III. Chicken genes and comments

Below is a table of genes and gene symbols. Allelic genes (genes that have the same location or locus on a chromosome, which are also genes that substitute for one another) are grouped together. I have tried to incorporate relevant and interesting comments about these genes in the comment section. I continue to update this and correct it....

**Chicken Genes of Common Interest**
Sex-Linked Genes (alleles)	Symbol	Comments
Sex-linked barring	B	Barring, cuckoo barring. Dominant. Causes white barring pattern in red and black, sometimes used as a black inhibitor, most notably in Leghorns. Cuckoo barring is also an inhibitor of tissue pigmentation and is responsible for the yellow shanks of Barred Rocks. Shanks of females can be darker. Barring shows a distinct dosage effect. B/B gives wider bars than heterozygotes have. Incorporation of the slow feathering gene results in a cleaner, more sharply defined barring.
	b⁺	Recessive wild-type gene. An allele of the sex-linked barring locus. Lack of barring.
Sex-linked dilution	B^Sd	Females that are hemizygous for B^Sd (having one B^Sd gene) have light blue and barred plumage as do the heterozygous males, however, homozygous males show a dosage effect and are essentially white. These homozygous males resemble dominant whites but differ in that they are epistatic to pheomelanin while dominant white is not.
comments		Sex-linked barring, B, sex-linked dilution, B^Sd and the wild-type, b⁺ are alleles of the same locus. The order of dominance is B^Sd > B > b⁺.
Brown eye	br	Not much is known about this gene and there may be a dominant inhibitor of brown eye. Many of the melanin-influencing genes have an effect on eye color.
Dwarf	dw	Recessive. Males are reduced in size by about 43%, females by 26-32%. Multiple alleles have been proposed. dw is responsible for some beneficial effects. dw homozygotes are more resistant to Marek's Disease and spirochetosis, fewer laying accidents, more aggressive immune response. Abnormal eggs are suppressed (soft-shelled, double yolks). Dwarfism, dw, does not effect mortality but does postpone the onset of lay in pullets up to two weeks. Although egg number and mass are slightly decreased by dw, feed efficiency (feed consumption per egg layed) in laying stocks is usually increased 13-25%.
	dw^B	Recessive but shows a dose effect; 'bantam' gene. Females reduced in size by 5-11% and males by about 5% in heterozygotes and 14% in homozygotes. Allelic with dw.
	dw^M	MacDonald dwarf. Reduces body weight by 13.5% and shank length by 9%. Allelic with dw.
	Dw⁺	Wild-type gene. Lack of dwarfing alleles. Allows 'normal' size to develop.
Silver and Red-Gold	S	This gene is called 'silver'. Inhibits red pigment, pheomelanin. The expression of silver is sometimes affected by hormonal levels and is considered to be incompletely dominant and highly influenced by modifying genes.
	s⁺	This gene is sometimes called 'gold'. Wild-type, recessive. Invokes red pigment.
Foot Color	Id	Light foot color. Dominant. Inhibits dermal melanin. Reported to have little influence on shank/foot color in birds with dark shanks due to E/E
	id^c	Recessive. This gene allows beak and sometimes plumage pigmentation in dominant white homozygotes.
	id^a	Allows green spots on shanks - this gene is not widely accepted and the effect of this gene may be due to the interaction of modifiers not allelic to this locus.
	id^M	Massachusetts mutation. Recessive. Unlike other alleles that belong to this locus, dermal melanin is present in shanks of day-old chicks. Other alleles take more time to express. The darkest shanks are produced in conjunction with E and i⁺. The combination of id^M, E and I produces a pale blue or green color by about three months of age.
	id⁺	Wild-type dermal melanin. Lack of dermal melanin inhibitors.
Sex-linked white skin	y	Recessive, causes white skin.
	Y⁺	Wild-type gene. Lack of recessive white skin mutation.
Feathering Rate Genes	k⁺	Sometimes called rapid feathering. Recessive.
	K	Late feathering gene
	K^s	Slow feathering gene
	Kⁿ	Very slow feathering or 'delayed' feathering gene. The order of dominance among the genes allelic to this locus is Kⁿ>K^s>K>k⁺. The slow feathering gene is believed to be associated with a bald patch on the back of the adolescent bird. The feathers do come in given enough time. Since this is likely due to a dose effect of the slow feathering gene, the homozygous males should be the most likely to exhibit the trait. In my personal flocks, I have both males and females exhibiting this. Many novice poultry keepers wrongly attribute the bald back phenotype with a picking problem.
Brown eggshell color inhibitor	pr	This recessive gene results in a lack of protoporphyrin pigment (the brown eggshell pigment) even in hens with polygenic brown eggshell color. It can be employed to remove undesirable tints from eggs of white shelled strains.

