in the ratio of the covert to primary feathers length, the length of the primary feathers, and the length of the tail (McGibbon, 1977a). Coverts in the fast-feathering phenotype are shorter than the primaries, whereas the coverts in the slow-feathering phenotype are equal in length to the primaries (compared in Fig. 10). Tail feathers do not appear on late feathering chicks until after around 21 days of age. Down feathers are not reported to have distinguishable differences. Studies from the early 1900s showed that the slow feathering phenotype is controlled by a sex-linked gene present in multiple breeds (Serebrovsky, 1922; Warren, 1925). Hetwing and Rittershaus (1929) assigned the gene locus the designation of K in their original German manuscript, referring to kurzer Flügel, with the literal translations “short wing”, as referenced by McGibbon (1977). Thus, the K allele is the dominant slow feathering phenotype, and the k allele is the wild-type fast (normal) feathering phenotype. A third allele of the feathering locus, with a more extreme feathering rate delay, has been reported, though no molecular analysis has been done. This third allele exhibits dominance over the other alleles. The symbol Kⁿ was assigned to this additional allele (Somes, 1969).

Fig 10 — Slow (left) and fast (right) feathering on day-old chick wings. Image courtesy of Hy-Line International.

The slow feathering phenotype has been associated with an endogenous retrovirus (ev21) on the chicken Z chromosome. However, the presence of this ev21 does not cause the slow feathering phenotype (Bacon et al., 1988; Levin and Smith, 1990; Takenouchi et al., 2018). Sequences homologous to the flanking regions of the ev21 integration site were found in all feathering morphotypes; however, this site remains unoccupied in fast feathering chickens. Some chicks from slow feathering parents can revert to fast-feathering because of changes at the ev21 locus classified as Type 1 (complete removal of ev21) and Type II (removal of the unoccupied repeat while ev21 remains intact) (Levin and Smith, 1990). Therefore, the presence of the ev21 insert does not produce slow feathering.

Late feathering has been confirmed to result from a 176,324 bp tandem duplication on the Z chromosome (Iraqi and Smith, 1995; Elferink et al., 2008). The duplication resides in portions of the prolactin receptor (PRLR) and sperm flagellar protein 2 (SPEF2) genes. This duplication of PRLR (dPRLR) is reduced by 149 amino acids on the C-terminal tail, which is hypothesized to be responsible for the delay in feather growth (Bu et al., 2013; Okamura et al., 2019). The sex-linked fast/slow feathering phenotype is also observed in turkeys. The same PRLR gene is affected, with slow feathering birds carrying a 5 bp deletion, leading to a truncated PRLR protein (Derks et al., 2018). These findings suggest that the absence of the C-terminus in PRLR is the cause of the slow feathering phenotype.

Feathered Shanks (Ptilopody). Feathers on the shanks or feet (ptilopody) is a characteristic of multiple breeds, including Brahma, Langshan, and Silkie chickens. The phenotype can be very variable, with five very different phenotypes described (Fig. 11). The mildest form displays a few small feathers on the outer toes and hocks, while the more extreme phenotype has heavily feathered toes and shanks (Somes, 1992). The feathering occurs only on the dorsal and side surfaces of the middle and outer toes and the outer and front surfaces of the shanks. These different phenotypes are exemplified within many poultry breeds, including the Langshan, which is an example of milder feathered shanks (Fig. 12), the Mille fleur d’Uccle with moderate coverage (Fig. 13), and the Cochin, which is the only breed with the more extreme phenotype. The fifth ptilopody phenotype is found only in the rare Pavloff breed, which has feathering on the inner, outer, and dorsal surfaces of the shanks and on the dorsal and side surfaces of all toes (Somes, 1992).

Fig 11 — Sketch of ptilopody phenotypes, from Somes (1992). Used with permission.

Fig 12 — Blue Langshan hen with feathered shanks (mild). Image courtesy of Jeannette Beranger/The Livestock Conservancy.

The genetic control of ptilopody has been extensively studied utilizing crosses between clean-legged and feathered shank breeds. These studies indicate that the gene governing ptilopody generally exhibits dominant inheritance, with two alleles at a single locus (Pti-1^B and Pti-1^L). However, segregation patterns in heavily feathered breeds suggest the involvement of two independently segregating loci (Pti-1, Pti-2; or S1S2). There may also be variable penetrance, indicating the presence of other ‘modifying genes’ within the genetic background (Punnett and Baily, 1918; Somes, 1992). The ptilopody phenotype found in the Pavloff breed appears to behave in a recessive manner (Somes, 1992).

Crosses utilizing Silkie, Langshan, or Beijing-You breeds as the source of the feathered legs and New Hampshire, Polish, broiler, or Houdan breeds as the source of the clean-legged variant have been used to identify the gene(s) responsible for feathered shanks (Dorshorst et al., 2010, Sun et al., 2015; Li et al, 2020). In addition, whole genome sequence comparison was done with feathered and clean-legged breeds (Bortoluzzi et al., 2020). These studies consistently report one or two specific regions on chromosome 13 and/or 15. On chromosome 13, feathered leg breeds have a 17 kb deletion involving a section of the H2AFY (H2A histone family, member Y) gene near PITX1 (paired-like homeodomain 1), which may impact PITX1 expression (Bortoluzzi et al., 2020; Li et al., 2020; Dorshorst et al., 2010). The second gene region is on chromosome 15 with a specific SNP variant, found in feather-legged breeds only, within a 297 bp highly conserved vertebrate element that is predicted to impact binding sites for transcription factors for TBX5 (T box transcription factor 5) expression (Domyan et al., 2016; Bortoluzzi et al., 2020; Li et al., 2020). Both PITX1 and TBX5 are transcription factors involved in limb pattern formation and/or arm-leg transformations (Spielmann et al., 2012; Royle et al., 2021).

Thus, as proposed in the very early studies on ptilopody in chickens, there appear to be two independent genes involved with the phenotype. It is worth noting that not all recent studies identified both regions, which is also consistent with the very early reports on the inheritance of feathered shanks in chickens. It is quite likely that different breeds have variation in one or both genes, which impacts the degree of feathering seen on their legs and toes. Interestingly, these same two loci (PITX1 and TBX5) have been reported to control foot feathering in pigeons, and the PITX1 variant in the pigeon has a 44kb deletion upstream of the gene (Domyan et al., 2016). This is an example of parallel evolution in chickens and pigeons.

Frizzle. The Frizzle phenotype has been known since at least the 1600s (Hutt, 1930). Frizzled feathers curl outward and upward, rather than downward toward the body. Altered feather morphology in the rachi, thickening of the barbs and barbules, and changes in the hooklets account for the curling (Ng et al., 2012). The frizzled trait is inherited as a single autosomal gene (denoted by F) with an incomplete dominance mode of inheritance. The Frizzle homozygote has a more extreme curling than the heterozygote, with increased fragility of the feathers (Hutt 1930). Because of the altered feather morphology, Frizzle has been considered a genetic variant with potential to improve heat tolerance (Sharifi et al., 2010; Zerjal et al., 2013; Adomako et al., 2014). The Frizzle chicken is not always recognized as a distinct breed, but is a phenotype found in some breeds, including the Lyonnaise Bantam (Fig. 14).

Fig 14 — Lyonnaise Bantam breed hen. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

The Frizzle mutation is due to a deletion in the alpha keratin gene KRT75 (Ng et al., 2012) located on chromosome 33. The in-frame 69 bp deletion includes the splice site between exon 5 and intron 5. With the removal of the splice site, a site within exon 5, with a similar sequence to the splice site, is utilized as a new splice site. The result is a deletion of 23 amino acids in a highly conserved region of the KRT75 protein, and birds with this deletion showed frizzled feathers. These studies were done utilizing European-derived breeds.

There are Chinese breeds of chickens that have a very similar Frizzle phenotype (Kirin, Qilin, Xiushui Yellow Frizzle), also inherited in an autosomal, incomplete dominant manner (Dong et al., 2018; Guo et al., 2018; Chen et al., 2022). This Chinese Frizzle mutation is caused by a 15bp deletion within exon 3 of another keratin gene, KRT75L4, leading to the deletion of 5 avian conserved amino acids in the transcript (Dong et al., 2018; Guo et al., 2018). This same 15 bp deletion within KRT75L4 was also found in the Xiushui Yellow Frizzle chicken (Chen et al., 2022). Both Frizzle-related genes are located within a cluster of keratin genes on chromosome 33. This confirms the previously reported linkage with Crest and Dominant White (Kerje et al., 2004; Ng et al, 2012). These two independent mutations resulting in similar phenotypes exemplify parallel genetic evolution.

Henny Feathering. Chickens display sexual dimorphism of plumage. Mature males have long, thin, pointed feathers on the neck, cape, back, and shoulders, with long, curved tail feathers. These same feathers in the female are shorter, more rounded, and the tail feathers do not curve. The ‘henny feathering’ (Hf) phenotype is characterized by males displaying the same plumage pattern as females. Other secondary male characteristics, such as comb and wattle development, are not affected (see Fig. 15). This trait is found in the Sebright breed, developed by John Sebright in the early 19th century (Hutt, 1949). The henny feathering phenotype of the Campine breed is allelic with the Sebright breed and is likely due to transfer of the trait from the Sebright breed (George et al., 1990). The trait is inherited in an autosomal incomplete dominant manner but is only observable in males (Somes et al., 1984).

Fig 15 — Sebright bantam rooster and hen. Both birds have a Rose-comb, but the female (front) is immature with a less developed comb. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

The unusual features of this trait led to multiple studies elucidating the mechanism. Skin transplantations maintained the henny feathering phenotype of the donor, thus indicating that the defect was present in the skin (Danforth, 1928). The aromatase enzyme (encoded by CYP19A1 gene, on chromosome 10) converts androgens into estrogens. In the chicken, aromatase is normally detected only in the hypothalamus in males and the hypothalamus and ovary in females. However, the henny feather phenotype shows additional aromatase expression in the skin (Leshin et al., 1983). Research revealed that the henny feathering phenotype was due to the presence of a second promoter that results in extragonadal aromatase expression (Matsumine et al., 1991). This additional promoter is the 3′LTR TATA box of an endogenous retroviral insert (erv; ev gene). This retroviral insert is a full-length erv, with high sequence identity to ev1 and ev21, present in the 5′UTR of the CYP19A1 gene of henny feathered birds, and has been assigned the name Hf_ERV (Li et al., 2019).

