Journal papers online - reference list

Posted by: KazJaps

Journal papers online - reference list - 01/21/11 01:28 AM

I thought I would start a list (with links) of journal papers online, so everyone can grab them while they can (access is often fleeting to old papers, or URLs change, not full publications available, etc).

jhered has released alot of old papers (full publications):

Inheritance of the Silver-Laced Wyandotte Plumage Pattern
(J Hered-1972-MOORE-179-84)
http://jhered.oxfordjournals.org/content/63/4/179.full.pdf

Melanotic: Key to a Phenotypic Enigma in the Fowl
(J Hered-1971-MOORE-215-9)
http://jhered.oxfordjournals.org/content/62/4/215.full.pdf

A NEW GENE DETERMINING THE COLUMBIAN FEATHER PATTERN In the Fowl.
(J Hered-1965-SMYTH-151-6)
http://jhered.oxfordjournals.org/content/56/4/151.full.pdf

Genetic Basis for Plumage Color Pattern in the New Hampshire Fowl
(J Hered-1970-SMYTH-280-3)
http://jhered.oxfordjournals.org/content/61/6/280.full.pdf

IRREGULAR MOSAICISM IN A HEN
(J Hered-1959-COCK-171-6)
http://jhered.oxfordjournals.org/content/50/4/171.full.pdf

The genetics of green spotting on shanks of Ancona chickens.
(J Hered-1978-MCGIBBON-97-100)
http://jhered.oxfordjournals.org/content/69/2/97.full.pdf

Linkage Relationships in Domestic Fowl
(J Hered-1973-SOMES-217-21)
http://jhered.oxfordjournals.org/content/64/4/217.full.pdf

White-wing, a lethal feather achromatic mutant in the fowl.
(J Hered-1979-SOMES-373-8)
http://jhered.oxfordjournals.org/content/70/6/373.full.pdf

Delayed Feathering, A Third Allele at the K Locus of the Domestic Fowl
(J Hered-1969-SOMES-281-6)
http://jhered.oxfordjournals.org/content/60/5/281.full.pdf

A genetic study of the buff Columbian color pattern in Prat chickens
(J Hered-1984-Campo-19-22)
http://jhered.oxfordjournals.org/content/75/1/19.full.pdf

Genetics of the Columbian plumage pattern in the Vasca chicken breed
(J Hered-1983-Campo-43-6)
http://jhered.oxfordjournals.org/content/74/1/43.full.pdf

Tardy feathering locus (f) located on chromosome 1 in the chicken.
(J Hered-1987-Bitgood-329-30)
http://jhered.oxfordjournals.org/content/78/5/329.full.pdf
-------------------------------------------
Poultry Science:

The Hypostatic Genotype of the Recessive White Prat Breed of Chickens
http://ps.fass.org/cgi/reprint/76/3/432.pdf

Further Tests for Genetic Linkages of Three Morphological Traits, Three Blood Groups, and Break Points of Two Chromosome Translocations on Chromosome One in the Chicken
(Bitgood et. al., 2001)
http://ps.fass.org/cgi/reprint/79/3/293.pdf

Molecular Characterization of the Smyth Chicken Sublines and Their Parental Controls by RFLP and DNA Fingerprint Analysis
http://ps.fass.org/cgi/reprint/80/1/1.pdf

----------------------------
Genetics:

PLUMAGE COLOR ALLELISM IN THE RED JUNGLE FOWL (GALLUS GALLUS) AND RELATED DOMESTIC FORMS
(Morejohn, V. 1954)
http://www.genetics.org/cgi/reprint/40/4/519.pdf

----------------------------

I've managed to freeze Adobe Reader (& PC suffering severe memory leakage, like its owner), so will get back to this list after a reboot smile .
Posted by: Wieslaw

Re: Journal papers online - reference list - 01/21/11 04:20 AM

Originally Posted By: KazJaps
White-wing, a lethal feather achromatic mutant in the fowl.
(J Hered-1979-SOMES-373-8)
http://jhered.oxfordjournals.org/content/70/6/373.full.pdf



I have seen a hen with white wings here:

http://www.youtube.com/watch?v=wiaGbXs-mbc&feature=related

Can it be another white wing mutation than the one described in the papers? It doesn't look lethal to me(well, at least not for the hen who's carrying it)
Posted by: KazJaps

Re: Journal papers online - reference list - 01/21/11 09:15 AM

I'll do some of the DNA sequenced mutations list, while I have the links handy:

-------------------------------

Chromosome Z:
- B : CDKN2A/B (abstract)
- Dw : GHR (growth hormone receptor)
- S : SLC45A2 (solute carrier family 45 member 2)(full paper)

Chromosome 1
- C : TYR (tyrosinase) (full paper)
- P : SOX5 (SRY-box 5) (full paper)
- Db : SOX10 (SRY-box 10) (abstract)

Chromosome 2
- Po : Lmbr1 (limb region 1)

Chromosome 7
- Lav : MLPH (melanophilin) (full paper)

Microchromosome 11
- E : MC1R (melanocortin-1 receptor) (abstract)

Microchromosome 24
- W : BCDO2 (beta-carotene dioxygenase 2)(full paper)

Linkage Group E22C19W28
- I : PMEL17 (Melanocyte protein Pmel 17) (full paper)


---------------------------
References & paper links:


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.
Full Paper pdf - 1.74 MB

Eriksson J, Larson G, Gunnarsson U, Bed'hom B, Tixier-Boichard M, Strömstedt L, Wright D, Jungerius A, Vereijken A, Randi E, Jensen P, Andersson L. 2008. Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken. PLoS Genet. 4(2):e1000010.
Full Paper –html text

Sex-linked barring in chickens is controlled by the CDKN2A /B tumour suppressor locus.
(Pigment Cell Melanoma Res. 2010 Aug;23(4):521-30. Epub 2010 Mar 29.)
Abstract only:
http://www.ncbi.nlm.nih.gov/pubmed/20374521

Genetic mapping of the sex-linked barring gene in the chicken.
(2009 Poultry Science 88 :1811–1817)
Full paper:
http://ps.fass.org/cgi/reprint/88/9/1811


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
Full paper

Mapping of the Recessive White Locus and Analysis of the Tyrosinase Gene in Chickens
(Sato et. al, 2007 Poultry Science 86:2126–2133)
full pdf paper

A single point-mutation within the melanophilin gene causes the lavender plumage colour dilution phenotype in the chicken.
(Vaez et al., BMC Genetics 2008, 9:7)
full text paper

Melanocortin 1-receptor (MC1R) mutations are associated with plumage colour in chicken
(Kerje et al., Anim Genet. 2003 Aug;34(4):241-8.)
abstract

Association of feather colour with constitutively active melanocortin 1 receptors in chicken
(Ling et al., Eur J Biochem. 2003 Apr;270(7):1441-9.)
full paper

The Dominant white, Dun and Smoky Color Variants in Chicken Are Associated With Insertion/Deletion Polymorphisms in the PMEL17 Gene
(Kerje et al., Genetics. 2004 Nov;168(3):1507-18.)
full paper
----------------------------
Possible candidates:

The "silver" Japanese quail and the MITF gene: causal mutation, associated traits and homology with the "blue" chicken plumage.
full paper.

