Poultry Genetics -Chromosome Linkages

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Linkages

Introduction on linkages
Linkages tables, categorised into chromosome groups
Map units

Chromosome Linkages Table

The following linkage map table is based on the following books:

1. Crawford (ed.) (1990) *Poultry Breeding and Genetics.*
2. Stevens, L. (1991) *Genetics and Evolution of the Domestic Fowl*.
3. Muir and Aggrey (ed.) (2003) *Poultry Genetics, Breeding and Biotechnology*, CABI Publishing.

# All hashed data is from the last book (Muir & Aggrey), & is based on the following quote from this book (page 499):

The classical linkage groups I, IV and Z correspond to chromosomes 1, 2 and Z, and linkage group II to linkage group E22C19W28. These results also clearly show that several of the linkages reported in the past are incorrect. For example, naked neck and blood group P are located not on chromosome 1 (linkage group 1) but on chromosome 3 and extension of eumelanin (MC1R) is not located on chromosome 1 but located on microchromosome 11 (Takeuchi et al., 1996; Sazanov et al., 1998; Kerje et al., 2003, unpublished).

*Note, the recessive white locus (Tyrosinase) map reference is from Dr Ron Okimoto (pers. comm.)
*Recent sequencing of the yellow skin allele:
Eriksson J, Larson G, Gunnarsson U, Bed'hom B, Tixier-Boichard M, et al. (2008) *Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken.* PLoS Genet 4(2): e1000010. doi:10.1371/journal.pgen.1000010

Quotes from the above article:

....yellow skin was previously assigned to chromosome 24.
An examination of this chromosomal region revealed an obvious candidate gene for yellow skin, BCDO2 located at position 6.26–6.29 Mbp.

*Due to the above information, I've included w locus on Microchromosome 24 (*) in the table below. It is obvious from growing discrepancies in data below that the old Linkage Maps in Crawford, etc (which most of the table below is based on) are outdated and need significant revision.

Locus	Map Unit Distance	Locus Description	Scientific Name - DNA sequenced	Comments/Ref
Group I : (# Chromosome 7)
Cp		Creeper
	0.4
R		Rose Comb	MNR2 (homeodomain protein) (& CCDC108 coiled-coil domain containing 108 )	Imsland et al. 2012
	30
U		Uropygial		linkage not given to lav
----------------------------	-----------	------------------		--------------
the below not linear
lav	32.5	Lavender	MLPH (melanophilin)	lav 32.5 map units to R Vaez et al., 2008
	?			linkage not given between lav & Mp
Mp	16			Mp 16 map units to R
the above not linear

Group II (# linkage group E22C19W28- new)
fr		Fray
	46
Cr		Crest	HOXC8 (Homeobox protein C8)	Wang et al., 2012
	12.5
I, I^D, I^S		Dominant White, Dun, Smoky	PMEL17 (Melanocyte protein Pmel 17)	Kerje et al., 2004
	17
F		Frizzle	KRT75 (α-Keratin)	Ng et al., 2012

Group III: (# Chromosome 1)

w		Yellow Skin		*sequenced on Microchromosome 24
	22
Ea-H		Blood Group H
	21
se		Sleepy Eye		se is 45 map units from P
	3
Ea-J		Blood Group J
p	36
O		Blue Egg-Shell
	4
Cha		Charcoal
	0.3
P		Pea Comb	SOX5 (SRY-box 5)	*Carefoot believed E locus linked to P -43 cM, this later determined incorrect. Wright et al, 2009. Sato et. al, 2010.
	32
Db		Dark Brown	SOX10 (SRY-box 10)	Gunnarsson et al. 2011.
	12
Ml		Melanotic		Ml is 45 + map units from P
	10
Pg		Pattern
	?
T		Tardy
	?
Ea-P		Blood Group P		(#Chromosome 3 -new)
	28
Na		Naked Neck		(#Chromosome 3 -new) Pitel et al. 2000
q	43
h		Hookless - Silkiness		possible Chromosome 3. Dorshorst et al 2010
	11
Fl		Flightless
	?
c		Recessive White	TYR (tyrosinase)	Tyrosinase (#Chromosome 1 -new) Chang et al, 2006. Sato et. al, 2007.