Muff and Beard. The Muff and Beard phenotype in the chicken consists of elongated feathers protruding from both sides of the face (muffs) and projecting down from under the beak (beard). They always occur together, though the muffs are easier to see than the beard (Fig. 16). The muff and beard phenotype also includes small wattles. It can be identified in day-old chicks, and heterozygote expression can be variable. Muff and Beard are inherited in an autosomal, incompletely dominant manner and were assigned the symbol Mb (Hutt, 1949). This trait is found in multiple breeds, including Faverolles and Crevecoeur.

The Mb mutation is caused by a complex structural variation with three duplications, one in tandem and two that are translocated on chicken chromosome 27 (GGA27). The duplications contain seven annotated genes, including HOXB7 (homeobox B7) and HOXB8 (homeobox B8) (Guo et al., 2016). HOX genes encode transcription factors that can activate or repress other genes and control patterning in the developing embryo. Birds with the Mb mutation have high ectopic expression of HOXB8 in the facial skin, indicating that upregulation of HOXB8 is responsible for the Mb phenotype. The structural variation of the Mb mutation has impacted the normal function of the HOXB8 gene (Yang et al., 2020; Zheng et al., 2023).

Naked Neck. The Naked neck chicken has a noticeable absence of feathers on the neck, reddened skin on the neck, and narrow feather tracts, resulting in an overall decrease in the number of feathers on the body (Fig. 17). The symbol Na is used for the naked neck gene (Hutt, 1949). It was initially reported as a dominant gene effect (Desta, T. T. The genetic basis and robustness of naked neck mutation in chicken. Trop. Anim. Health Prod. 53:95. doi:10.1007/s11250-020-02505-1 Davenport, 1914); however, heterozygotes can be distinguished from homozygotes by a tuft of feathers (bow tie) on the neck. Furthermore, the degree of feather reduction on the body is greater for Na homozygotes than heterozygotes, thus defining Naked neck as an incomplete dominant trait (Crawford, 1976; Classen and Smyth, 1977). Because of the physical similarity of the Naked neck phenotype to the domestic turkey, they were initially thought to be turkey/chicken hybrids and were called Turken. The decreased feather coverage of Na birds led to the hypothesis that these birds might be more thermotolerant. There have been numerous reports on the development of thermotolerant birds for locations with hot and humid environmental conditions utilizing the Na gene (Merat, 1986; Desta, 2021; Fernandes et al., 2023).

Fig 17 — Naked Neck rooster (homozygous). This bird also has a single comb. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

The Na mutation is due to the insertion of a 180 bp segment from chromosome 1 into chromosome 3. This insertion is located approximately 260Kb downstream of BMP12 (bone morphogenetic protein 12) gene (also called GDF7; growth differentiation factor 7). Naked neck embryos show increased BMP12 expression in the skin, suggesting that the presence of the insert has a long-range cis-regulatory effect on BMP12, causing increased BMP12 expression. The elevated BMP12 expression results in inhibition of feather placode development (Mou et al., 2011).

Scaleless. The scaleless (sc/sc) mutation was first observed in chicks of the New Hampshire breed from the University of California, Davis in 1954 (Abbott and Asmundson, 1957). The scaleless phenotype is characterized by very smooth skin and a lack of feathers. This phenotype is called ‘scaleless’ as it lacks all derivatives of scales, which include feathers, spurs, and scales on the legs, toes, and foot pads (Fig. 18). Nails, beak, comb, and wattles appear to be normal, with a few feathers scattered across the body. The scaleless phenotype is due to a single recessive mutation (Abbott and Asmundson, 1957). Initial embryonic tissue studies suggested that the physiological defect was due to the scaleless epidermal layer failing to respond to signals from the underlying dermal tissue for subsequent formation of the epidermal placode (Brotman, 1977; Goetinck, 1963; Song and Sawyer, 1996). Subsequent studies suggest that the scaleless mutation impairs gene expression required to stabilize placodes for subsequent feather development (Houghton et al., 2007).

Fig 18 — Scaleless chicken. This bird also has a single comb. Image from Wells et al. (2012).

The scaleless mutant has been used extensively to understand skin and feather development in the chicken and the evolutionary development of scales (Wu et al., 2018). Scaleless mutants are the ideal subject to study the skin development of chickens and have displayed the required reciprocal signaling between the dermal and epidermal tissue layers for skin patterning. Further studies on sc/sc developing skin show a dense dermal layer, but a lack of epidermal placode formation (Wells et al., 2012). The mutation responsible for the scaleless phenotype was located on chromosome 4. A single SNP (c.535A>T) within exon 3 of FGF20 (Fibroblast growth factor 20) was homozygous in all scaleless birds, absent in WT samples of different breeds. This SNP results in a STOP codon (p.R179X), causing premature termination of the FGF20 protein. The missing part of the protein includes a highly conserved region important for fibroblast growth factor signaling (Wells et al., 2012).

Silky. The Silkie chicken is unique among chicken breeds due to its multiple novel phenotypic variations not commonly seen in other domesticated breeds, including their distinctive fluffy plumage (Fig. 19). These chickens are thought to have originated in China and are named after the “silk-like” appearance of their feathers. Reports of chickens with silky feathers were mentioned by Marco Polo in the thirteenth century (Hutt, 1949). The silky phenotype impacts the structure of all feathers, with more delicate shafts and long and frequently bifurcated barbs. The barbules are elongated and irregularly arranged; thus, the feathers lack the normal flat web and appear silky or woolly (Somes, 1990).

Fig 19 — Silkie rooster. This bird also has a walnut comb, moderate feathered shanks, and melanistic (black) skin. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

The Silkie feathering trait is also known as hookless (h) due to a lack of barbicel formation on the branches of the feather. It is inherited as an autosomal recessive trait (Hutt, 1949). The silky-feather locus was first mapped to a 15.7 Mb region on chromosome 3 (Dorshorst et al., 2010). Further examination of genome sequence information in that region from multiple chickens with and without the silky phenotype identified a single SNP variant unique to all birds with silky feathers. This single distinguishing SNP was located 103bp upstream of the coding sequence of the gene Prenyl (decaprenyl) Diphosphate Synthase, Subunit 2 (PDSS2). Decreased expression of PDSS2 was found in silky-feather skin, and this specific SNP is proposed to impact a regulatory site for PDSS2 (Feng, 2014).

Skeletal

Chickens have historically served as an important model organism for studying skeletal development because of their rapid embryonic growth and easy access to the developing tissues of the embryo. The structure and morphogenesis of the avian skeleton are influenced by both genetic and environmental factors. As vertebrates, chickens share conserved developmental pathways with mammals, which makes them a valuable comparative model for studying skeletal patterning and congenital malformations (Eames et al., 2004; Gravellec et al., 2011). The utilization of chickens in skeletal research offers the ability to access and manipulate the embryo directly within the egg. Techniques such as in ovo electroporation, surgical manipulation, and grafting allow for targeted investigation of gene function and tissue interactions during limb and axial skeleton formation (Hamburger and Hamilton, 1951; Saunders and Reuss, 1974). Genetic mutations affecting skeletal traits, including dwarfism, chondrodystrophy, and other axial or limb abnormalities, have provided insight into the molecular regulation of cartilage and bone development. These models have enhanced our understanding of vertebrate skeletogenesis and contributed to the identification of candidate genes relevant to human skeletal disorders (Mohajeri et al., 2021; Schock et al., 2015). As such, the chicken continues to serve as a powerful and versatile system for exploring the genetic basis of skeletal variation.

Cleft Palate. The chicken cleft primary palate (cpp) mutation was found within a stock at the University of California Davis in 1966. The phenotype involved craniofacial abnormalities, with abnormality of the frontonasal prominence, resulting in a severely truncated upper beak (Schock et al., 2016). The genetic control is autosomal recessive, with embryonic lethality towards the latter part of incubation (Youngworth and Delany, 2020). It is likely that much of the embryonic mortality is due to the abnormal upper beak, which the chick requires for hatching. Genetic analysis utilizing a high-density SNP panel and several generations of segregating progeny identified a 200kb region on chromosome 11 most likely to contain the causative gene and mutation. Only one cpp-linked variant within that region was predicted to significantly impact gene function, a single base pair deletion, expected to result in a frameshift mutation in the gene ESRP2 (epithelial splicing regulatory protein 2). Mutations in this gene have been linked to cleft lip and palate in humans (Carroll et al., 2020; Stelzer et al., 2016).

A second cleft palate phenotype in chickens was reported by Juriloff and Roberts (1975). The trait was semi-lethal, with embryonic mortality associated with the more severe cleft phenotype. Maternal dietary riboflavin deficiency resulted in a higher incidence of the defect in chicks. Selection in subsequent generations for cleft palate greatly increased the frequency of the phenotype, even on a normal maternal diet. It was proposed that the cleft palate phenotype was controlled by three recessive loci, one of which was exposed by disturbed riboflavin metabolism. Unfortunately, the stock containing this genetic defect no longer exists.

Cleft lip and palate are one of the most common human birth defects, occurring at a rate of approximately 1:1000 (Cobourne, 2004). The genetic bases of these defects are complex, and multiple genes have been identified that impact the development of cleft lip and palate in humans (Kohli and Kohli, 2012). Several animal models for cleft palate exist, including in mice, rabbits and chickens (Jaruga et al., 2022).

Creeper. The Creeper phenotype in the chicken has been known for centuries (Cutler, 1925; Gordon et al., 2015). Creeper chickens have shortened long bones (up to 31% reduction compared to non-creepers), with abnormalities of endochondral ossification (Landauer and Dunn, 1930; Hutt, 1949). Additional morphological changes include decreased wing size, smaller body weight, and occasionally curled toes (Landauer and Dunn, 1930; Jin et al., 2016). The pronounced shortening of the leg bones gives the appearance of the chicken “creeping” when in motion (Fig. 20).