-----------------------

I'll double-check, edit, and add to the list another day.
Posted by: Henk69

Re: Journal papers online - reference list - 01/22/11 02:10 AM

Originally Posted By: Wieslaw
I have seen a hen with white wings here:

http://www.youtube.com/watch?v=wiaGbXs-mbc&feature=related

Can it be another white wing mutation than the one described in the papers? It doesn't look lethal to me(well, at least not for the hen who's carrying it)


Reminds me of christmas with my sisters... wink
Warning for violence here.

Kazjaps, thank you, I will make this a sticky.
Posted by: Htul

Re: Journal papers online - reference list - 01/22/11 06:03 AM


A gene for yellowish-white down in the red junglefowl

Morejohn (1953) J Hered 44(2): 47-52 http://jhered.oxfordjournals.org/content/44/2/47.full.pdf

I would consider this to be an essential read for sceptics of the existence of a separate ey
Posted by: KazJaps

Re: Journal papers online - reference list - 01/22/11 07:44 AM

I see you've found the ey paper too smile

I'll give the jhered link to the archives index page:
http://jhered.oxfordjournals.org/content/by/year

----------------------------------

To continue the jhered list (full papers):

Sunsuit, A Mutation Reducing Plumage In The Fowl.
(F. B. Hutt And J. Long)(J Hered-1950-HUTT-145-50)
http://jhered.oxfordjournals.org/content/41/6/145.full.pdf

Genetic Basis Of The Erminette Breed Of Fowls.
(F. B. Hutt, J Hered-1964-HUTT-200-6)
http://jhered.oxfordjournals.org/content/55/5/200.full.pdf

Wild Type Plumage Pattern In The Fowl
(Elliot Kimball, J Hered-1952-KIMBALL-129-32)
http://jhered.oxfordjournals.org/content/43/3/129.full.pdf

Alphabetical list of the genes of domestic fowl.
(RALPH G. SOMES, JR.) (J Hered-1980-SOMES-168-74)
http://jhered.oxfordjournals.org/content/71/3/168.full.pdf

Inheritance Of Albinism In The Domestic Fowl.
(D. C. WARREN)(J Hered-1933-WARREN-379-83)
http://jhered.oxfordjournals.org/content/24/10/379.full.pdf

Inheritance Of Pinkeye In The Fowl.
(D. C. WARREN)(J Hered-1940-WARREN-291-2)
http://jhered.oxfordjournals.org/content/31/6/291.full.pdf

Sexual Dimorphism In Single Comb Rhode Island Red Down Color.
(T. C. BYERLY and J. P. QUINN)(J Hered-1936-BYERLY-319-22)
http://jhered.oxfordjournals.org/content/27/8/319.full.pdf

Snow-White Down In The Chick
(F. B. Hutt)(J Hered-1951-HUTT-117-20)
http://jhered.oxfordjournals.org/content/42/3/117.full.pdf

Green shanks and adult mortality in chicken.
(W. H. MCGIBBON)(J Hered-1979-MCGIBBON-44-6)
http://jhered.oxfordjournals.org/content/70/1/44.full.pdf
Posted by: KazJaps

Re: Journal papers online - reference list - 01/22/11 09:00 AM

*continued jhered list (full papers):

A Gene for Partial Feather Achromatosis in the Fowl
(K. W. WASHBURN AND J. ROBERT SMYTH JR.)(J Hered-1967-WASHBURN-131-4)
http://jhered.oxfordjournals.org/content/58/3/131.full.pdf

The DAM chicken: a model for spontaneous postnatal cutaneous and ocular amelanosis
(]. R. Smyth, Jr., R. E. Boissy, K. V. Fit)(J Hered-1981-Smyth-151-6)
http://jhered.oxfordjournals.org/content/72/3/151.full.pdf

Inheritance of Spotting in the Down Plumage of Gold Columbian Chickens.
(RALPH G. SOMES, JR.)(J Hered-1969-SOMES-353-6)
http://jhered.oxfordjournals.org/content/60/6/353.full.pdf

Hereditary Congenital Baldness: A Sex-Linked Trait in the Domestic Fowl.
(R. G. Somes, Jr)(J Hered-1989-Somes-493-6)
http://jhered.oxfordjournals.org/content/80/6/493.full.pdf

Genetics of the Fowl: 12—Sex-Linked, Imperfect Albinism
(C. D. MUELLER AND F. B. Hutt)(J Hered-1941-MUELLER-71-80)
http://jhered.oxfordjournals.org/content/32/2/71.full.pdf

Inheritance of the henny-feathering trait of the Sebright bantam chicken.
(R. G. Somes, Jr., F. W. George, J. Baron, J. F. Noble, J. D. Wilson)(J Hered-1984-Somes-99-102)
http://jhered.oxfordjournals.org/content/75/2/99.full.pdf

Ametapodia, a Dominant Mutation in the Fowl.
(R. K. COLE)(J Hered-1967-COLE-141-6)
http://jhered.oxfordjournals.org/content/58/3/141.full.pdf

The Genetics Of The Domestic Fowl.
Abstracted by L. C. DUNN, Storrs Agr. Exp. Station, from the
translation of B. F. GLESSING, Bureau of Animal Industry, U. S. Department of Agriculture.
(J Hered-1928-DUNN-511-9)
http://jhered.oxfordjournals.org/content/19/11/511.full.pdf
* This has research from Serebrovsky