**Autosomal Linkage Group 1 Genes**
Autosomal Genes	Symbol	Comments
Creeper	Cp	Short legged condition. Lethal in homozygous state. Dominant.
	cp⁺	Recessive, wild-type gene. Lack of creeper trait.
Rose comb	R	Associated with poor fertility in some homozygous breeds. Dominant.
	r⁺	Wild-type gene. Recessive. Lack of rose comb trait.
Lavender	lav	Recessive lavender has been associated with poor feather quality and even lack of feathers in some breeds. Lavender dilutes both black and red; changes black to grey and red to cream. Blue fowls termed "self blue" are normally lavender homozygotes. A mating of two lav homozygotes (blue fowls) will produce blue offspring. Lavender causes dilution by inhibiting the transfer of pigment granules from melanocytes, which produce them, to the feather structure. Lavender expression in homozygotes is present in chicks and adults.
	Lav⁺	Dominant, wild-type gene. Lack of lavender trait.

**Autosomal Linkage Group 2 Genes**
Autosomal Genes	Symbol	Comments
Crest	Cr	Crest feathers are similar in shape and texture to hackle feathers. There may be more than one allele. Incompletely dominant.
	cr⁺	Wild-type gene. Lack of crest.
Pied / Mottle	mo (pi)	The pied pattern is recessive black and white as in Exchequer Leghorn. Research has shown that the pied and mottle patterns are due to the mottle gene. It is no longer accepted that 'pied' is a distinct gene from mottle, however it is not known why the mottle gene causes the pied pattern in some birds and the typical mottle pattern in others. Mottle causes a white tip at the distal end (end farthest from the skin) of the feather. Chicks with extended black and mottle (E/E mo/mo) as in the Exchequer Leghorn will often have black restricted from the belly and sometimes the head.
	Mo⁺	Wild-type gene. Dominant. Lack of mottling.
Dominant white	I	Incompletely dominant. Influences eye pigment. Inhibits black pigment, eumalanin. This gene is ‘leaky’ and will allow black specks through. Generally not as efficient at producing a solid white bird as are two copies of recessive white. Heterozygotes of dominant white, I/i⁺ are often grey with the grey color visible in the chick down. Dominant white dilutes, but does not eliminate, epidermal melanin.
Smoky	I^S	The smoky gene is an allele belonging to the dominant white locus. Smoky is dominant to dominant white in both chick down and adult plumage in that extended black with I/I^S (E/E I/I^S)results in grey chick down and adult plumage. Research to date indicates that i+/I^S heterozygotes express more the wild-type phenotype with respect to this gene indicating a recessive character with respect to the wild-type. Smoky is dominant on the chick down of I^S/i+ heterozygotes in that down that should be black is grey. The melanosomes resulting from the expression of smoky resemble those resulting from Andalusian Blue. Smoky dilutes black much more than red/gold. An important difference between Smoky and Andalusian Blue is that Smoky in the homozygote state produces a grey/blue bird while Andalusian Blue homozygotes are splash. Therefore, Smoky fowl will breed true.
	I^D	This gene is often called 'Dun'. Incompletely dominant, off-white. Allelic with dominant white.
	i⁺	Wild-type gene. Lack of dominant white.
Frizzle	F	Incompletely dominant. The action of the frizzle gene is localized in the feather follicle. It causes a structure abnormality in the feather and abnormalities of internal organs (enlarged heart, spleen, gizzard and alimentary canal) are common.
	f⁺	Recessive, wild-type gene. Lack of frizzle.