Fig 20 — Japanese Bantam breed hen with creeper. This bird also has a single comb. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

The Creeper trait (Cp) is inherited as an autosomal dominant with lethality for homozygotes. Homozygotes for the Creeper allele typically cease to develop beyond day 4 of the embryonic stage (Landauer, 1944). Heterozygotes (Cp/+) are selectively bred for aesthetic purposes in breeds such as the Japanese Bantam, Scots Dumpy, and Khazak (Dohner, 2001; Rostamzadeh Mahdabi et al., 2021). Early mapping studies found that the gene for Creeper was closely linked with the gene for Rose-comb, and this linkage relationship is often used as the first example of autosomal linkage (Landauer, 1933). Cp has been mapped to a 25 kb causative deletion on chromosome 7 (Kinoshita, 2020) containing the IHH (Indian hedgehog) gene (Jin et al., 2016). IHH is known as a key component of bone development (Shi et al., 2015). Cp/+ individuals experience a downregulation of IHH, and Cp/Cp individuals experience a complete loss of IHH, which results in shortened legs and wings. The 25 kb deletion also includes the non-homologous end-joining factor 1 (NHEJ1) gene, which is suggested to lead to embryonic death in Cp/Cp individuals when downregulated, as the loss impacts DNA double-strand break repair, resulting in apoptosis at an early embryonic age (Kinoshita et al., 2020).

Dwarfism. The occurrence of dwarfism in chickens had been reported from multiple sources of Rhode Island Red, Barred Plymouth Rock, New Hampshire, Cornish, and White Leghorn breeds (Upp, 1934; Hutt, 1959; Bernier and Arscott, 1972). However, the inheritance mechanisms underlying many of these dwarf phenotypes have not been thoroughly studied. In foundational studies, some dwarfism mutants were observable at hatch compared to non-mutants due to their smaller size. Other mutants could not be differentiated from normal-sized birds until two weeks of age or older (Hutt, 1959). Mature body weights of dwarfs are approximately 70% of their non-dwarf siblings (Fig. 21). It is now known that there are both autosomal and sex-linked forms of dwarfism in the fowl, with multiple genetic variants causing the dwarf phenotypes.

Fig 21 — Olandsk dwarf (breed). The specific type of dwarfism (autosomal or sex-linked) is unknown. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

The most studied autosomal form of dwarfism was first identified in a White Leghorn flock at Cornell University in 1964 (Cole, 2000). The phenotype is described as a proportional reduction in overall size. This phenotype is differentiated from the Creeper mutant in that the Creeper phenotype solely impacts the distal skeletal elements. Autosomal dwarfism is inherited in a recessive manner, with the defined gene symbol ‘adw’ (autosomal dwarfism) assigned by Cole (2000). The mutation impacts mature body weight in both males and females by around 30%, is shown to delay sexual maturity (+2 weeks), and requires an extended incubation time (18 h) for hatch rate to reach 85% (Cole, 2000).

The adw mutation was mapped to chromosome 1, close to the HMGI-C (high mobility group protein 1-C) gene associated with a pygmy phenotype in mice (Zhou et al., 1995; Ruyter-Spira et al., 1998a). Thus, HMGI-C was considered a strong candidate gene for the adw locus. However, no genomic sequence differences were found between adw and unaffected birds for the HMGI-C gene, nor were there differences in its gene expression or subsequent protein levels (Ruyter-Spira, 1998b). Further fine-mapping studies identified the gene TMEM263 (transmembrane protein 263) as the adw locus, with a nonsense mutation causing a premature termination of the protein at the first membrane-spanning helix (Wu et al., 2018). This gene has been identified as being involved with bone mineral density in mammals (Estrada et al., 2012).

Multiple examples of sex-linked dwarfism (SLD) have been identified in independent populations. Unfortunately, the literature does not always clearly identify the original source of the specific dwarfism under study. Those with well-identified genetic mutants are described herein.

The Georgia strain of sex-linked dwarfism has a T to C mutation in a 5′ splice donor site of the growth hormone receptor gene (GHR). This causes a splicing error, resulting in the lack of full-length functional GHR protein (Huang et al., 1993). The same mutant was reported in the Gifu20 dwarf strain, though the specific source of this strain was not given (Tanaka et al., 1996). The Connecticut strain SLD (commercial broiler origin) is due to a 1773 bp deletion within the GHR gene, which impacts 27 highly conserved amino acids and a STOP codon at the 3′ end of the coding region. This results in the substitution of amino acids, producing an abnormal carboxy terminus of the GHR protein (Agarwal et al., 1994). The Connecticut strain mutation has the same mutation as reported in the S2 line (Huang et al., 2016). The Cornell strain SLD (White Leghorn) is due to a missense mutation within the extracellular domain. A conserved phenylalanine is replaced with a serine, impacting a growth hormone binding site (Hull et al., 1999). A fourth SLD has been found in a White Leghorn stock in France. There were three SNP differences between the dwarf and normal phenotypes resulting in three amino acid changes; lysine at amino acid position 34 was replaced by asparagine (K34N), valine was replaced by leucine at amino acid position 35 (V35L), and serine was replaced at amino acid 199 by an isoleucine (S199I). The S199I variant impacts a highly conserved region near the junction between the extracellular and transmembrane domains in a region essential for receptor activity. The mutated GHR had impaired plasma membrane expression and binding activity (Duriez et al., 1993).

Growth hormone (GH) encourages growth through cell surface receptor (growth hormone receptor; GHR) binding as an initial step in a cascade of events that results in insulin-like growth factor production. Disruptions to this pathway can lead to dwarfism due to failures of receptor recognition or signal transmissions. Laron syndrome (idiopathic short stature) in humans (autosomal recessive) has multiple genetic forms, most of which are caused by different mutations within the human growth hormone receptor. Over 90 mutations of GHR in humans are known to impact stature, including deletions, missense, nonsense, frameshift, and splice site mutations (Lin et al., 2018). The SLD mutations in the chicken all impact the function of the growth hormone receptor and thus are all animal models for Laron syndrome.

Limbless. Limbless is an autosomal recessive mutation in which the embryo lacks wings and legs (Fig. 22). It is an embryonic lethal trait, and the symbol ‘am’ for amelia was initially assigned to the trait. This was later changed to ‘ll’ for limbless. The mutant originated in a commercial Rhode Island Red chicken line. The limb buds initially develop, but the apical ectodermal ridge (AER) of the ectoderm does not form, at which point the limb buds regress completely. The limbless embryos also had a shortened upper beak (Prahlad et al., 1979). The limbless genetic defect is expressed in the ectoderm, not the mesoderm, as shown by embryonic ectopic tissue transplantation studies (Carrington and Fallon, 1988).

Chromosomal mapping studies narrowed the genetic region responsible for the limbless phenotype to a 2.9 Mb region on chromosome 2 (Robb et al., 2011). This region contained 14 identified genes and was syntenic with a region of the human genome with a WNT3 (Wnt family member 3) mutation causing tetra-amelia in humans (Niemann et al., 2004). The transcription factors Sp6 (Sp 6 transcription factor) and Sp8 (Sp 8 transcription factor) are essential for the normal formation of limbs. Mutations of these genes result in failure of the maturation of the AER in mice (Haro et al., 2014). Robb et al. (2011) proposed Sp8 or Sp9 as possible candidate genes for the limbless phenotype in the chicken. In the most recent chicken genome build (Gallus gallus bGalGal1.mat.broiler.GRCg7b, accessed Dec 31, 2024), Sp8 is located within the 2.9 Mb region on chromosome 2, identified, while Sp9 and Sp6 are on different chromosomes; thus, Sp8 is a likely candidate. Unfortunately, the specific genetic defect causing the limbless phenotype is not known. The chicken limbless mutant has been used extensively as a model system for limb development, as the lack of limbs can be studied in this mutant without any surgical intervention (Lizarraga et al., 1999; McQueeney et al., 2002).

Nanomelia. Nanomelia (nm) is a lethal trait resulting in embryonic death around 17-19 days of development and is inherited in a recessive manner. Homozygous embryos exhibit a condition marked by shortened limbs, cartilage abnormalities, and underdeveloped cranial skeletons. Nanomelia was initially discovered in an F₂ generation of a cross between Buff Cochin and White Leghorn chickens (Landauer et al., 1965). Subsequent studies found defective synthesis of cartilage chondroitin sulfate proteoglycan and lack of proteoglycan core protein in nanomelic embryos (McKeown and Goetinck, 1979; Argraves et al., 1981).

Nanomelia is due to a single SNP variant that results in a STOP codon that prematurely terminates translation in the ACAN (aggrecan) gene, affecting the synthesis of aggrecan, a large (> 200kDA) proteoglycan found in cartilage. This multi-component molecule contains three globular domains (G1, G2, and G3), an inter-globular domain, a keratan sulfate attachment domain, and a chondroitin sulfate attachment domain (Kiani et al., 2001). Together, these domains bind a gel-like hyaluronan structure to hydrate and provide structural support for cartilage (Kiani et al., 2002). Velleman and Clark (1992) studied the genetic linkage between nanomelia and aggrecan. It was determined that nanomelia chondrocytes synthesize a shortened aggrecan core protein, which impacts cartilage formation (Li et al., 1993; Velleman, 2000). The location of the STOP codon within the ACAN gene impacts coding of the chondroitin sulfate attachment domain, prior to the G3 region, resulting in a shortened molecule lacking the G3 domain. Kiani et al. (2001) showed that the chondroitin sulfate attachment domain, together with the G3 region, plays a role in product secretion. Nanomelic embryos showed a 94% decrease in detectable aggrecan protein levels compared to normal embryos (Stirpe et al., 1987). The lack of aggrecan in the extracellular matrix space of nanomelic chondrocytes results in dehydration and loss of mechanical and functional strength of cartilage involved in expanding tissue for bone growth, causing impairment in long bone development (Pennypacker and Goetinck, 1976). The nanomelia mutation has provided significant information on the importance of aggrecan in cartilage development. Defects in this gene are known to result in skeletal anomalies in Dexter cattle (Cavanagh et al., 2007) and multiple human skeletal disorders (Dateki, 2017).

Polydactyly. Polydactyly is an inherited condition in which birds have more than the standard four digits on their feet (Figs. 23 and 24). It can be variable in form, but the most common type reported appears as a duplication of the first digit (inner toe). It is a required standard trait for several breeds of chickens, including Silkie, Dorking, and Houdan (American Standard of Perfection, 1993). Polydactyly is inherited in an autosomal dominant manner, with the gene symbol Po used (Warren, 1944; Dunn and Jull, 1927). Polydactyly has been referred to as incompletely dominant (Somes, 1990) due to a deficiency of heterozygotes observed in some breed crosses, however, researchers have suggested that the observation of additional phalanges in some heterozygotes are the missing Po birds, which are exhibiting a lower expression of the trait (Dunn et al., 2011; Warren, 1944).