A Red-Eye Mutation In White Plymouth Rocks.
(E. Roberts, W. E. Shaklee And H. F. Falls)(J Hered-1952-ROBERTS-201-4)
http://jhered.oxfordjournals.org/content/43/5/201.full.pdf

A "new" allele at the C pigment locus in the fowl.
(J. A. Brumbaugh, T. W. Bargar, W. S. Oettin)(J Hered-1983-Brumbaugh-331-6)
http://jhered.oxfordjournals.org/content/74/5/331.full.pdf

Further Studies of Prenatal, A Sex-Linked Lethal in Fowl.
(RALPH G. SOMES, JR)(J Hered-1969-SOMES-185-6)
http://jhered.oxfordjournals.org/content/60/4/185.full.pdf

----------------Turkeys--------------
Potential Uses Of Parthenogenetic Development in Turkeys.
(J Hered-1969-OLSEN-346-8)
http://jhered.oxfordjournals.org/content/60/6/346.full.pdf

Sex-Linked Albinism In The Turkey
(F. B. HUTT AND C. D. MuELLER)(J Hered-1942-HUTT-69-77)
http://jhered.oxfordjournals.org/content/33/2/69.full.pdf

------------------------

A Triple-Allele Series And Plumage Color In Turkeys
(V. S. Asmundson, 1945)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1209290/pdf/305.pdf

------------------------
Genetics:

Alleles Of The Mallard Plumage Pattern In Ducks.
(R. George Jaap, 1933)
http://www.genetics.org/cgi/reprint/19/4/310.pdf

-----------------------
THE INHERITANCE OF SHANK COLOR IN CHICKENS.
(C. W. KNOX, 1935)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1208630/pdf/529.pdf

GENETICS OF THE FOWL. 11. A FOUR-GENE AUTOSOMAL LINKAGE GROUP
(F. B. HUTT, 1932)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1208371/pdf/82.pdf
Posted by: M. J. Conley

Re: Journal papers online - reference list - 01/22/11 04:41 PM

Thanks KazJaps, excellent
Posted by: Htul

Re: Journal papers online - reference list - 01/25/11 05:32 AM

Genetic variation of chicken MC1R gene in different plumage colour populations.
Guo XL, Li XL, Li Y, Gu ZL, Zheng CS, Wei ZH, Wang JS, Zhou RY, Li LH, Zheng HQ.
Br Poult Sci. 2010 Dec;51(6):734-9.

Abstract only



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
Sakae Takeuchi, , Hideyuki Suzuki, Masafumi Yabuuchi and Sumio Takahashi


Abstract only

Association of a Glu92Lys substitution in MC1R with extended brown in Japanese quail (Coturnix japonica).

Nadeau NJ, Minvielle F, Mundy NI.
Anim Genet. 2006 Jun;37(3):287-9.

Full paper
Posted by: Henk69

Re: Journal papers online - reference list - 02/02/11 12:34 AM

F.B. Hutt
Genetics of the Fowl
1949

http://chla.library.cornell.edu/cgi/t/te...image&seq=1
Posted by: IPF

Re: Journal papers online - reference list - 02/02/11 10:46 AM

This wonderfully useful book (Hutt) is available, reprinted, from http://www.nortoncreekpress.com/genetics_of_the_fowl.html
for $49.95. A large chunk (most?) of the research on phenotypic characters in chickens was complete by this publication date, so the book is remarkably complete. Very very few things in it are conspicuously out of date.
Posted by: KazJaps

Re: Journal papers online - reference list - 02/03/11 12:22 AM

Identifying the ptilopody (feathered shank) loci of the chicken.
Somes RG Jr.
J Hered. 1992 May-Jun;83(3):230-4.
full paper

--------------
On the Inheritance of some Characters of the Silky Fowl.
DUNN, L. C, and JULL, M. A. 1927.
Jour. Genet. XIX, 1, pp28-63.
full paper

---------------

Bantam genetics: distribution of traits in a Sebright-
Mille Fleur cross.

Danforth CH. 1929.
J Hered. 20:573–582.
full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/03/11 12:26 AM

Articles:

Gunnarsson, U. 2009. Genetic Studies of Pigmentation in Chicken. Acta Universitatis
Upsaliensis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of
Medicine 428. 44 pp. Uppsala. 978-91-554-7439-3.
download full paper

Commentary: Vitiligo – Lessons learned from the Smyth line chicken (2007)
Gisela F. Erf, Ph.D., Professor.
http://paspcr.med.umn.edu/Commentary/Erfcommentary.pdf
* photos of Smyth’s eb Brown line & DAM (delayed amelanosis) line


Spanish Breeds (Campo et al. research):
Abstracts:


Genetics of the black-tailed red plumage pattern in Villafranquina chickens.
Campo JL, Alvarez C.
Poult Sci. 1988 Mar;67(3):351-6.
abstract

Genetics of the Birchen and Blue plumage patterns in Leonesa chickens.
Campo, J.L.; Alvarez, C.
Poult Sci. 1993 Jul;72(7) p. 1218-1223
abstract

Photos of various Spanish Breeds (pdf):
http://www.inia.es/gcontrec/pub/gallinas_1054897707500.pdf

Photos of Leonesa chickens (pdf):
download full article-pdf
Posted by: KazJaps

Re: Journal papers online - reference list - 02/03/11 01:56 AM

This is a very good read wink

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

I imagine this is the paper that Black_Feather was referring to in this previous post:
The Coop: Mottling and linkages

Quote:
Moreover a publication suggests (but does not prove) some genes for other traits :

- Fm : EDN3 (Endothelin 3, on chromosome 20)

- Po : SHH (Sonic HedgeHog, on chromosome 2), instead of LMBR1

- Id : VCAN (Versican) or B4GALT1 (beta1,4-Galactosyltransferase) on chromosome Z


---------------------
Some others on DNA sequencing...

A missense mutation in the GHR gene of Cornell sex-linked dwarf
chickens does not abolish serum GH binding.