Group IV (#Chromosome 2 -new)
D^V, D^C		Duplex Comb		chromosome 2 - Dorshorst et al 2010
	27
M		Multiple Spurs
	33
Po, Po^d		Polydactyly, Duplicate	Lmbr1 (limb region 1)	chromosome 2 - Dorshorst et al 2010 Might be SHH (Sonic HedgeHog) instead of Lmbr1 Dunn et al., 2011

Rp		Rumpless	Irx1 and Irx2 (Iroquois homeobox)	Rooksana et al, 2012

#Chromosome 3 -new
Ea-P		Blood Group P		(#Chromosome 3 -new)
	28
Na		Naked Neck	BMP12/GDF7 (bone morphogenetic protein 12)(growth differentiation factor 7)	(#Chromosome 3 -new) Mou et al. 2011
	43
h		Hookless - Silkiness		possible Chromosome 3. Dorshorst et al 2010
	11
Fl		Flightless		possible Chromosome 3. due to close linkage with h - hookless


*Group V: (Z Chromosome -sex chromosome)*

ro		Restricted Ovulator
	3
sh		Shaker
p	14
n		Naked
	7
px		Paroxysm
	1.9
ln		Liver Necrosis
	3.1
dw^B, dw^M, dw		Dwarf	GHR (growth hormone receptor)	Hull et al, 1999
	3.4
wl		Wingless
	0.6
pn		Prenatal Lethal
	3
ev21		Endogenous viral 21	EV21 (ALVE21) (Endogenous viral 21)	Tixier-Boichard et al., 1997. Bacon et al., 1988
Kⁿ, K^s, K		Slow Feathering	PRLR and SPEF2 (prolactin receptor) (sperm flagellar 2)	Elferink et al., 2008
	1.1
S, S^al-s, s^al		Silver, Imperfect Albinism	SLC45A2 (solute carrier family 45 member 2)	Gunnarsson et al, 2007.
	4
lk		Lady Killer
	12
Li		Light Down
	7
y		Recessive White Skin
	13
br		Brown Eye
q	27
Id, id^a, id^c,id^M		Dermal Melanin Inhibitor	VCAN (Versican) or B4GALT1 (beta1,4-Galactosyltransferase)	Might be VCAN or B4GALT1 - not substantiated. Dorshorst et al, 2010
	14
B^Sd, B		Sex-linked Dilution, Barring	CDKN2A/B (Cyclin-dependent kinas inhibitor 2A/B)	Hellström et al, 2010
	13
ko		Head Streak

*Group VI: (W Chromosome -sex chromosome- females only)*


Group VII (Chromosome 6)
the below not linear
Gc, Alb
Ade-A
Pgm-2
the above not linear
ig		Inhibitor of Gold (Cream)	COMTD1 (catechol-O-methyltransferase domain containing 1)	Eriksson, 2012
Group VIII (Chromosome 7)
Ade-B			adenine synthesis B

Group X (Microchromosome 17)

p
B-G

Ea-B
	0.4
B-F		MHC
R-Rs 1
B-L
lr-GAT
NOR		Nucleolar organiser region
q

Ea-B

Chromosome 8
		fishy taint	FMO3 (flavincontaining mono-oxygenase 3)	Honkatukia et al. 2005 Hamid et al, 2012

Chromosome 10
Hf		Henny-feathering	CYP19A1 (cytochrome P450, family 19, subfamily A, polypeptide 1)	ref: OMIA

#Microchromosome 11

E, E^R, E^R- Fay, e^Wh, e⁺, e^b, e^s, e^bc, e^y, e^q		E Series	MC1R (melanocortin-1 receptor)	Takeuchi et al. 1996. Kerje et al., 2003. Ling et al., 2003
	26
mo		Mottled		ref. Brumbaugh & Hollander, 1965

Microchromosome 12
Bl		Blue	MITF	*possible candidate - not sequenced in chickens. Minvielle et al., 2010

Microchromosome 13
Pti		Feathered legs		Chromosome 13 - Dorshorst et al 2010

#Microchromosome 15
Et		Ear Tuft	TBX1, partial GNB1L (T-box 1)	Rooksana et al, 2012

Microchromosome 20
Fm		Fibromelanosis	EDN3 (Endothelin 3)	Chromosome 20 - Dorshorst et al 2010 *might be EDN3 - not substantiated Dorshorst et al., 2011. Shinomiya et al., 2011.
*Microchromosome 24
w		Yellow skin	BCDO2 (beta-carotene dioxygenase 2)	*see ref. above Eriksson et al., 2008

Full Reference List:

Bacon LD, Smith E, Crittenden LB, Havenstein GB. (1988) Association of the slow feathering (K) and an endogenous viral (ev21) gene on the Z chromosome of chickens. Poult Sci. 1988 Feb;67(2):191-7. [URL]

Brumbaugh, J. A., and W. F. Hollander (1965) A further study of the E pattern locus in the fowl. Iowa State J.of Science, 40; 51-64