Fig 23 — Morphology of a polydactyly mutant (±) at embryonic day 10 from the University of California-Davis (Robb et al., 2011). Image used with permission. Phenotypically, the embryo is exhibiting preaxial polydactyly characterized by unilateral duplication on both feet.

Fig 24 — Houdan (breed) hen with polydactyly. Image courtesy of Jeannette Beranger/The Livestock Conservancy.

Based on different phalanx origination points of the additional toe(s) and toe size variability, subtypes of polydactyly have been designated in various publications (Warren, 1944; Zhang et al., 2016; He et al., 2017). Subtype I consists of an extra toe located between toe one and two, which is described as being characteristic of Beijing-You, Silkie, and Jiningbairi Chinese breeds. Subtype II is characterized as an additional toe developing from the first phalanx of toe one and is found in the European Houdan breed (Zhang et al., 2016). He et al. (2017) expanded on Warren’s (1944) subtype designation to incorporate extra toe length and origin point of Beijing fatty chickens. However, it is not clear if these different subtypes of polydactyly are consistently identified or truly breed specific.

Numerous studies have identified a specific SNP variant in the Silkie breed on chromosome 2 associated with the polydactyly phenotype. This SNP lies within the ZRS (zone of polarizing activity regulatory sequence), which is a limb-specific cis-regulatory element for the gene Shh (Sonic hedgehog) located within an intron of the Lmbr1 (limb development membrane protein 1) gene (Dunn et al., 2011). This same SNP variant was found in other polydactylous breeds, including White Sultan, Beijing-You, and Jiningbairi, but not Faverolle, Houdan, or Dorking, suggesting that there is another variant associated with the development of polydactyly in these breeds (Dorshort et al., 2010; Zhang et al., 2017). Aberrant FGF (fibroblast growth factor) signaling, independent of ectopic Shh, which is associated with Po has been found in Dorking chickens (Bouldin and Harfe, 2009; Dorshorst et al., 2010). This second causative variant has yet to be identified, though it is within the same chromosome 2 region as the original SNP (Zhang et al., 2016). This is another example of a trait with parallel evolution, where different mutations have evolved that produce the same phenotype.

Extra fingers or toes are found in multiple species and are one of the more common congenital limb anomalies in humans (Umair et al., 2018; Al-Qattan, 2018). The polydactyly observed in chickens is the same phenotype as preaxial polydactyly (PPD), in which additional digit(s) occur on the preaxial (inner) side of the hand or foot. PPD in other animal species is also due to variation within the ZRS, showing the value of the chicken as an animal model for understanding limb development (Al-Qattan, 2018; Lettice et al., 2008).

Rumpless. Rumplessness is a phenotypic trait characterized by a truncated appearance at the hindquarters of the bird (Fig. 25; Zwilling, 1942). Multiple forms of rumplessness exist, and the exact type of rumplessness appears to be breed-specific with regard to both morphology and genetics. Commonly, phenotypic rumplessness is associated with missing internal and external features, including tail feathers, caudal vertebrae, and the uropygial gland. Rumplessness has also been identified in chickens with missing or modified tail feathers. Genomic and breeding studies indicate that the genetic cause of rumplessness and the phenotypic traits acquired are breed-dependent.

The Araucana chicken breed, originating from South America, is recognized by the American Poultry Association and American Bantam Association (Ekarius, 2007). The breed is characterized by ear tufts, blue eggshells, and must be rumpless according to breed standards. The Araucana Rumpless gene (RP) is autosomal dominant (Dunn and Landauer, 1934). Noorai et al. (2012) mapped a 2.14 Mb haplotype on Gga 2, found to be common amongst a diverse population of Rumpless Araucana. Variation within Irx1 (iroquois homeobox 1) and Irx2 (iroquois homeobox 2), two candidate proneural genes, was identified within the Rumpless birds. These genes are known to be associated with developmental repatterning (Cavodeassi et al., 2001). Further studies indicate the presence of one or both of two SNPs in the proximal regulatory region of Irx1 and Irx2, caused misexpression of these genes producing the RP phenotype (Noorai et al., 2012; Freese et al., 2014; Noorai et al., 2019).

The Chinese Piao chicken is similar to the Araucana in that both breeds have the same missing anatomical features (Wang et al., 2021) as well as autosomal dominant inheritance. However, the two breeds are considered to be genetically unrelated. The strongest candidate gene regions associated with Rumpless Piao chickens were found on chromosome 2, located near-but distinct from-the region associated with Rumplessness in the Araucana breed (Guo et al., 2023). The Piao Rumpless birds does not have the Irx1 and Irx2 variants found within the Rumpless Araucana breed. A causal loss-of-function variation of a novel gene (Rum; rumpless) was found unique to the Piao chicken that downregulates the gene MSGN1 (Mesogenein 1) and TBX6 (T-box 5) during tail somite formation, resulting in the rumpless phenotype (Guo et al., 2023).

The Hongshan chicken, an indigenous breed of China, is similar to the Araucana in that individuals of the breed may appear rumpless (Wang et al., 2017); however, Hongshan chickens contain the typical number of vertebra and have a uropygial gland. The rumpless phenotype in Hongshan appears to be solely due to a modification of tail feathering, which designates the rumpless Hongshans as a unique morphology compared to the Araucana rumpless chickens. Specifically, the main tail feather maintains a frizzy texture, contributing to the bird’s truncated appearance. A study utilized selective breeding to identify Hongshan rumplessness as a sex-linked trait (Wang et al., 2017). A pseudogene in the targeted 71.8–72 Mb region is associated with feather development in the Wnt/β-catenin signaling pathway.

Talpid. Named for the phenotypically similar webbed paws of the Talpidae (mole) family, the talpid mutants are autosomal recessive pleiotropic mutations in poultry characterized by a polydactyl morphology (Cole, 1942; Hunton, 1960; Schock et al., 2016). The talpid mutations discussed here (talpid2 and talpid3) also cause craniofacial and other morphological defects, which differ based on the mutation type. Both talpid2 and talpid3 are lethal in ovo. While described as a similar phenotype, the originally described talpid phenotype identified by Cole (1942) was reported as extinct in 1959 by Ede and Kelly (1964).

First described in 1959, talpid2 craniofacial deformities include facial clefting, dwarfing, and exposed viscera (Abbott et al., 1959). Similarly to talpid3, talpid2 has been shown to also lack functional primary cilia and cranio-facial Shh signaling disruption (Brugmann et al., 2010; Chang et al., 2014). Limb expression of the Shh signaling pathway proceeds in talpid2 mutants (Caruccio et al., 1999). A 19 bp deletion on GGA1 within C2CD3 (C2 Domain Containing 3 Centriole Elongation Regulator) produces a premature STOP codon that is suggested as the causative mutation for the characteristic talpid2 defects (Chang et al., 2014). Though both talpid3 and talpid2 mutations disrupt cilia, Chang et al. (2014) determined that the proteins containing the mutations are different, thus resulting in different morphologies in craniofacial mutations.

Schock et al. (2016) identified talpid3 as a lethal recessive allele in a flock kept at Wye College in Kent, UK. The talpid3 mutation is the more widely studied mutant. In this mutation, craniofacial defects are specifically along the midline, causing a deformation of the beak and migration of the eyes to the midline (Ede and Kelly, 1964). Identification of the talpid phenotype can be made by embryonic day 3 (E3), and it is lethal around E6 (Ede and Kelly, 1964). The gene was mapped to GGA5 on gene KIAA0586 (protein talpid 3) where a thymine residue insertion leads to a subsequent frame-shift and STOP codon (Davey et al., 2006). Gene expression of the craniofacial and limb morphologies differs, with Hedgehog (Hh) signaling demonstrating both a loss and a gain of function (Buxton et al., 2004). Normal craniofacial development is directed through the Sonic Hedgehog signaling (Shh). The talpid3 mutants lack Shh expression domains in the head, yet the limbs experience a gain of function of Shh (Buxton et al., 2004; Davey et al., 2006). Yin et al. (2009) identified the loss of primary cilia resulting from the talpid3 mutation as the basis for the Shh signaling defect.

The study of the talpid mutations is important, as both are used as animal models for human-relevant disease. For example, talpid3 and talpid2, respectively, are used as models for Joubert syndrome, a disease caused by cilia deformation, and oral-facial-digital syndrome, another ciliopathy causing facial deformities including cleft palate (Schock et al., 2015; Stephen et al., 2015). An interesting study by Harris et al. (2006) identified the initial development of tooth formation in talpid2 chicks, hypothesized as being due to the talpid2 mutation impacting regional boundary signaling in the jaw.

Wingless. A lethal phenotype in which embryos were lacking wings was reported in birds of the White Leghorn breed in 1943. In addition to the lack of wings, these embryos also had abnormalities of the legs and toes, craniofacial defects, partial absence of lungs, air sacs, and kidneys, and abnormal (clubbed) toes. This trait showed considerable variability in the severity of expression. It was inherited as an autosomal recessive, and the symbol wg was assigned (Waters and Bywaters, 1943; Hutt, 1949). This wingless mutant is no longer available for study, and the causative gene is unknown.

A second autosomal recessive wingless mutation was found in an unrelated flock synthesized from four chicken breeds (Rhode Island Red, White Leghorn, Dorking, Red Jungle Fowl) and was given the moniker of wingless-2 (wg-2) (Zwilling, 1956). The phenotype was very similar to that of the original wingless, showing variability in expression with lack of wings, legs, and kidneys. However, the lungs and air sacs were unaffected. Extensive embryological studies identified the absence of the apical epidermal ridge in these embryos which is essential for normal limb bud development (Zwilling, 1956).

Initial studies narrowed the genomic region containing the causative mutation to a 227 Kb region on chromosome 12 which contained 6 candidate genes (Webb et al., 2018). Comparison of sequence information within this candidate gene region identified a single SNP consistently associated with the mutant phenotype. This SNP is in exon 2 of the RAF1 gene, and results in a STOP codon within the RAF1 transcript. Protein expression studies showed lack of RAF1 protein in wg-2 homozygous embryos (Youngworth and Delany, 2019). RAF1 is a component of the MAPK pathway and mutations in this pathway cause multiple developmental syndromes, called RASopathies (Uniprot, 2024; Rauen, 2013).

