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Linkages

 


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on chromosome 1 but located on microchromosome 11 (Takeuchi et al., 1996; Sazanov et al., 1998; Kerje et al., 2003, unpublished).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discrepancies in data below that the old Linkage Maps in Crawford, etc (which most of the table below is based on) are outdated and need significant revision.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, ID, IS
  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)
DV, DC
 
Duplex Comb   chromosome 2 -
Dorshorst et al 2010
 
27
     
M
  Multiple Spurs    
 
33
     
Po, Pod
  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
     
dwB, dwM, 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, Ks, K
 
Slow Feathering PRLR and SPEF2
(prolactin receptor)
(sperm flagellar 2)
Elferink et al., 2008
 
1.1
     
S, Sal-s, sal
 
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, ida, idc,idM
Dermal Melanin Inhibitor VCAN (Versican) or B4GALT1 (beta1,4-Galactosyltransferase) Might be VCAN or B4GALT1 - not substantiated.
Dorshorst et al, 2010
 
14
     
BSd, 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, ER, ER- Fay, eWh, e+, eb, es, ebc, ey, eq
  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
 
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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