K L Hull, J A Marsh and S Harvey
Journal of Endocrinology (1999) 161, 495–50
full paper

Autosomal Albino Chicken Mutation (ca/ca) Deletes Hexanucleotide (−ΔGACTGG817) at a Copper-Binding Site of the Tyrosinase Gene
T. Tobita-Teramoto, G. Y. Jang, K. Kino, D. W. Salter, J. Brumbaugh and T. Akiyama
2000 Poultry Science 79:46–5.
full paper

Complete association between a retroviral insertion in the tyrosinase gene and the recessive white mutation in chickens.
Chung-Ming Chang, Jean-Luc Coville, Gérard Coquerelle, David Gourichon, Ahmad Oulmouden, and Michèle Tixier-Boichard
BMC Genomics. 2006; 7: 19.
full paper

Flesh color association with polymorphism of the tyrosinase gene in different Chinese chicken breeds.
Zhang JQ, Chen H, Sun ZJ, Liu XL, Qiang-Ba YZ, Gu YL.
Mol Biol Rep. 2010 Jan;37(1):165-9. Epub 2009 May 13
full paper


Quantitative effects of an intronic retroviral insertion on the transcription of the tyrosinase gene in recessive white chickens.[
Chang CM, Furet JP, Coville JL, Coquerelle G, Gourichon D, Tixier-Boichard M.
Anim Genet. 2007 Apr;38(2):162-7. Epub 2007 Mar 12.
abstract paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/03/11 02:36 AM

European Graduate School in Animal Breeding and Genetics: PhD Projects
PhD Projects – full paper

----------------------------
ASIP -agouti locus

Characterization of Japanese Quail yellow as a Genomic Deletion Upstream of the Avian Homolog of the Mammalian ASIP (agouti) Gene.
(Genetics 178: 777–786 (February 2008))
http://www.genetics.org/cgi/content/full/178/2/777
Quote:
ASIP expression in chicken: Dorsal and ventral skin samples were taken from 10 chickens, 2 males with a mottled phenotype and 8 females with a Columbian phenotype.

......The presence of an apparently functional ASIP gene in chickens poses the question of why no good candidates for mutations at this gene are known among the large numbers of described pigmentation variants (Smyth 1990).


The ASIP locus is found on Chromosome 20:

Recessive black Is Allelic to the yellow Plumage Locus in Japanese Quail and Associated With a Frameshift Deletion in the ASIP gene.
(Genetics 178: 771–775 (February 2008))
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248368/pdf/GEN1782771.pdf
Quote:
The Y locus in the Japanese quail was mapped on the QL10 linkage group homologous to GGA20 in chicken (Gallus gallus) (Miwa et al. 2005), where an ASIP-like sequence was found (Klovins and Schioth 2005)
.

Ref:
Mapping of plumage colour and blood protein loci on the microsatellite linkage map of the Japanese quail.
(Miwa et. al. 2005)
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.2005.01335.x/full

Agouti-related proteins (AGRPs) and agouti-signaling peptide (ASIP) in fish and chicken.
Klovins J, Schiöth HB., 2005.
(Ann N Y Acad Sci. 2005 Apr;1040:363-7.)
http://www.ncbi.nlm.nih.gov/pubmed/15891063
Posted by: KazJaps

Re: Journal papers online - reference list - 02/03/11 04:33 AM

Testing Homology of Loci for Two Plumage Colors, “lavender” and “recessive white,” With Chicken and Japanese Quail Hybrids.
F. Minvielle, D. Gourichon and J. L. Monvoisin
J Hered (2002) 93 (1): 73-76
full paper

Lavender, a chick melanocyte mutant with defective melanosome translocation: a possible role for 10 nm filaments and microfilaments but not microtubules.
Mayerson PL, Brumbaugh JA.
J Cell Sci. 1981 Oct;51:25-51.
full paper

Adendritic melanocytes: a mutation in linkage group II of the fowl.
Brumbaugh JA, Chatterjee G, Hollander WF.
J Hered. 1972 Jan-Feb;63(1):19-25.
full paper

The Gene Action and Function Of Two Dopa Oxidase Positive Melanocyte Mutants of the Fowl
J. A. Brumbaugh and K. W. Lee.
Genetics. 1975 Oct;81(2):333-47.
full paper
*about pk – pink-eye & I Dominant White.

Heterokaryon analysis of the genetic control of pigment synthesis in chick embryo melanocytes.
Wilkins LM, Brumbaugh JA, Moore JW.
Genetics. 1982 Nov;102(3):557-69.
full paper
*tested c, pk, Bl, ey and I

The inheritance of the peculiar pigmentation of the silky fowl
W. Bateson and R. C. Punnett (1911)
Journal of Genetics Volume 1, Number 3, 185-203
full paper

Genetics of Buff and Related Color Patterns of the Fowl.
Brumbaugh, J. A., and W. F. Hollander (1966)
Poultry Science Vol.45: p.p.451-457
full paper (1.6 MB)
Posted by: KazJaps

Re: Journal papers online - reference list - 02/03/11 04:41 AM

Henny-feathering journal papers:

Aromatase mRNA in the extragonadal tissues of chickens with the henny-feathering trait is derived from a distinctive promoter structure that contains a segment of a retroviral long terminal repeat. Functional organization of the Sebright, Leghorn, and Campine aromatase genes.
Matsumine H, Herbst MA, Ou SH, Wilson JD, McPhaul MJ.
J Biol Chem. 1991 Oct 25;266(30):19900-7.
full paper

Data on the Genetics of Vulture Hock, Hen Feathering and "Crooked Neck" in the Domestic Fowl.
MORLEY A. JULL AND JOSEPH P. Quinn
J Hered (1931) 22 (5): 147-154.
full paper
* good B/W photos in this one

The Production of Hen-feathered Brown Leghorns by Breeding.
Jull, M. A., and Quinn, J. P. 1930
Jour..Hered. XXI, 4 pp. 176-186.
full paper
*very good B/W photos also

The Genetic Factor For Hen-Feathering In The Sebright Bantam.
T. H. Morgan (1920
Bid. Bui. XXXIX, 4, pp. 257-259
full paper

The Testis And Thyroid In A Hen-Feathered Silver-Grey Dorking Cock.
Gwynneth Buchanan
Journal of Experimental Biology 4,73-80 (1926)
full paper

Inheritance of the henny feathering trait in the golden Campine chicken: evidence for allelism with the gene that causes henny feathering in the Sebright bantam.
George FW, Matsumine H, McPhaul MJ, Somes RG Jr, Wilson JD.
J Hered. 1990 Mar-Apr;81(2):107-10.
full paper