A sex-linked wingless mutant found in descendants of the Light Sussex breed has also been described (Pease, 1962). This trait had variable expression, ranging from minor defects of the wings to complete lack of both wings and legs. Missing phalanges, syndactyly, and distortion of the feet were also reported (Lancaster, 1968). The symbol ‘ws’ was assigned to this gene. There was no apparent involvement of the internal organs. As with the wg-2 mutation, the ws mutant embryos have an absence of the apical ectodermal ridge (Hinchliffe and Ede, 1973). It is likely that this mutation no longer exists, as no other recent publications using this mutation have been found.

Cellular

The phenotypes described in this section are distinct from the common phenotypic variants widely recognized in various domestic chicken breeds. Instead, they encompass unique traits originally referred to as blood or biochemical polymorphisms, or those associated with specialized lines selectively developed for specific biological studies, such as traits linked to virus receptors. For many of these specialized phenotypes, the underlying genes and variants have now been identified, making them valuable additions to this document. Tumor virus receptors have provided critical insights into viral entry mechanisms in cells, while blood types, among the earliest characterized blood biochemical polymorphisms, have recently been linked to specific genetic loci. Additionally, several of the phenotypic variants discussed above are now understood to arise from endogenous retroviral elements integrated into the chicken genome. These additions provide a deeper understanding of the genetic basis for chicken genetic diversity and its relevance to poultry research and breeding. While not an exhaustive list, the examples provided offer valuable insights into the genetic mechanisms behind important and functional traits in chickens. They also demonstrate how chickens serve as an effective model organism for studying human gene functions.

Blood types

Different blood types are due to antigenic differences on blood cells between individuals of the same species. Human blood types were first identified by Landsteiner and Miller (1924) during investigations of mortality related to blood transfusions. The first human blood system discovered was the ABO system, with multiple other blood systems being subsequently defined including the Rhesus (Rh) system (Landsteiner and Wiener, 1940). There are 13 blood type systems known in the chicken, (A, B, C, D, E, H, I, J, K, L, N, P and R) identified alphabetically in the order in which they were discovered (McDermid, 1964; Taylor et al., 2016). Variants within each of the blood types were originally identified serologically by red blood cell agglutination after mixing with specific polyclonal sera (Fulton, 2020). Many of these alloantigens have been found to impact immunological traits, including resistance to coccidiosis, antibody response following immunization, and size of the bursa of Fabricius (Briles, 2004). Reviews of avian blood groups are available, including their impact on multiple traits (Dietert et al., 1992; Briles et al., 2004; Taylor et al., 2016).

Recently, the genes and gene variants responsible for multiple chicken blood systems have been identified, and DNA-based detection methods have been developed. This information will allow further studies on the impact of these genes on various production and disease-related traits.

A System . The chicken blood system A was identified at the same time as the B system, with nine serologically defined alleles recognized (Briles et al., 1950a). Using a GWAS (genome wide association study) and genome sequence information from samples of known A system serology, the responsible gene for the A blood system has recently been identified as the complement component 4 binding protein, membrane (C4BPM), located on chromosome 26 (Fulton et al., 2022). Furthermore, the actual genetic variants that result in the specific serological alleles were defined. The C4BPM gene is a member of the Regulators of Complement Activation (RCA) gene cluster, syntenic with human RCA, which regulates the initiation of the complement cascade. Gene variants in the human RCA are reported as influencing disease outcomes, including malaria (Cooling, 2015). Chicken lines divergently selected from a common base for immune response also differ in frequency of A blood system alleles, suggesting that A blood system can play a role in immune response in chickens, including coccidiosis (Johnson and Edgar, 1984; Martin et al., 1990).

B System (MHC region). The most studied chicken blood system is the B system, which is highly polymorphic and highly antigenic (Fulton et al., 2016). The B system, now known to be the chicken Major Histocompatibility Complex (MHC-B system), is a cluster of immune-related genes located on chicken chromosome 16 (Schierman and Nordskog, 1961; Miller and Taylor, 2016). The chicken MHC is considered one of the best models for MHC-associated disease resistance (Halabi and Kaufman, 2022), and variants within the MHC are well-known to confer resistance to multiple bacterial, parasitic, and viral pathogens. Serological differences are due to variation within multiple genes of the MHC, and 27 serologically defined alleles were identified (Briles and Briles, 1982). A SNP panel, encompassing a 230K bp region of the MHC has identified over 100 different haplotypes and novel MHC recombinants in multiple commercially utilized and indigenous chicken breeds (Fulton et al., 2016; Fulton et al., 2017; Iglesias et al., 2019; Tarrant et al., 2020; Manjula et al., 2020). A thorough review of the chicken MHC-B function is available (Miller and Taylor, 2016).

D System. The chicken blood system D was initially identified in 1950 (Briles et al., 1950b; Briles, 1951) with further details reported by Briles and co-workers (1963). It has five serologically defined alleles (Briles and Gilmour, 1979). Classical recombination studies identified the gene responsible for the D system location on chromosome 1, but no further information was known (Bitgood et al., 1991). GWAS analysis and sequence information resulted in the identification of the gene CD99 (cluster of differentiation 99) as encoding the protein of the chicken D blood system (Fulton et al., 2023). This gene is located on chicken chromosome 1, confirming the previous chromosome location reported. In humans, CD99 is part of the Xg^a human blood system (Yeh et al., 2018).

E System. The chicken blood system E is closely linked to the A blood system, with genetic distance estimates of 0.5 – 1.0 cM calculated from classical recombination studies (Briles et al., 1968; Kopti et al., 1997). There are 11 E system alleles defined by serology (Briles and Gilmour, 1979). With the location of the A system allele defined, this allowed identification of the most likely candidate gene for the chicken E blood system to be FCAMR (Fc fragment of IgA and IgM receptor) (Fulton et al., 2022).

I System. Identification of the chicken blood system I was first reported in 1962 (Briles, 1962). Eight alleles identified through serology were subsequently reported (Briles and Gilmour, 1979). The gene responsible for the I system was identified as RHCE (Rh blood group, CcEe antigen) via DNA sequence data combined with GWAS analysis utilizing DNA samples with known I system alleles (Fulton et al., 2024). This gene, located on chromosome 23, encodes one of the proteins involved in the human Rh blood system (Avent and Reid, 2000).

Hypolipidemia. A novel white-skinned phenotype was identified within a closed breeding flock of White Leghorns at the University of Wisconsin. This phenotype is characterized by white skin, a white beak, and colorless blood plasma, which result from a deficiency of carotenoids (McGibbon, 1981; Attie et al., 2002). The mutation was initially designated as 'y' for "recessive to yellow skin," and later named WHAM (Wisconsin Hypo-Alpha Mutant) (Poernama et al., 1990). The mode of inheritance was determined to be sex-linked.

WHAM chickens exhibited significantly lower levels of lipoprotein cholesterol compared to controls, with heterozygous birds displaying intermediate cholesterol levels (Poernama et al., 1990). A similar phenotype is observed in humans with Tangier disease, a condition characterized by extremely low cholesterol levels caused by defects in phospholipid and cholesterol efflux due to mutations in the ABCA1 gene (Bodzioch et al., 1999). The ABC (ATP-binding cassette) proteins transport multiple substrates across the plasma and intracellular membranes. The genomic region containing the ABCA1 gene in chickens is syntenic to the human region containing ABCA1. Sequence analysis of the chicken ABCA1 gene revealed a single SNP resulting in a glutamic acid (E) to lysine (K) substitution at amino acid position 89 (E89K) (Attie et al., 2002). This amino acid is highly conserved across species, from humans to fish, and the mutation disrupts lipid export from the cell (Attie et al., 2002).

The WHAM chicken mutant represents the first spontaneously occurring animal model for HDL deficiency syndromes such as Tangier disease (Poernama et al., 1990). It is considered an important model for advancing our understanding of lipoprotein transport and metabolism.

Endogenous Retroviruses (erv; ev genes). Retroviruses insert their genetic material into host cell genomic DNA, where it can then be replicated to produce more viruses. If the insertion is in germ cells, then these retroviral inserts are inherited in Mendelian fashion and are identified as endogenous retroviruses or ALV subgroup E (ALVE). The chicken-specific endogenous retrovirus originated from the avian leukosis virus (ALV; ASLV), and specific genomic integrations are called erv (endogenous retrovirus) or ev genes. Integration of ALV into the chicken genome can result in the production of infectious viral particles and can interfere with gene expression, all of which may impact various production-relevant traits (Astrin et al., 1978; Chang et al., 2006; Fulton et al., 2021; Crittenden et al., 1984). Over time, mutations can accumulate in these retroviral insertions, causing loss of segments of the viral genome and subsequent inactivity (Mason et al., 2020). The presence of ALVE was originally determined by Southern blotting, with chicken genomic DNA and viral-specific probes (Astrin, 1978). PCR-based tests were then developed to detect specific ALVE insertions (Benkel, 1998). More recently, a bioinformatic pipeline was developed that identifies the presence of ALVE remnants through analysis of genomic sequence information (Mason et al., 2020). The presence of many ALVE has been detected in multiple chicken breeds, including commercial poultry, wild jungle fowl and indigenous breeds (Aarts et al., 1991; Grunder et al., 1995; Benkel and Rutherford, 2014; Mason et al., 2020; Wang et al., 2023).

An extensive review of endogenous retroviruses is beyond the scope of this review. They are included herein as some of the genetic causes of phenotypes described are due to retroviral inserts that impact gene expression (see Table 1). A more comprehensive review of endogenous retroviral elements in the chicken genome can be found in Mason et al. (2016).

Tumor Virus Receptors. The Avian sarcoma and leukosis virus (ASLV) is an avian oncogenic virus and infection results in decreased production, increased mortality, and formation of tumors in multiple organs. It was the first model for transmissible neoplastic disease and the role of viruses in cancer in the early 20th century (Payne and Nair, 2012). This retrovirus is classified into 6 major subgroups identified as A through E and J. Subgroup E is also referred to as endogenous retrovirus (erv; also called ev), which are present as stable genetic elements within the chicken genome. The presence and impact of ev genes within the chicken have been previously discussed, and several of the aforementioned unique phenotypes in the chicken are due to the presence of an ev insertion in the genome impacting normal gene function. The study of receptors specific for the different viral subgroups and the effects of specific protein variation within these receptors on viral binding has been critical in understanding the mechanisms of viral infection and viral-cell membrane fusion (Barnard et al., 2006; Munguia and Federspiel, 2008; Federspiel, 2019).

