Poultry Genetics -Chromosome Linkages

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Last updated: 1 Nov, 2010

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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on chromosome 1 but located on microchromosome 11 (Takeuchi et al., 1996; Sazanov et al., 1998; Kerje et al., 2003, unpublished).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discrepancies in data below that the old Linkage Maps in Crawford, etc (which most of the table below is based on) are outdated and need significant revision.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
Group I : (# Chromosome 7)
Cp		Creeper
	0.4
R		Rose Comb
	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
	?			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
	12.5
I, I^D, I^S		Dominant White, Dun, Smoky	PMEL17 (Melanocyte protein Pmel 17)
	17
F		Frizzle

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.
	32
Db		Dark Brown	SOX10 (SRY-box 10)	Db is 32 Map units from P
	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)
q	43
h		Hookless - Silkiness
	11
Fl		Flightless
	?
c		Recessive White	TYR (tyrosinase)	Tyrosinase (#Chromosome 1 -new)

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

*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)
	3.4
wl		Wingless
	0.6
pn		Prenatal Lethal
	3
Kⁿ, K^s, K		Slow Feathering
	1.1
S, S^al-s, s^al		Silver, Imperfect Albinism	SLC45A2 (solute carrier family 45 member 2)
	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.
	14
B^Sd, B		Sex-linked Dilution, Barring	CDKN2A/B (Cyclin-dependent kinas inhibitor 2A/B)
	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

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

#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)
	26
mo		Mottled		ref. Brumbaugh & Hollander, 1965
Chromosome 20
Fm		Fibromelanosis	EDN3 (Endothelin 3)	*might be EDN3 - not substantiated
*Microchromosome 24
w		Yellow skin	BCDO2 (beta-carotene dioxygenase 2)	*see ref. above

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