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

Dorshorst B, Okimoto R, Ashwell C. (2010) Genomic Regions Associated with Dermal Hyperpigmentation, Polydactyly and Other Morphological Traits in the Silkie Chicken. J Hered. 2010 May-Jun;101(3):339-50 [URL]

Dorshorst B, Molin AM, Rubin CJ, Johansson AM, Strömstedt L, Pham MH, Chen CF, Hallböök F, Ashwell C, Andersson L. (2011) A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in the chicken. PLoS Genet. 2011 Dec;7(12):e1002412. Epub 2011 Dec 22. [URL]

Dunn IC, Paton IR, Clelland AK, Sebastian S, Johnson EJ, McTeir L, Windsor D, Sherman A, Sang H, Burt DW, Tickle C, Davey MG. (2011) The chicken polydactyly (Po) locus causes allelic imbalance and ectopic expression of Shh during limb development. Dev Dyn. 2011 May;240(5):1163-72. doi: 10.1002/dvdy.22623. Epub 2011 Apr 4. [URL]

Elferink MG, Vallée AA, Jungerius AP, Crooijmans RP, Groenen MA. (2008) Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken. BMC Genomics. 2008 Aug 20;9:391. [URL]

Eriksson J, Larson G, Gunnarsson U, Bed'hom B, Tixier-Boichard M, et al. (2008) Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken. PLoS Genet 4(2): e1000010. doi:10.1371/journal.pgen.1000010. [URL]

Eriksson, J (2012) Genetic and Genomic Studies in Chicken: Assigning Function to Vertebrate Genes. Acta Universitatis Upsaliensis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 732. 55pp. Uppsala. ISBN 978-91-554-8246-6. [URL]

Gunnarsson U, Hellström AR, Tixier-Boichard M, Minvielle F, Bed'hom B, Ito S, Jensen P, Rattink A, Vereijken A, Andersson L. (2007). Mutations in SLC45A2 Cause Plumage Color Variation in Chicken and Japanese Quail. Genetics. 175, 867-77. [URL]

Gunnarsson U, Kerje S, Bed'hom B, Sahlqvist AS, Ekwall O, Tixier-Boichard M, Kämpe O, Andersson L. (2011) The Dark brown plumage color in chickens is caused by an 8.3-kb deletion upstream of SOX10. Pigment Cell Melanoma Res. 2011 Apr;24(2):268-74. doi: 10.1111/j.1755-148X.2011.00825.x. Epub 2011 Jan 25. [URL]

Hamid MA, Wang X, and Zhao X. (2012) Genotyping of flavin-containing mono-oxygenase 3 (FMO3) gene by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and mismatch amplification mutation assay (MAMA-PCR) in chickens. African Journal of Biotechnology Vol. 11(7), pp. 1823-1828, 24 January, 2012. [URL]

Hellström AR, Sundström E, Gunnarsson U, Bed'Hom B, Tixier-Boichard M, Honaker CF, Sahlqvist AS, Jensen P, Kämpe O, Siegel PB, Kerje S, Andersson L. (2010) Sex-linked barring in chickens is controlled by the CDKN2A /B tumour suppressor locus. Pigment Cell Melanoma Res. 2010 Aug;23(4):521-30. doi: 10.1111/j.1755-148X.2010.00700.x. Epub 2010 Mar 29. [URL]

Honkatukia M, Reese K, Preisinger R, Tuiskula-Haavisto M, Weigend S, Roito J, Mäki-Tanila A, Vilkki J. (2005) Fishy taint in chicken eggs is associated with a substitution within a conserved motif of the FMO3 gene. Genomics. 2005 Aug;86(2):225-32. [URL]

Hull, K.L, Marsh, J.A. and Harvey, S. (1999) A missense mutation in the GHR gene of Cornell sex-linked dwarf chickens does not abolish serum GH binding. Journal of Endocrinology (1999) 161, 495–50. [URL]

Imsland F, Feng C, Boije H, Bed'hom B, Fillon V, Dorshorst B, Rubin CJ, Liu R, Gao Y, Gu X, Wang Y, Gourichon D, Zody MC, Zecchin W, Vieaud A, Tixier-Boichard M, Hu X, Hallböök F, Li N, Andersson L.(2012) The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility. PLoS Genet. 2012 Jun;8(6):e1002775. Epub 2012 Jun 28. [URL]

Kerje S, Lind J, Schütz K, Jensen P, Andersson L. (2003) Melanocortin 1-receptor (MC1R) mutations are associated with plumage colour in chicken. Anim Genet. 2003 Aug;34(4):241-8. [URL]