Four distinct genes influencing susceptibility to infection by various ASLV virus subgroups have been identified in the chicken. The cell surface proteins encoded by these genes serve as receptors for specific viral subgroups, facilitating viral entry into host cells. The tva locus provides susceptibility to ASLV subgroup A, while the tvb locus allows ASLV subgroups B, D and E to infect cells. Additionally, the tvc locus mediates susceptibility to ASLV subgroup C viruses. The ASLV-J virus subgroup arose through a recombination event between an endogenous retrovirus (erv) and exogenous ALV virus (Sacco et al., 2004). The receptor utilized by the ASLV-J has been referred to as tvaj (Chen et al., 2015). The viral envelope protein binds to this receptor, enabling the virus to enter the cell. The resistance forms of each of these receptors are recessive and contain variations that either block the expression of the receptor or prevent the virus from binding.

TVA. The tva locus is a member of the low-density lipoprotein receptor (LDLR) gene family and is located on chicken chromosome 28, near the tvc locus (Bates et al., 1993; Elleder et al., 2005). It has been assigned the name CD320 (ENSGALG00015024750) within Ensembl genome browser (https://oct2024.archive.ensembl.org/Gallus_gallus_GCA_016700215.2/Gene/Summary?db=core;g=ENSGALG00015024750;r=28:875732-880588;t=ENSGALT00015060384; accessed Feb. 2025). Specific naturally occurring variants of this locus have been shown to impact the ability of the virus to bind and infect cells. Two variants of the tva locus that impart resistance to ASLV-A infection were found in two different resistant chicken lines. A single base pair change (tva^r) resulted in a cysteine to tryptophan change in the LDLR region (Cys40Trp). This amino acid change prevents the formation of an important disulfide bond thus impacting protein folding and reducing the binding affinity between tva protein and ASLV-A envelope glycoprotein. An independent mutation with a 4bp deletion in exon 1 (tva^r2) changes a reading frame which prevents expression of the TVA receptor (Elleder et al., 2004). Additional resistance variants with reduced susceptibility have been identified (tva^r3, tva^r4, tva^r5 and tva^r6). These involve short intronic deletions within the tva gene which introduce a premature STOP codon, creating resistance to ASLV-A because the impacted splicing shortened the protein (Ritchey et al., 2012; Chen et al., 2015). The tva gene is orthologous to CD320, which is a cellular receptor for Vitamin B12/cobalamin complex in humans. Gene knockouts of tva in chickens resulted in ASLV-A resistance and cobalamin/vitamin B12 metabolism disorder (Krchlíková et al., 2021; Koslova et al., 2021).

TVB. The tvb locus has been identified as part of the tumor necrosis factor receptor family (TNFR) (Brojatsch et al., 1996; Adkins et al., 2000) and is labelled as TNFRSF10B (ENSGALG00000000452) in Ensembl genome browser (https://oct2024.archive.ensembl.org/Gallus_gallus_GCA_000002315.5/Gene/Matches?g=ENSGALG00000000452;r=22:1415487-1422100; accessed Feb. 2025). It is located on chromosome 22. There are two distinct alleles, each conferring resistance to different ASLV subgroups. The tvb^s1 (wild-type) variant allows infection by ASLV subgroups B, D, and E. However, the tvb^s3 allele permits infection only by subgroups B and D. The tvb^s3 allele has a Cys62Ser change, which impacts a disulfide bond, ultimately preventing binding of subgroup E envelope (Adkins et al., 2000). The tvb^r allele confers complete resistance to all three viral subtypes. It consists of a single base pair mutation that results in an in-frame STOP mutation, resulting in a truncated protein that does not allow infection by any of these subtypes (Klucking et al., 2002). Additional mutations (tvb^r4, tvb^r5) are, 2 and 1 bp, respectively, insertions within exon 4 that change the amino acid sequence of the tvb protein and result in premature STOP codons in exons 5 and 7. The truncated protein does not confer resistance, but does decrease susceptibility to ALVE-B, D, and E infection (Li et al., 2018). An erythrocyte isoantigen (labelled as R) was detected using specific alloantisera and was associated with susceptibility to ASLV subgroup B (Crittenden et al., 1970). It is likely that the R antigen is the same as the tvb locus. A subsequently detected R2 allele is probably one of the tvb^r variants (Bacon et al., 1996).

TVC. The tvc locus has been identified as a member of the butyrophilin subfamily and has the name BTN1A1(ENSGALG00010027725) in Ensembl genome browser (https://oct2024.archive.ensembl.org/Gallus_gallus/Gene/Summary?db=core;g=ENSGALG00010027725;r=28:1216361-1222907; accessed Feb. 2025). It is located on chromosome 28, close to the tva locus. One resistance allele (tvc^r) has been described. It has a single nucleotide change in codon 55 that changes a cysteine to a STOP codon. This results in a truncated protein that cannot be used as a receptor by ASLV-C (Elleder et al., 2005).

TVJ. The ASLV subgroup J virus was found to utilize the cell surface expressed product of the NHE1 (Na+/H+ exchanger type 1) gene on chromosome 23 as its viral receptor (Chai and Bates, 2006). Multiple chicken lines were found to be susceptible. However, quail and other avian species were resistant (Payne et al., 1991; Payne et al., 1992). Comparison of the NHE1 sequence between resistant and susceptible avian species, combined with in vitro mutagenesis studies, revealed that the tryptophan at position 38 was essential for ASLV-J susceptibility (Kucerova et al., 2013; Lee et al., 2017). Removal of this specific amino acid through the use of CRISPR/Cas9 editing of the NHE1 gene resulted in resistance to ALV-J virus and is an excellent example of the application of gene editing to improve disease resistance in livestock species (Koslova et al., 2020; Kheimar et al., 2021).

Fishy Taint. Fishy taint in eggs is due to a combination of a genetic mutation and a dietary ingredient. It is found in eggs from brown eggshell breeds when fed diets high in fish meal or rapeseed meal (Hobson-Frohock et al., 1973). The unpleasant fishy odor is due to the accumulation of TMA (trimethylamine) in the egg. Fishy flavor in milk is known in Swedish Red and White dairy cows (Lundén et al., 2002a). In humans, fish-odor syndrome (trimethylaminuria; TMAU) is characterized by secretion of TMA in breath and body fluids (Mitchell and Smith, 2001). Canola meal has high levels of sinapine, which is hydrolyzed by enteric bacteria to choline and sinapic acid. This choline is further broken down into TMA. The TMA is then oxidized in the liver to an odorless form (TMA n-oxide) by the enzyme FMO3 (flavin-containing mono-oxygenase 3) and then excreted by the kidneys (Ward et al., 2009). A defective FMO3 enzyme results in the accumulation of TMA, which is subsequently excreted into egg yolks, resulting in the fishy odor.

The human TMAU condition is known to be due to mutations in the FMO3 gene (Dolphin et al., 1997; Akerman et al., 1999), with multiple loss-of-function variants identified (Hernandez et al., 2003; Makiguchi et al., 2023). Close examination of the FM03 gene in cows showed a variant within the gene present only in the affected cows producing fishy odor milk (Lundén et al., 2002b). A GWAS utilizing microsatellite markers identified chicken chromosome 8 as a possible candidate region, and FMO3 was identified as being close to that same region. Sequencing of affected and non-affected individuals revealed a single base pair change in FMO3 that was associated with fishy taint in eggs. This change results in an amino acid change in an evolutionarily conserved region (FATGY motif), thus impacting the function of the FMO3 gene (Honkatukia et al., 2005).

Soft tissue

Eye. Eye development is a complex and tightly regulated process, and disruptions often lead to highly visible and measurable phenotypes, making the eye a particularly powerful system for investigating genetic, developmental, and degenerative mechanisms (e.g., Trejo-Reveles et al., 2018). In addition to experimental models, multiple reports of genetically linked eye defects have been documented in chickens, several of which have been recognized as valuable models for studying ocular development and human eye diseases (Hocking and Guggenheim, 2013). The three variants included here—rc, rdd, and rge—each result in blindness but arise through distinct genetic mechanisms. In all cases, mutations in the same or homologous genes are known to cause similar inherited retinal diseases in humans. These naturally occurring chicken models provide important insights into the genetic basis of vision loss and have been used to explore potential therapeutic approaches.

Blindness (rc). The rc mutation is an autosomal recessive mutation that causes blindness in hatched chicks. It was found in an experimental Rhode Island Red line and called rc, as the hypothesis was that the rods and cones failed to develop (Cheng et al., 1980). Further work determined that while the chicks were blind at hatch, the histology of the retinas was normal. Degeneration of the retina is observed at seven days post-hatch and continues until 6-8 months of age, at which time the photoreceptor cell layer is absent (Ulshafer and Allen, 1985). Due to this retinal degeneration, this blindness mutation has also been referred to as rd (Semple-Rowland and Cheng, 1999). Additional studies have shown that this mutation also impacts multiple organs, including the thymus, liver, kidney, heart, and male gonads (Cerruti Sola et al., 1997; Rabkin and Cheng, 1992; Arshami and Cheng, 2007).

Studies showed that rc chickens have low levels of a retina-specific guanylate cyclase enzyme, encoded by the gene GUCY2D (initially called photoreceptor guanylate cyclase, GC1). This is due to a deletion of sequence encoding exons 4-7 of GUCY2D and subsequent insertion in reverse orientation of a portion of exon 9. These changes result in a lack of a functional enzyme, or a null allele. (Semple-Rowland et al., 1998). Leber’s congenital amaurosis (LCA) is an autosomal recessive disease in humans that results in blindness at birth. Several defects in GUCY2D (missense, frameshift, insertion) have been identified as responsible for some of the LCA familial blindness phenotypes (Perrault et al., 1996; Perrault et al., 2004).

The rc chicken is considered as an animal model for inherited retinal degeneration (Valdez et al., 2009), more specifically for LCA type 1 (Perrault et al., 1996; Wisely et al., 2017). Lentiviral vector expression of GUCY2D in rc chickens restored cell function and vision to photoreceptor cells, thus validating the rc chicken as a model for the development of possible gene therapies to restore vision (Williams et al., 2006; Verrier et al., 2011).