Inheritance of the henny-feathering trait of the Sebright bantam chicken.
Somes RG Jr, George FW, Baron J, Noble JF, Wilson JD.
J Hered. 1984 Mar-Apr;75(2):99-102.
full paper
*posted previously in this thread (some B/W photos)

Abstracts only

Hen-feathering mutation HF*H may act as a eumelanising factor and modify the expression of autosomal barring.
Carefoot WC.
Br Poult Sci. 2002 Jul;43(3):391-4.
abstract paper

Aromatase expression in extragonadal tissues of the Sebright chicken is controlled by a retroviral promoter.
McPhaul MJ, Matsumine H, Herbst MA, Wilson JD.
Trans Assoc Am Physicians. 1991;104:141-9.
abstract paper

Feather growth in Sebright bantams of henny, intermediate, and cocky plumage.
Juhn M.
J Exp Zool. 1949 Oct;112(1):109-23, incl pl.
first page only

Developmental pattern of increased aromatase activity in the Sebright bantam chicken.
George FW, Wilson JD.
Endocrinology. 1982 Apr;110(4):1203-7.
abstract paper

Characterization of the increased estrogen synthesis in skin fibroblasts from the Sebright bantam.
Leshin M, Noble JF, George FW, Wilson JD.
J Steroid Biochem. 1983 Jan;18(1):33-9.
abstract paper

The Sebright bantam chicken and the genetic control of extraglandular aromatase.
Wilson JD, Leshin M, George FW.
Endocr Rev. 1987 Nov;8(4):363-76.
abstract paper

Studies on the Relation of Gonadic Structure to Plumage Characterisation in the Domestic Fowl.--III. The Laying Hen with Cock's Plumage.
F. A. E. Crew
Proceedings of the Royal Society of London. Series B, Containing Papers of a Biological Character
Vol. 101, No. 712 (Jul. 1, 1927), pp. 514-518
abstract paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/03/11 10:54 AM

Duplex comb in the chicken: a multi-allelic trait.
Somes RG Jr.
J Hered. 1991 Mar-Apr;82(2):169-72.
full paper
*with B/W comb photos

Some Observations on High Cavernous Nostrils in the Chicken.
J Hered-1991-Somes-172-4
full paper
*with B/W comb photos

Creeper and single comb linkage in the fowl.
TAYLOR, L. W.
Jour. Hered. 25 :205-206. 1934
full paper

The Linkage of Polydactyly with Multiple Spurs and Duplex Comb in the Fowl.
F. B. Hutt and C. D. Mueller
The American Naturalist
Vol. 77, No. 768 (Jan. - Feb., 1943), pp. 70-78
abstract paper

GENETICS OF THE FOWL: 15. Multiple Spurs, a Mutation Linked with Duplex Comb.
F. B. HUTT
J Hered (1941) 32(10): 357-364
full paper

GENETICS OF THE FOWL:11. A FOUR-GENE AUTOSOMAL LINKAGE GROUP
F. B. HUTT
Ja 1933 Genetics: 18: 82
full paper
*posted previously

GENETICS OF THE FOWL:11 A Linkage Map for Six Chromosomes.
F. B. HUTT AND W. F. LAMOREUX
Journal of Heredity 1940 Vol. 31 pp. 231-235
full paper
*with many photos of mutations

NINE INDEPENDENTLY INHERITED AUTOSOMAL FACTORS IN THE DOMESTIC FOWL.
D. C. WARREN
GENETICS: 18: 68 Ja 1933
full paper

LINKAGE RELATIONS OF AUTOSOMAL FACTORS IN THE FOWL
D. C. WARREN
GENETICS 34: 333 May 1949
full paper

A CASE OF CLOSE AUTOSOMAL LINKAGE IN THE FOWL
A. S. SEREBROVSKY AND S. G. PETROV
J Hered (1928) 19 (7): 305-306.
full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/15/11 09:47 AM

Creeper, Cornish Lethal, etc

A lethal mutation in Dark Cornish fowl.
Walter Landauer
Storrs Agric. Exp. Station.
1935 Journal of Genetics 31:237-242 .
full paper

Maternal effects on expression of Lethality in the creeper chicken.
Yoshihisa Fujio.
Japan. J. Genetics. Vol. 1, No. 5: 347-354 (1976).
full paper

Studies on the Creeper Fowl. Xv. Maternal Inheritance in Survival of Embryos From Reciprocal Crosses Involving the Creeper Factor.
Walter Landauer And C. I. Bliss
Storrs Agricultural Experiment Station, Storrs, Conn.
GENETICS 28: 218 May 1943.
full paper

Studies on the Creeper fowl. XI. Castration and length of bones of the appendicular skeleton in normal and Creeper fowl.
Walter Landauer
The Anatomical Record: Volume 69, Issue 2, pages 247–253, September 1937.
abstract

Reptilian Fowls: A Study in Atavistic Heredity.
J Hered (1925) 16(10): 353-356
Ira Eugene Cutler
full paper
*creepers

On The Identification of Segregated Phenotypes in Progeny From Creeper Fowl Matings.
Dorothea Rudnick And Viktor Hamburger
Storrs Agricultural Experiment Station,
GENETICS 25: 215 March 1940
full paper

The developmental potencies of eye primordia of homozygous Creeper chick embryos tested by orthotopic transplantation.
Kenneth Gayer, Viktor Hamburger
Journal of Experimental Zoology, Volume 93, Issue 2, pages 147–183, July 1943
first page

Transplantation of Limb Primordia of Homozygous and Heterozygous Chondrodystrophic ("Creeper") Chick Embryos.
Viktor Hamburger
Physiological Zoology Vol. 14, No. 3 (Jul., 1941), pp. 355-365
abstract paper

Experimental analysis of the Creeper condition in chickens: Effect of embryo extract on elongation, protein content, and incorporation of amino acids by cartilaginous tibiotarsi.
William A. Elmer
Developmental Biology: Volume 18, Issue 1, July 1968, Pages 76-92
abstract paper

Length of Survival Of Homozygous Creeper Fowl Embryos.
Walter Landauer
Science 15 December 1944: Vol. 100 no. 2607 pp. 553-554
abstract paper

Studies On The Creeper Fowl: I
Walter Landauer and Dunn
full paper

Studies On The Creeper Fowl: Viii. The Effect Of Bone Extract On Skeletal Growth And The Phosphatase Content Of The Bones.
Walter Landauer, Elizabeth Upham, and Fay Rubin
J. Biol. Chem. 1935 108: 121-126.
full paper

A Semi-Lethal Mutation In Fowl Affecting Length Of The Upper Beak And Of The Long Bones
Walter Landauer
Genetics. 1941 July; 26(4): 426–439
full paper

A New Recessive Ametapodia Mutation in the Chicken
J,R. Smyth Jr., G.P.Sreekumar, C.A.Coyle, and J.J. Bitgood.
The Journal of Heredity 2000 91(4) 340-342
full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/15/11 09:53 AM

Modifiers of feathers, etc.