Kerje S, Sharma P, Gunnarsson U, Kim H, Bagchi S, Fredriksson R, Schütz K, Jensen P, von Heijne G, Okimoto R, Andersson L. (2004) The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion polymorphisms in the PMEL17 gene. Genetics. 2004 Nov;168(3):1507-18. [URL]

Ling MK, Lagerström MC, Fredriksson R, Okimoto R, Mundy NI, Takeuchi S, Schiöth HB. (2003) Association of feather colour with constitutively active melanocortin 1 receptors in chicken. Eur J Biochem. 2003 Apr;270(7):1441-9. [URL]

Minvielle F, Bed'hom B, Coville JL, Ito S, Inoue-Murayama M, Gourichon D. (2010) The "silver" Japanese quail and the MITF gene: causal mutation, associated traits and homology with the "blue" chicken plumage. BMC Genet. 2010 Feb 25;11:15. doi: 10.1186/1471-2156-11-15. [URL]

Mou C, Pitel F, Gourichon D, Vignoles F, Tzika A, et al. (2011) Cryptic Patterning of Avian Skin Confers a Developmental Facility for Loss of Neck Feathering. PLoS Biol 9(3): e1001028. doi:10.1371/journal.pbio.1001028 [URL]

Ng CS, Wu P, Foley J, Foley A, McDonald ML, Juan WT, Huang CJ, Lai YT, Lo WS, Chen CF, Leal SM, Zhang H, Widelitz RB, Patel PI, Li WH, Chuong CM. (2012) The Chicken Frizzle Feather Is Due to an a-Keratin (KRT75) Mutation That Causes a Defective Rachis. PLoS Genet. 2012 Jul;8(7):e1002748. Epub 2012 Jul 19. [URL]

Pitel F, Berge R, Coquerelle G, Crooijmans RPMA, Groenen MAM, et al. (2000) Mapping the naked neck (NA) and polydactyly (PO) mutants of the chicken with microsatellite molecular markers. Genet Sel Evol 32: 73–86. [URL]

Rooksana E. Noorai, Nowlan H. Freese, Lindsay M. Wright, Susan C. Chapman, and Leigh Anne Clark. (2012) Genome-Wide Association Mapping and Identification of Candidate Genes for the Rumpless and Ear-tufted Traits of the Araucana Chicken. PLoS One. 2012; 7(7): e40974. [URL]

Sato S, Otake T, Suzuki C, Saburi J, Kobayashi E. (2007) Mapping of the recessive white locus and analysis of the tyrosinase gene in chickens. Poult Sci. 2007 Oct;86(10):2126-33. [URL]

Sato S, Otake T, Suzuki C, Uemoto Y, Saburi J, Hashimoto H, Kobayashi E. (2010) Sequence analysis of a pea comb locus on chicken chromosome 1. Animal Genetics. Volume 41, Issue 6, pages 659–661, December 2010. [URL]

Shinomiya A, Kayashima Y, Kinoshita K, Mizutani M, Namikawa T, Matsuda Y, Akiyama T. (2011) Gene Duplication of endothelin 3 is Closely Correlated with the Hyperpigmentation of the Internal Organs (Fibromelanosis) in Silky Chickens. Genetics. 2012 Feb;190(2):627-38. doi: 10.1534/genetics.111.136705. Epub 2011 Nov 30. [URL]

Takeuchi S, Suzuki H, Yabuuchi M and Takahashi S. (1996) A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the chicken. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression Volume 1308, Issue 2, 14 August 1996, Pages 164-168. [URL]

Tixier-Boichard M, Boulliou-Robic A, Morisson M, Coquerelle G, Horst P, Benkel B. (1997) A deleted retroviral insertion at the ev21-K complex locus in Indonesian chickens. Poult Sci. 1997 May;76(5):733-42. [URL]

Vaez M, Follett SA, Bed'hom B, Gourichon D, Tixier-Boichard M, Burke T. (2008) A single point-mutation within the melanophilin gene causes the lavender plumage colour dilution phenotype in the chicken. BMC Genet. 2008 Jan 15;9:7. doi: 10.1186/1471-2156-9-7. [URL]

Wang Y, Gao Y, Imsland F, Gu X, Feng C, et al. (2012) The Crest Phenotype in Chicken Is Associated with Ectopic Expression of HOXC8 in Cranial Skin. PLoS ONE 7(4): e34012. doi:10.1371/journal.pone.0034012. [URL]

Wright D, Boije H, Meadows JRS, Bed'hom B, Gourichon D, et al. (2009) Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens. PLoS Genet 5(6): e1000512. doi:10.1371/journal.pgen.1000512. [URL]

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