Blindness (Rdd). In a strain of commercial laying birds, retinal abnormalities were noted that were apparent at hatch with progressive deterioration and eventual blindness in adult birds (Randall and McLachlan, 1979; Randall et al., 1983). This defect was inherited in a recessive manner with abnormalities of the retina observable shortly after 8 days of embryonic development, followed by photoreceptor degeneration as birds age (Randall et al., 1983; Finnegan et al., 2010). This non-lethal blindness phenotype was called rdd for retinal dysplasia and degeneration and resembles pathological abnormalities observed in severe forms of human retinitis pigmentosa (Finnegan et al., 2010).

Subsequent work determined that the rdd mutation was sex-linked. The initial matings to determine the mode of inheritance involved sighted cocks being mated with non-sighted hens, and the progeny segregation pattern was consistent with either sex-linked or autosomal inheritance mode of inheritance. The eventual reverse mating of non-sighted cocks with sighted hens revealed the sex-linked inheritance of the phenotype. Linkage analysis using microsatellite markers on the Z chromosome narrowed the causative region to 12.5 Mbp, which includes several potential candidate genes responsible for this phenotype. (Burt et al., 2003). More detailed analysis of this region, utilizing additional microsatellite markers, further refined the region to 3Mb, which contained 14 possible candidate genes. The gene MPDZ (multiple PDZ domain crumbs cell polarity complex component) lies within this region in the chicken genome. Variants within this gene are known that cause two recessively inherited disease phenotypes in humans, retinitis pigmentosa (RP) and Leber Congenital Amaurosis (LCA) (Hollander et al., 1999; Lotery et al., 2001). MPDZ sequence information of affected chickens identified a C to T substitution resulting in a premature STOP codon within the MPDZ gene that was present only in the non-sighted birds, thus identifying the causative gene and the variant (Ali et al., 2011).

Blindness (rge). Retinopathy globe enlarged (rge) results in poor vision and eventual blindness, with affected birds being identified as early as three weeks of age. The phenotype was first observed in UK commercial chicken flocks (Curtis et al., 1987). As the birds aged, pupil reactivity to light became increasingly sluggish and diminished, accompanied by posterior subcapsular lens opacities and an atrophic pectin. Abnormal collagen alignment was also noted, along with enlargement of the eye globe and corneal flattening (Boote et al., 2009). This defect is inherited in an autosomal recessive manner and was initially mapped to a region on chromosome 1 (Inglehearn et al., 2003). Subsequent work identified an in-frame 3-bp deletion within the ubiquitously expressed gene GNB3, leading to the deletion of a single codon (D153del), as the causative mutation (Tummala et al., 2006). It is hypothesized that this mutation leads to an unstable form of the GNB3 protein that is rapidly degraded (Tummala et al., 2011). GNB3 encodes a G protein involved in transducing extracellular signals across the plasma membrane. Variants in GNB3 are associated with night blindness in humans (Vincent et al., 2016), and the chicken rge mutant is considered a valuable animal model for studying eye disease (Ritchey et al., 2012).

Muscle

Muscular Dystrophy. A heritable form of muscular dystrophy was reported in a commercial flock of New Hampshire birds in 1953. These birds had been selected for heavy breast muscling. Affected birds failed to raise their wings and rise from a flat surface when placed in the supine position (Asmundson and Julian, 1956). Subsequent refinements of the test measured how many times the birds could consecutively right themselves (exhaustion test) (Julian, 1973). It can be observed in day-old chicks and progressively worsens as the chicks age. Affected birds can survive and reproduce. While the mode of inheritance was initially reported as recessive, further testing with the exhaustion test identified heterozygotes in older birds; thus, the trait is considered codominant. The gene name AM was assigned for Abnormal Muscling. Severe pathological changes are observed in the fast-twitch muscles, particularly the muscles of the breast and forearm (see review by Kikuchi, 2020). Abnormal embryonic myofibrils can be observed four days before hatch (Allen and Murphy, 1979). The original mutant was outcrossed into several different genetic backgrounds, which consequently modified the phenotype due to background genes (Wilson et al., 1979; Asmundsen et al., 1966; Kikuchi et al., 1981).

Initial studies identified a 1 Mbp region on the long arm of chicken Chromosome 2 as the location of the AM gene using segregating resource populations and microsatellite markers (Yoshikawa et al., 2004; Matsumoto et al., 2007). Genomic sequence analyses identified the AM gene as WWP1 (WW domain containing E3 ubiquitin protein ligase 1) with a single missense mutation (R441Q) resulting in protein degradation in muscle cells (Matsumoto et al., 2008; Imamura et al., 2016). This variation lies within an amino acid sequence that is highly conserved among tetrapods and thus is hypothesized to impact an important functional region of the WWP1 protein. This gene has not been previously reported to impact muscular dystrophies in other species, though variants within this gene in humans are associated with increased risk of developing certain cancers (Lee et al., 2020).

Ovary

Restricted Ovulator. A White Leghorn male, producing 50% of daughters that failed to lay eggs, was identified at DeKalb Agriculture Research Inc. in the 1970s (Jones et al., 1975). The original male, his sons, and laying daughters appeared to be normal, but the non-laying females displayed abnormal ovarian morphology, lacking a follicular hierarchy, with the follicles never achieving maturity, and may have dark or dull yellow coloration. The affected hens had 5-fold higher levels of serum cholesterol and triglycerides (extreme hyperlipidemia) and were more likely to develop atherosclerotic aortas than normal hens (Ho et al., 1974). The term ro, for ‘restricted ovulator’ was used to identify this trait, and it was identified as being sex-linked (McGibbon, 1977b).

The cause of the ro (R/O) phenotype was determined to be a lack of a receptor on the avian oocyte responsible for binding and transportation of multiple lipoproteins into the oocyte (Nimpf et al., 1989; Stifani et al., 1990). This receptor was originally named LR8 (LDLR relative, with 8 receptor binding domain) (Bujo et al., 1994). Sequence homology identified this receptor as the equivalent of the mammalian very low-density lipoprotein receptor (VLDLR), and the name was subsequently changed (Bujo et al., 1995; Steyrer, 1990; Schneider et al., 1998). The VLDLR gene is located on the chicken Z chromosome, which confirms the initial genetic report of being sex-linked. The specific variant within the VLDLR gene in the ro chicken is a non-synonymous SNP, which results in a cysteine to serine (C682S) change, that produces an unpaired cysteine, with greatly reduced expression of VLDLR on the oocyte surface (Bujo et al., 1995). A mutation in the same position (C646Y) in humans results in familial hypercholesterolemia (FH) (Leitersdorf et al., 1990). A PCR detection assay has been developed to identify the specific ro variant in the chicken (Bujo et al., 1996; Elkin et al., 2003).

The ro mutant has been a very important animal model, providing insights into multiple processes, including reproduction (VLDL receptor and follicular maturation), hypercholesterolemia (model for human familial hypercholesterolemia), cholesterol metabolism, and atherosclerosis. (Nimpf et al., 1989; Toda et al., 1981; Schneider et al., 1998). The ro chicken is a unique animal model for investigating ovarian cancer, with a nine-fold decrease in ovarian cancer rate in ro chickens compared to normal hens at 38 months of age (Giles et al., 2010; Johnson and Giles, 2013). A thorough review of the restricted ovulator chicken can be found in Elkin et al. (2012).

Other

Blue Shell. The chicken eggshell comes in two major colors, brown or white, and is breed-specific. However, blue and green eggshell-producing breeds exist. The genetics of this novel shell color was first described by Punnett (1933) as being due to an autosomal dominant gene. He assigned the gene name ‘O’ (Oocyan; precursor of bilirubin) due to the presence of oocyanin throughout the eggshell. The presence of the O gene on a white shell background results in blue color, and on a brown shell background results in an olive-green color (Fig. 26). Blue/green shell colors are found in the Mapuche fowl of Chile, and in their descendant breeds in both Europe and North America, which includes the Araucana. The blue/green eggshell is also reported in certain Asian breeds, including the Dongxiang and Lushi breeds (Wang et al., 2013). Using specific crosses utilizing chromosomal translocations, the location of the O gene was reported on chromosome 1 within 3.1 map units of the gene for pea comb (Bitgood, 1985).

Fig 26 — Blue egg shells are indicated by an asterisk (*). Image courtesy of Jeannette Beranger/The Livestock Conservancy.

The blue eggshell variant found within the Mapuche and its derived breeds was determined to be due to the presence of an incomplete endogenous retroviral (erv) insertion (lacks the retroviral pol gene) in the flanking region of the SLC01B3 gene and in the opposite orientation (Wragg et al., 2013). The Asian blue eggshell variant also has an incomplete erv present in the same flanking region (∼4.2kb: lacking the pol gene and part of gag and env genes) (Wang et al., 2013). While the blue eggshell phenotypes are identical, there are distinct genetic differences between them for the causative mutation. The insertion sites are not identical, being 23 bp apart, and there are sequence differences between the two EAV-HP inserts. Furthermore, there is a SNP within the homologous host sequence upstream of the erv integration site that is unique to the South American sources. However, the impacts of these erv insertions are the same. They result in the overexpression of the SLCO1B3 gene in the uterus (shell-forming gland) and oviduct, suggesting that the presence of the retroviral sequence acts as an enhancer. In the blue eggshell birds, this gene is expressed in the uterus (shell-forming gland), and its encoded protein is responsible for bile acid and bilirubin transport, providing further evidence for the overexpression of the SLC01B3 gene impacting the blue eggshell color. The location of the SLC01B3 gene is chr 1: 65.22-65.25 MBP, and the SOX5 gene (pea comb) is at chr 1: 65.71-66.18, confirming the close genetic linkage previously reported (Bitgood, 1985).

The observation of the blue shell phenotype in both Asian and South American chickens has led to the hypothesis of a historical genetic exchange of chickens between these two continents (Gongora et al., 2008). The determination that the two blue shell phenotypes are due to different genetic variations negates that hypothesis. The genetic results showing that the variants causing the phenotype are different between the two sources are an example of parallel molecular evolution. The observation of two independent integration events in almost identical genomic locations suggests that this may be a preferred EAV integration site (Desfarges and Ciuffi, 2010).