The Bare Necks.
DAVENPORT, C. B.
Jour. Hered. 5:374. 1914.
full paper

The "penguin" guinea fowl.
McCrady, E. Jr
Jour. Hered. 23:201-207. 1932
full paper

The "Frizzle" Character of Fowls. Its Expression and Inheritance.
Landauer, W. and L. C. Dunn
Jour. Hered. 21:290-305. 1930.
full paper

Genetics of the fowl V. The modified frizzle.
F. B. Hutt
Journal of Genetics Volume 32, Number 2, 277-285 1936
full paper

Soluble Derivatives of Feather Keratin. Isolation, Fractionation And Amino Acid Composition.
B. S. Harrap And E. F. Woods
Biochem. J. (1964), 92, 8
full paper

Scaleless, an Inherited Ectodermal Defect in the Domestic Fowl.
U. K. Abbott And V. S. Asmundson.
J. Hered. 48, 63-70 1957.
full paper

Hairy, A Gene Causing Abnormal Plumage In The Turkey.
J. Robert Smyth Jr.
J Hered (1954) 45 (4): 197-200.
full paper

Genetics of fowl IX. Naked, a new sex-linked mutation.
Hutt, F. B., And P. D. Sturkie.
J. Hered. 29:371-379. 1938.
full paper

A New Type Of Autosomal Nakedness In The Domestic Fowl.
Paul D. Sturkie.
J. Hered. 33: 202-208. 1942.
full paper

“Sporadic Flightless" Fowls.
Roy L. Mayhew
J Hered ]1934. 25 (10) 409-10.
full paper

Sunsuit, a mutation reducing plumage in the fowl.
F. Hutt and J. long.
Jour. Hered. 41:145-150. 1950.
full paper
*posted before.

Downless Chickens.
A. S. Serebrovsky And S. G. Petroff
J Hered 1929. p.331-2
full paper

"Porcupine" Pigeons”. Studies on Inheritance in Pigeons—VIII.
L. J. Cole and L. E. Hawkins.
J Hered. 1930. 21: 51-60
full paper

“Porcupine Chickens”.
Nelson F. Waters.
J Hered 1967. 163-4
full paper

Woolly Feathering In The Fowl
D. G. Jones and Walter Morgan
J Hered (1956) 47 (3): 137-141
full paper

The inheritance of "stringy," an abnormal feather condition in white Leghorn chickens.
Buss Eg, Bohren Bb, Warren Dc.
J Hered. 1950 Jun;41(6):143-4.
full paper

A Heritable Variation of Feather Structure in the Fowl.
Warren D.C.
Jour. Hered. 29: 91-93. 1938.
full paper

An Inherited Feather Defect in the Fowl.
Warren D.C.
J Hered. 1949 Oct;40(10):266
full paper

Non-heritable downlessness in chickens.
Warren, D. C.
J. Hered. 21:408. 1930.
full paper

Flightless- A Heritable Variation In the Domestic Fowl.
D.C. Warren.
J Hered (1932) 23 (11): 449-452
full paper

The Lethal Nature of Flightlessness in the Fowl.
Warren, D. C.
1937 J Hered. 28:16-18
full paper

Inheritance Of Rate Of Feathering In Poultry.
D. C. Warren
J Hered (1925) 16(1): 13-18
full paper

The Inheritance Of Rumplessness In The Domestic Fowl.
L. C. Dunn
J Hered (1925) 16(4): 127-134
full paper

Two Types Of Rumplessness In Domestic Fowls: A Morphological Comparison.
Walter Landauer And L. C. Dunn
J Hered (1925) 16(5): 153-160
full paper

Recessive and Sporadic Rumplessness of Fowl: Effects on Penetrance and Expressivity.
Walter Landauer
The American Naturalist Vol. 89, No. 844 (Jan. - Feb., 1955), pp. 35-38
first page only

Studies Of Inheritance In Pigeons: V—Lace of Silky, a sex-Linked Character.
Dewey G. Steele
J Hered (1925) 16(9): 321-337
full paper

---------added below-----
Retarded Feathering In The Fowl: A New Factor Affecting Manner of Feathering.
D. C. Warren
J Hered (1933) 24 (11): 431-434
full paper

Ear tuftedness: a lethal condition in the Araucana fowl.
Ralph G. Somes, Jr. and Mary S. Pabilonia
J Hered (1981) 72(2): 121-124
full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/15/11 09:56 AM

Combs

Mendel's Principles of Heredity
William Bateson:
1909 University Press, Cambridge.
google book preview: Bateson-page 61_combs
download all book- pdf (36.7MB)

The genetic architecture of a female sexual ornament.
Wright D, Kerje S, Brändström H, Schütz K, Kindmark A, Andersson L, Jensen P, Pizzari T. Evolution. 2008 Jan;62(1):86-98.
full paper

INHERITANCE OF SIDE SPRIGS. Data on the Inheritance of Side Sprigs on the Combs of Single. Comb White Leghorns.
V. S. Asmundson.
J Hered (1926) 17(8): 281-284
full paper

A Comb-inhibiting gene. An Inhibitor of the Development of the Pea and Walnut Combs in Domestic Fowl.
Petroff, S.G.,
1929 J. Hered. 20 (11): 540- 542.
full paper

-------added below---------

Spike Blade — A Heritable Single Comb Variation In The Fowl.
D. C. Warren
J Hered (1939) 30(6): 257-260
full paper

The Association Of Comb And Crest Characters In The Domestic Fowl.
Morley A. Jull
J Hered (1930) 21(1): 21-28
full paper

Breast Ridge, Associated with Pea and Walnut Comb, as an Aid in Identifying Comb Type.
R. D. Crawford
Poult Sci 1961. 40:262-263
full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/19/11 11:41 PM

Historical Books:
* Note: due to the very large file size of many of the following books, it’s best to download by ‘right-clicking’ on the link, then ‘save target as’ (Internet Explorer) or ‘save link as’ (Firefox or Chrome), etc.
*Except for the html book "Mendelism", by Punnett (not pdf, so just click on the link).