**Autosomal Linkage Group 3 Genes**
Autosomal Genes	Symbol	Comments
Skin Color	w	Yellow skin color. Recessive.
	W⁺	Dominant wild-type gene. Autosomal white skin gene. Prevents the transfer of xanthophyll into the skin, beak and shanks but does not effect the eye iris, egg yolk or blood serum. This gene is considered to be the wild-type because it is present in the Jungle Fowl.
Blue eggshell	O	The action of the blue eggshell gene is dominant to the action of the white eggshell gene, o. Blue and brown egghell genes present simultaneously give a shade of green on the exterior of the egg. The blue eggshell color permeates the shell while brown is primarily an exterior coating.
	o	Recessive wild-type gene. Lack of blue eggshell color gene. Causes white eggshells in the absence of brown eggshell color genes.
Pea comb	P	Dominant. Sometimes referred to as triple comb. Heterozygotes often display a prominant central ridge with much smaller lateral points.
	p⁺	Wild-type gene. Recessive. Lack of pea comb.
Naked neck	Na	Incompletely dominant. Turkens. Causes bare skin on the neck which becomes reddish toward sexual maturity. Heterozygotes show a small tuft of feathers on the neck above the crop, which is almost missing in the homozygote. The Na allele is associated with increased tolerance for heat, which is probably due to the 30% reduction in overall plumage for heterozygotes and 40% for homozygotes. Na is also associated with a small increase in meat yield and lower body fat content. An increase in embryonic mortality of up to 10% is attributed to Na.
	na⁺	Recessive, wild-type gene. Lack of naked neck. Allows full feathering.
Silkie	h	Recessive. The barbs of the feathers are highly modified giving the silkie a 'woolly appearance.
	H⁺	Dominant, wild-type gene. Lack of silkie trait. Allows normal feather structure.
Melanotic	Ml	Dominant. Black intensifyer, one of the genes which, in concert with Pg and other genes, is responsible for plumage patterns. There is speculation that there may be more than one eumelanin intensifying gene similar to Ml and non-allelic.
	ml⁺	Recessive, wild-type gene. Lack of melanotic eumelanin enhancing gene.
Pattern gene	Pg	Dominant. This is the pattern gene which, together with other genes is responsible for the patterns of plumage. The pattern gene doesn’t seem to express in the absence of Ml in combination with some of the E locus alleles. See text. The pattern gene with the Db and Co Columbian-like restrictors is believed to be responsible for autosomal barring.
	pg⁺	Recessive. Wild-type gene. Lack of pattern gene.
Dark brown	Db	Incompletely dominant. Changes black down of E, E^R to reddish-brown. Adults males exhibit a Columbian-type pattern of black, modifies red to orange-tan. Db is a better restrictor of black in males than females.
	db⁺	Wild-type gene. Recessive. Lack of dark brown-type Columbian restriction.

**Autosomal Linkage Group 4 Genes**
Autosomal Genes	Symbol	Comments
Duplex comb	D^v, D^c	Dominant alleles. The superscripts 'v' and 'c' indicate the 'V' and 'cup' shaped phenotypes and are considered to be separate genes.
	d⁺	Recessive, wild-type gene. Lack of duplex trait.
Multiple spurs	M	Dominant. Causes more than one spur per shank on males.
	m⁺	Wild-type gene. Recessive. Lack of multiple spur trait.
Polydactyly	Po	Dominant. Having too many toes. The fifth toe develops on top of the first toe and is longer than the first toe. There are several degrees of expression of this gene.
	Po^d	Duplicate polydactyly. Dominant to the wild-type allele. An extra toe is present as well as an elogation and splitting of the original first toe. Extreme expression can accompany this gene in which the most extreme cases the entire foot is duplicated.
	po⁺	Wild-type, recessive. Allows normal foot.