Epileptiform Seizures. The epileptiform seizures mutation in the chicken was first reported in 1970 (Crawford, 1970). It was found in a strain of the Fayoumi breed of chickens. Epileptic seizures, similar to grand mal events in humans, occur through the life of the bird, beginning at hatch. They can be induced by intermittent light stimulation with strobe lights, and start with excited vocalization, followed by random pecking, loss of leg muscle control, and a period of unconsciousness (Crawford, 1990). After waking, the bird is lethargic and unresponsive to further stimulation. It is one of only two animal genetic models for photosensitive epilepsy, the other species being a primate (Papio papio) (Killam et al., 1967). Chickens with this mutation have been used as models for human epilepsy, as the birds respond in a similar manner to epilepsy medications (Guy et al., 1992). This nervous system mutation was given the moniker of epi (later changed to Fepi) and was determined to have autosomal recessive inheritance (Crawford, 1990).

A mutation within the SV2A gene on chromosome 25 was identified as the causative mutation of this epilepsy. A dinucleotide change (c581-4, CC>TG) in the splice acceptor site within intron 2 results in a lack of exon 3 in the alternatively spliced variant, ultimately resulting in a codon frameshift, which then results in a premature termination codon and a severely truncated protein (Douaud et al., 2011). This variant is located within a region that is highly conserved across species. Mice lacking the SV2A gene appear normal at birth but experience severe seizures and die by the third week of life (Crowder et al., 1999). Thus, this chicken model is the only non-lethal animal model for a defect in SV2A impacting epileptic seizures. The protein encoded by the SV2A gene is identified as impacting secretion in neural and endocrine cells and as a possible receptor for botulinum neurotoxin type A1. However, it is not reported as being involved with epilepsy (GeneCards SV2A; May 2023).

Phenotypes for which the genomic region only is identified

There are numerous other mutations identified in the chicken for which their chromosomal location and/or potential candidate genes have been identified, but the actual responsible variant is still not known. These unresolved cases are summarized in Table 2 and highlight the need for continued genomic investigation. Table 2 summarizes 11 of these, showing their approximate chromosomal location and a reference describing attempts to identify the responsible gene. Additional resources, such as detailed sequencing and the current access to more complete chicken genome sequences, would likely assist in identifying the genetic cause (Warren et al., 2023). Many of these share a common phenotype with known human pathologies and may provide additional animal models for investigations into abnormal development. For example, scleroderma is an autoimmune disease of the skin and internal organs in humans. The scleroderma chicken displays all of the human disease characteristics and is considered to be one of the best animal models for this disease (Ek et al., 2012). The sex-linked single gene defect Coloboma was originally named due to the eye defects observed. However, the mutation phenotype extends to multiple other tissues and organs, resulting in dwarfism, truncated limbs, exposed viscera, addition or loss of foot digits, and cleft palate (Robb et al., 2013).

Discussion

The primary purpose of this manuscript is to provide an open-access, consolidated resource that summarizes the genes and the genetic variation known to underlie a broad range of phenotypic traits found in chickens (excluding plumage color variants). Many of the best-characterized traits, such as those influencing comb type (pea, rose, duplex), feather morphology (frizzle, crest, muff and beard), skeletal development (creeper, dwarfism, polydactyly), and disease resistance (tumor virus receptor loci), have defined genetic bases, with causative mutations identified as single nucleotide polymorphisms (SNPs), insertions or deletions (indels), or endogenous retroviral (ev) insertions. Notably, distinct ev insertions have been implicated in several traits, including recessive white feathers, henny feathering, and the blue eggshell phenotype.

Advances in genome assemblies and sequence data for chickens now make it technically feasible to resolve many of these remaining questions. The recent development of two novel haploid de-novo genome assemblies, (broiler (GRCg7b) and layer (GRCg7w)) resulted in structural adjustments among microchromosomes, extended the W chromosome, and enhanced telomere sequence placements. Furthermore, the identification of an additional microchromosome brings the total number of autosomes to 39 (Warren et al., 2023). These advances not only facilitate resolving outstanding genetic questions, but also enhance our ability to apply this knowledge directly in commercial breeding programs.

Beyond serving as a comprehensive reference, some of the phenotypic variants in this collection serve as functional tools for trait selection, which have significantly impacted genetic breeding programs in commercial poultry. For example, traits of particular interest in improving resistance to heat stress include frizzle, naked neck, and scaleless. Scaleless mutants, for instance, allow for a potential benefit for meat production in tropical climates. High temperatures s1ress the growth of feathered broilers, which necessitate the use of cooling systems for housing, resulting in additional costs and labor. The sc/sc featherless broilers are more heat-tolerant, with production parameters, including livability and body weight gain, being greater than those of full-feathered birds under heat stress (Somes, 1982; Azoulay et al., 2011). In another example, due to the sex-linked nature of the slow (K) and fast (k) feathering phenotype, which allows for the easy distinction between male and female chicks at hatch, feathering rate is used extensively in commercial settings to determine sex at hatch needed for different production systems. This rapid sexing method works well, provided that the parental birds contain the appropriate feathing locus combination (demonstrated in Fig. 27).

Fig 27 — This figure shows the genetic constituency of grandparent and parent flocks used to produce commercial chicks that can be feathered sexed. A). Feathering status of the four grandparent lines. B). Feathering status of the male and female parents used to produce feather sexable chicks. C). Feathering status of commercial chicks produced from the correct feathering genetics parents.

Wang et al. (2021) make an interesting hypothesis that the rumplessness characteristics may positively impact fertility traits, as breeding becomes easier and less obstructed. As a result, high levels of fertility and hatchability may be unconsciously selected through the breeding of rumpless birds. It is important to note that while some rumpless breeds can boast a high reproductive yield, this is not the case for all rumpless breeds.

The recessive white trait, due to an ALVE insertion, is used in the broiler industry to provide white-feathered plumage. This variant minimizes the appearance of dark pin feathers at time of processing. The white phenotype is due to a retroviral insertion within intron 4 of the tyrosinase gene, which subsequently disrupts the production of feather pigments (Chang et al., 2006). A second selection example using plumage phenotype is the fast/slow feathering used extensively in both the layer and broiler industry, which expresses at day of hatch and, with appropriate parental matings, can be used to rapidly identify the sex of day-old chicks (see Fig. 10).

The sex-linked dwarf phenotype has been used in the past for commercial production of both meat and eggs as the dwarfs have lower feed requirements, lower space requirements, and thus lower costs of production (Bernier and Arscott, 1972; Marks, 1983; Sadjadi et al., 1983). Using sex-linked dwarf females crossed with non-dwarf males produces normal-sized commercial birds, leveraging the dwarf trait in the dams for improved production efficiency. Ultimately, the dwarf phenotype in chickens has played a role in developing specialized breeds while also being used for its practicality within commercial production systems.

Additional strategic breeding has been conducted at a commercial level, targeting the removal of the recessive FM03 variant to eliminate fishy taint in eggs. Selection measures to emphasize the blue eggshell gene for niche markets, and selection of viral receptor variance to enhance disease resistance across flocks provide other examples of application of the genetic information within breeding flocks. These applications underscore the tangible value of maintaining genetic diversity, as the traits that are leveraged commercially today were once rare or specialized variants primarily held in research collections.

The limiting factor is no longer technology but access to birds exhibiting rare or legacy phenotypes. Over the past several decades, many unique chicken mutants, especially those with reduced viability or limited commercial importance, have been lost (Fulton and Delany, 2003; Pisenti et al., 2001; Miller, 2004). These lines were often preserved by academic institutions and were essential for understanding developmental biology, gene function, and vertebrate morphogenesis. Examples include the sex-linked lady-killer mutant (Sheridan, 1964; Sheridan, 1979) and both dominant and recessive forms of ametapodia (Smyth et al., 2000). The loss of such lines severely constrains future opportunities for discovery. Similarly, the extinction of specialized lines in other avian species, such as the parthenogenetic turkey line (Harada and Buss, 1981), represents a major setback. That line would have enabled researchers to investigate asexual reproduction, embryonic development, and possibly discover new breeding or conservation methods.

Despite these losses, the diversity of known chicken mutants still offers valuable insight into vertebrate biology. By compiling this information into a single reference, the manuscript aims to support researchers, breeders, and educators in understanding the genetic basis of traits that affect both scientific research and applied poultry production. In addition to well-characterized variants, we also highlight several phenotypes for which the chromosomal regions have been identified and gene candidates proposed, though the precise genetic variation responsible for the phenotype has not yet been identified.

Chickens are uniquely suited for in vivo studies because of their embryonic accessibility and accurate developmental staging. Therefore, it is essential to preserve and characterize remaining genetic stocks. Ongoing collaboration between academic, government, and commercial institutions, along with targeted sample collection and genome sequencing of rare phenotypes, will be essential to preserving this valuable natural resource for both fundamental and applied scientific research.

CRediT authorship contribution statement

Janet E. Fulton: Conceptualization, Project administration, Writing – original draft, Writing – review & editing. Amy M. McCarron: Writing – original draft, Writing – review & editing. Abigail Mullen: Writing – original draft, Writing – review & editing. Lowdan Ali: Writing – original draft, Writing – review & editing. Katy J. Tarrant: Project administration, Writing – original draft, Writing – review & editing.

Disclosures

There are no conflicts of interest to disclose.

Footnotes

Section: Genetics and Genomics

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PERMALINK

A review of genetic variation underlying chicken phenotypic diversity

Janet E Fulton

Amy M McCarron

Abigail Mullen

Lowdan Ali

Katy J Tarrant

Abstract

Introduction

Table 1.

Fig. 1.

Table 2.

Mutant phenotypes

Integument–combs

Fig. 13.

Fig. 2.

Fig. 9.

Fig. 3.

Fig. 16.

Fig. 4.

Fig. 5.

Fig. 6.

Feathers

Fig. 7.

Fig. 8.

Fig. 10.

Fig. 11.

Fig. 12.

Fig. 14.

Fig. 15.

Fig. 17.

Fig. 18.

Fig. 19.

Skeletal

Fig. 20.

Fig. 21.

Fig. 22.

Fig. 23.

Fig. 24.

Fig. 25.

Cellular

Blood types

Soft tissue

Muscle

Ovary

Other

Fig. 26.

Phenotypes for which the genomic region only is identified

Discussion

Fig. 27.

CRediT authorship contribution statement

Disclosures

Footnotes

References

ACTIONS

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