The Poultry Manual.
Sturges, T.W. 1909.
London, Macdonald and Evans.
full book (19.4 MB pdf)

The Book of Poultry.
Wright, Lewis. 1891
Cassell & Co. Lt. London.
full book (53.9 MB pdf)

The Poultry Book.
1873 Tegetmeier, W. B.
George Rutledge & Sons, London.
full book (31.8MB pdf)

Inheritance in poultry.
C. B. Davenport
Carnegie Institution of Washington publication -- no. 52. 1906
full book (8.9 MB pdf)

Inheritance of characteristics in domestic fowl.
C. B. Davenport
Carnegie Institution of Washington publication -- no. 121. (1909)
full book (5.7 MB pdf)

Mendel's Principles of Heredity.
Bateson. W. 1909.
University Press, Cambridge.
full book- pdf (36.7MB pdf)
* posted previously

The variation of animals and plants under domestication. 2d ed.
Charles Darwin. 1875.
London: John Murray.
full book Vol 1 (77 MB pdf)
full book Vol 2 (81 MB pdf)

The origin of species by means of natural selection, or the preservation of favoured races in the struggle for life.
Charles Darwin.
1876. 6th ed., with additions and corrections.
London: John Murray.
full book (113.7 MB pdf)

Classic Papers in Genetics.
1959. James Arthur Peters.
Englewood Cliffs, N.J., Prentice-Hall
full book (18.9 MB pdf)


* Mendelism.
Punnnet, R. 1911
The Macmillan Company, New York
full ebook – html
Posted by: KazJaps

Re: Journal papers online - reference list - 02/20/11 01:11 AM

Genetic Studies in Poultry I. Inheritance of leg-feathering.
Punnett R.C. and Bailey P.G. 1918
J Genet. Volume 7, Number 3, 203-213.
full paper

Genetic studies in poultry. V. On a case of pied plumage.
R. C. Punnett and M. S. Pease. 1927
Journal of Genetics. Volume 18, Number 2, 207-218
full paper

Genetic studies in poultry. VI. The Gold Barred Rock.
R. C. Punnett and M. S. Pease. 1928
Journal of Genetics. Volume 19, Number 3, 337-350
full paper

Genetic studies in poultry VII. Notes on Polydactyly.
R. C. Punnett and M. S. Pease. 1929
Journal of Genetics. Volume 21, 341-366
full paper

Genetic studies in poultry IX. The Blue egg.
R. C. Punnett. 1933.
Journal of Genetics. Volume 27, Number , 465-470.
full paper

Genetic Studies in Poultry. X: Cream Plumage.
Punnett R.C.
J Genet. 1948 Jan;48(3):327-32.
full paper

Genetic Studies in Poultry. XI: The Legbar.
Punnett R.C.
J Genet. 1940 Jan;41(1):1-8.
full paper

Genetic studies in poultry XIII. Recessive Black.
R. C. Punnett. 1957.
Journal of Genetics. Volume 55, Number 3, 562-569.
full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/20/11 01:30 AM

Pathogenesis of the Henny Feathering Trait in the Sebright Bantam Chicken. Increased Conversion of Androgen to Estrogen in Skin.
Fredrick W. George and Jean D. Wilson,
J Clin Invest. 1980 July; 66(1): 57–65.
full paper

Henny feathering in the fowl - a fresh interpretation.
Punnett, R. C.
1937 J. Genet. 35: 129-140.
full paper

Note on a Sex-linked Down character in Ducks.
R.C. Punnett.
1932. J. Genet. 25, 191-194
full paper

Sex-Linked Genes in the Fowl.
John W. Macarthur
1933. Genetics 18: 210 .
full paper

VI—Dominance in Poultry.
R.A. Fisher, F.R.S. (1935)
Philosophical Transactions of the Royal Society of London, B, 225: 197-226,
full paper

A Case of Lateral Asymmetry in the Domestic Fowl.
F.A.E. Crew.
Journal of Genetics. Volume 20, Number 2, 179-186
full paper

Crest and Hernia in Fowls due to a Single Gene without Dominance.
R.A. Fisher
Science, 80: 288-289, (1934)
full paper

Breast Ridge in Domestic Fowl, a New Dominant Character Linked with Pea Comb, or Another Expression of the Pea Comb Gene?
S. S. Munro and Igor L. Kosin.
The American Naturalist Vol. 74, No. 753 (Jul. - Aug., 1940), pp. 382-384
first page only
abstract only

Rose comb: an example of operational over-dominance in the domestic fowl.
Thomas W. Fox, Roy D. Crawford and J. Robert Smyth Jr.
Genetical Research (1964), 5: 379-383
abstract paper
Quote:
The pleiotropic effect of the rose-comb gene (R) on fertility when combined with artificial selection against the single-comb type (r) results in an interesting example of operational over-dominance. An evaluation of the equilibrium frequency of the rose-comb gene based on this over-dominance concept provides a plausible explanation for the relatively high frequency of single-comb birds appearing in the Wyandotte breed of fowls.


Influence of Homozygosity for Rose Comb on Fumarase, Aconitase, Isocitric Dehydrogenase And Malic Dehydrogenase Activity in Spermatozoa of the Domestic
Fowl (Gallus Domesticus).