**Other Autosomal Genes**
Autosomal Genes	Symbol	Comments
Autosomal barring	Ab	Non-sex-linked barring. Sometimes called 'parallel pencilling'. This is not a real gene, rather autosomal barring is due to combinations of Pg, Co, Db with e^b, E^R, and e^bc. See text.
Breda combless	bd	Recessive. Birds with this gene are almost completely lacking comb and wattles. Females are considered to be completely combles and males have a tiny comb.
	Bd⁺	Dominant, wild-type gene. Lack of breda combless trait. It is believed that this gene is necessary for chickens to produce a comb.
Blue	Bl	Incompletely dominant. Andalusian blue-dilutes black: blue pigment is a modified black. Two nigrum genes, E, and one Bl gives a blue chicken; two Bl genes gives splash.
	bl⁺	Wild-type gene. Recessive. Lack of blue eumelanin dilution gene, Bl.
Brachydactyl	By	Dominant. Abnormally short digits (toes).
Recessive white genes	c	Thought to give a cleaner white than dominant white. Varieties of White Plymouth Rock, Wyandotte, Minorca, Orpington, Jersey Giant, Dorking, Langshan, Silky and others often carry recessive white genes. Many varieties carry both dominant and recessive white. Allows dark eyes. Pigmentation in chick down varies.
	c^re	Recessive white allele that allows red eyes.
	c^a	Autosomal albinism. Alellic with the recessive white genes. Evident via lack of eye pigment. Some melanin present in chick down.
	C⁺	Wild-type gene. Dominant. Lack of recessive white mutations.
	Comments about the C locus	The order of dominance among the recessive white alleles is: C⁺>c>c^re>c^a. The presence of other pigment inhibiting or enhancing genes will influence the chick down color. Some adults have a grey color.
Champagne blond	Cb	Dominant. Inhibits pheomelanin (red / gold). The presence of the gene is not observable on the wild-type down
	cb⁺	Wild-type gene. Recessive. Lack of chanpagne blond dilution.
Columbian	Co	Incompletely dominant.Confines black to hackle and tail in both sexes (called Columbian restriction). Thought to cause a gradient in color from head to tail. Modifies Wheaten to Buff Columbian. Has no effect on extended black, E.
	co⁺	Wild-type gene. Lack of Columbian restriction. Recessive.
Red diluter	Di	Dominant. Dilutes red, changes red to buff.
	di⁺	Wild-type gene. Lack of red diluter. Recessive.
Dark	Dk	A proposed gene of an allelemorphic series that darkens the shade of red. Pheomelanin enhancer(s). Dk^l was proposed for the dark brown Leghorn and dk⁺ for the wild-type allele.
Ginger	Gr	This gene may be Columbian, Co, or closely related. This may not be a distinct gene.
Grey	no symbol	Recessive, dilutes black to brown/grey.
The E-locus alleles	E	Often called 'extended black', 'nigrum' or 'self black'. Extends black, changes red to black, red inhibitor.
	E^R	Birchen. Resembles extended black, E, but with non-black breaks on head and hackle. Body is black with some stippling (flecks/dots) of other color. Used as red inhibitor in Leghorn.
	e^b	Partridge (brown). Sometimes represented as e^p, females have non-salmon breast with stippling. Males are wild-type.
	e^Wh	Dominant wheaten. Female body varies from light salmon to wheat color, some black may be present. Males are wild-type.
	e⁺	Wild-type. Female: breast is salmon brown and devoid of stippling, body is black and brown in stippled pattern. Males: black breast and abdomen; non-black hackle, saddle and wings.
	e^s	Speckled. Resembles e^b but with less pronounced stippling. Males are wild-type.
	e^y	Recessive wheaten. Female: resembles dominant wheaten with more coarse black stippling on breast and back. Males are wild type.
	e^bc	Buttercup allele. Resembles the e^b phenotype.
	Comments on E-locus alleles	The order of dominance among the generally accepted E-locus alleles is: E>E^R>e⁺>e^b>e^s>e^bc>e^y. The birchen allele is incompletely dominant to dominant wheaten and the wild-type alleles. Additional alleles have been proposed for the E-locus but research to verify these as separate alleles has not been done. As of this writing, the buttercup allele has been sequenced and has been found to be the same sequence as the e^b allele. The buttercup phenotype then is due to modifiers or interactions with other genes. Every E-locus allele influences adult female phenotype. However, all the adult male phenotypes are the same as wild-type except for extended black and birchen.
Ear tuft	Et	Dominant. Lethal in homozygous state. Thought to be associated with birth defects, particularly in the ear structures.
	et⁺	Wild-type gene. Recessive. Lack of ear tufts.
Erminette	no symbol	Black spots and flecks, variable black and white feathers, similar to pied.
Fibromelanosis	Fm	Dominant. Sounds like a disease. The name was suggested by F. Hutt in the 1940s to emphasize the association with connective tissue pigmentation. This gene is responsible for the deep skin pigmentation of silkie. Fm is strongly influenced by dermal melanin inhibitors such as the sex-linked Id mutation.
	fm⁺	Wild-type gene. Recessive. Lack of fibromelanosis.
Long tail	Gt, mt	The Gt gene (dominant) allows continual growth of tail and saddle feathers. The mt gene allows certain tail and saddle feathers to be nonmolting.
Henny plumage	Hf	Dominant. The term comes from 'hen feathering' in which male plumage is indistinguishable from female plumage.
	hf⁺	Wild-type gene. Recessive. Lack of henny feathering.
Cream	ig	Dilutes red. Recessive. A major pheomelanin dilution gene. The gene symbol derives from "inhibitor of gold".
	Ig⁺	Wild-type gene. Dominant. Lack of cream dilution.
Lace	Lg	This is not a real gene. See text. Partridge Rock, Silver Pencilled Rock.
Beard-Muff	Mb	Incompletely dominant. Characteristic of Ameraucana, Easter Egg Chickens (faux-Araucana)
	mb⁺	Wild-type gene. Recessive. Lack of beard-muff.
frizzle modifyer	mf	Recessive. Reduces/modifies the effect or expression of the frizzle gene. This gene can modify frizzle heterozygote expression to the point that they are almost indistinguishable from the wild type. Modifies the extreme expression of the frizzle homozygote.
	Mf⁺	Wild-type gene (uncertain). Dominant. Lack of frizzle modifyer.
Recessive melanotic	mi	Enhances black, (helps) change red to black. E + mi gives a black chicken.
	Mi⁺	Wild-type gene. Dominant. Lack of recessive melanotic enhancing.
Mottle	mo	Recessive. Makes a white tip on end of feather. Changes a black bird to Mottled and a Buff Columbian to a Mille Fleur. Dilutes epidermal melanin. There may be several alleles corresponding to this locus or non-allelic modifying genes.
	Mo⁺	Wild-type gene. Dominant. Lack of mottling.
Mahogany	Mh	Dominant. Mahogany restricts eumelanin and enhances the color of red. Rhode Island Red is a good example. Restricts black in the back and wing of both males and females. Down color seemes to be unaffected by mahogany.
	mh⁺	Wild-type gene. Recessive. Lack of mahogany.
Pink-eye dilute	p^K	Dilutes both feathers and eye color. Recessive.
Recessive polydactyly	po-2	Recessive. A number of extra toes can be present even ascending the shank. Associated with leg deformities, significant decrease in hatchability and much higher post-natal mortality.
Feathered legs	Pti-1, Pti-2	Dominant. Two different feathered leg genes. Research has shown that these genes are most likely not allelic (they belong to different loci of the chromosome). When both are present, heavy feathering as in Cochin, Sultan, Belgian d’Uccle. If only one is present, the feathering is weaker as in Langshan, Faverolle, Breda. Genes demonstrate a dose effect.
Recessive feathered legs	pti-3	The recessive leg feathering gene was identified in a Russian breed referred to as the Pavlov breed. Test matings confirmed the recessive nature of this gene.
Dominant Rumplessness	Rp	No coccyx (tail vertebra), reduces hatchability.
	rp⁺	Wild-type gene. Recessive. Lack of dominant rumplessness. Fowls usually have tails.
Recessive Rumplessness	rp-2	A skeletal mutation commonly called 'roachback'.
Red spash white	rs	Recessive. Two copies of this gene give a white bird with spashes of red and black. Chicks are white with a red head spot. This gene may be extinct now. It was first isolated in a line of Rhode Island Reds, but it was not maintained nor has it be re-identified.
Recessive black	sg	Not much is known about this gene. Eumelanin intensifier. There may be a number of genes that play this role.
Spurlessness	sl	Recessive. Fowls have no spurs.
Snow-white down	sw	Recessive. The chick down is white rather than yellow.
Vulture hocks	v	Recessive. Long and stiff feathers on the posterior area of the tibia. Characteristic of Belgian Bearded d'Uccle, Breda, Sultan.
Dorking white	wh	Recessive.
Woolly	wo	Recessive.

Glossary

Allele One of a number of possible alternative forms of genetic information at a gene locus [1]. A member of a set of genes that all have the same location on a given chromosome. For example, extended black and birchen are allelic genes ( to each other) because they are both found at the E locus or location.

Epistasis (also epistacy) suppression of the effect of a gene by a nonallelic gene [3]. A gene for trait A somehow having an effect on triat B is an example of epistasis.

Gene The unit of heredity [1]. A piece of DNA in a chromosome that contains the coded information for a trait.

Generation notation: The original members of a mating are referred to as the parental (P) generation. The first generation of progeny from the parental cross is referred to as the first filial generation, F1. The progeny of a cross in which one or both of the parents are from the F1 generation is an F2 generation (F1 x F1 = F2) and so on [1].

Heterosis The deviation between the cross and midparent means [2]. The difference in some property, for example rate of lay, between a cross bred line and the average for the parent lines. For example, “hybrid vigor” can be thought of as an effect of heterosis.

1. J.J. Pasternak, An Introduction to Human Molecular Genetics, Mechanisms of Inherited Diseases, Fitzgerald Science Press, Bethesda, MD 1999.

2. R.W. Fairfull in Poultry Breeding and Genetics, R.D. Crawford, ed., Elsevier, 1990, page 913.

3. Webster’s Seventh Collegiate Dictionary

Websites:

Poultry Genome Project http://poultry.mph.msu.edu/

Poultry Genetics Board http://www.insidetheweb.com/messageboard/mbs.cgi/mb55754

UCDavis http://animalscience.ucdavis.edu/extension/avian/pfs1b.htm

MSState http://www.msstate.edu/dept/poultry/avianemb.htm