R. B. Buckland, F. H. Wilcox and C. S. Shaffner
J. Reprod. Fert. (1969) 18, 89-95.
full paper

White skin: a Z-linked recessive mutation in the fowl.
W. H. McGibbon
J Hered (1981) 72(2): 139-140
full paper

Inheritance of Silkiness in Fowls. History and Description of the Sporadic Occurrence of Silky Feathered Birds among Normally Feathered Ones, and Their Relation.
Sarah V. H. Jones
J Hered (1921) 12 (3): 117-128.
full paper

The Inheritance of Shank-Feathering in the Domestic Fowl.
W. V. Lambert And C. W. Knox
Poult Sci 1929. 9:51-64.
full paper

Genetic Tests on the Association of Brachydactyly and Ptilopody in Fowl.
Paul F. Goetinck
J Hered (1971) 62 (1): 28-30.
full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/20/11 02:21 AM

Lethal Mutations


Missing upper beak: a new lethal mutation in domestic fowl.
F. G. Silversides, M. S. Umrtla, and R. D. Crawford.
The Journal of Heredity 73:295-296. 1982.
full paper

A multiple trait semilethal in fowl.
McGibbon WH, Shackelford RM.
J Hered. 1972 Jul-Aug;63(4):209-11.
full paper

Nanomelia, A Lethal Mutation Of The Fowl.
Walter Landauer
J Hered (1965) 56 (3): 131-13
full paper

Prenatal, A Sex-Linked Lethal Mutation of the Fowl.
Ralph G. Somes, J R ., And J. Robert Smyth, J R.
J Hered (1967) 58 (1): 25-29
full paper

Ectrodactyly: A New Embryonic Lethal Mutation in the Chicken.
U. K. Abbott And J.A. MacCabe.
J Hered 1966. p207-11
full paper

Kyphoscoliosis in a Long-Term Selection Experiment with Chickens.
Lewis W. Taylor
Avian Diseases Vol. 15, No. 2 (Apr. - Jun., 1971), pp. 376-39
first page only

Hereditary Hypothyroidism in the Domestic Fowl.
R.K. Cole
Genetics 53: 1021-1033 June 1966
full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/20/11 02:26 AM

Evaluation of diversity between different Spanish chicken breeds, a tester line, and a White Leghorn population based on microsatellite markers.
S. G. Dávila1, M. G. Gil, P. Resino-Talaván and J. L. Campo
Poult Sci 2009. 88:2518-2525.
abstract paper

The action of the sex linked barring gene on Spanish chickens with gold plumage.
JL Campo and F Orozco
Genet Sel Evol. 1980; 12(3): 233–239.
full paper

Inheritance of a new albino mutation in Brazilian free-range black chickens.
Jorge W; Cunha L.M.
Rev. Bras. Cienc. Avic. vol.10 no.3 Campinas July/Sept. 2008.
full paper

Linkage mapping of phenotypic markers and marker identification in MHC in a cross between red junglefowl and Obese strain chicken.
Malin Lindås
full paper

Retarded pigmentation. A new gene affecting down colour and pattern.
Pease, M.; Cock, A.
Autosexing annual, 1952. 1951 pp. 9-12 pp.
abstract paper
Quote:
Light Sussex were crossed with Brussbars and the plumage pattern of the latter recovered by backcrossing. The Brussbars so extracted usually bred true but 2 exceptional ♂ chicks with pure white plumage appeared among their progeny. As adults they became indistinguishable from normal Brussbars. The character behaves as a simple autosomal recessive. In the ♀ its action reduces the width but not the sharpness of the dark stripes in the down. J. S. S. BLYTH.


Carefoot, W.C. 1981. Notes on the “wheaten” plumage phenotype of the domestic fowl.
Brit Poult Sci 22:499-502
abstract paper

Test for linkage between the eumelanin dilution blue (B1), the extended black (E) allele at the E-locus and the linked pea comb (P) and eumelanin extension (M1) genes in the domestic fowl.
Carefoot WC.
Br Poult Sci. 1990 Sep;31(3):465-72.
abstract paper
Quote:
Thirty-four crossovers occurred among the 97 progeny between P and E suggesting linkage of approximately 35 units. A further mating was made from among segregants in the backcross which confirmed P-E linkage with 17 crossovers in 55 gametes. Combining the tests produced a linkage value of approximately 34 units.


Research note: linkage relationship between the pea comb (P) and extended black (E) loci of the chicken.
Smyth, J.R. Jr. (University of Massachusetts, Amherst, MA); Ponce de Leon, F.A.
Poultry science (Jan 1992) v. 71(1) p. 208-210
abstract paper
Quote:
The linkage relationship between the autosomal genes, extended black (E) and pea comb (P), were estimated from the cross E/ey P/p+ X e(b)/e(y) p+/p+ in the coupling phase. Reciprocal crosses yielded a total of 545 chicks and indicated that the E and P loci were genetically linked by 45.5 +/- 2.14 (SE) crossover units (P 0.05). The two reciprocals resulted in similar estimates (45.6 and 45.3), although significant individually only at the 0.10 level of probability. Intra-allelic segregation at both loci closely approximated the expected 1:1 ratio. These data provide additional evidence that the E and P loci are linked in linkage Group III on Chromosome 1


An Autosomal Genetic Linkage Map of the Chicken.
I. Levin, L. Santangelo, H. Cheng, L B. Crittenden, and J. B. Dodgson
full paper

Comparative Mapping of the Chicken Genome Using the East Lansing Reference Population.
Eugene J. Smith, Leslie A. Lyons, Hans H. Cheng, And Steven P. Suchyta.
1997 Poultry Science 76:743–747
full paper

A preliminary linkage map of the chicken genome.
Bumstead N, Palyga J.
Genomics. 1992 Jul;13(3):690-7.
abstract paper

New Microsatellite Markers on the Linkage Map of the Chicken Genome.
R. P. Rfl. A. Crooijmans, A. J. A. van Kampen, J. J. van der Poel, and M.A.M. Groenen.
The Journal of Heredity 1994 85(5)
full paper

Siegel, P.B., Dodgson, J.B. & Andersson, L. 2006. Progress from chicken genetics to
the chicken genome.
Poult Sci 85:2025-2060
full paper

Plumage Color Inheritance of the Indian Blue Peafowl (Pavo cristatus): Blue, BlackShouldered, Cameo, and Oaten.
R. G. Somes, Jr. and R. E. Burge
J Hered-1991-64-8
full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/20/11 03:06 AM

Genetic Control of Melanin Pigmentation in the Fowl.
Dr. J. Robert Smyth, Jr. 1976
full paper

Melanin Pigmentation: Its Biological Roles, Inheritance and Expression in the Chicken.
Dr. J. Robert Smyth, Jr. 1994
full paper

Bovan history (2009).
full article
*has photos of commercial parent line stock, plus early Exchequer Leghorn stock.
Posted by: KazJaps

Re: Journal papers online - reference list - 02/26/11 08:35 PM

Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds.
William M. Muir, Gane Ka-Shu Wong, Yong Zhang, Jun Wang, Martien A.M. Groenen, Richard P.M.A. Crooijmans, Hendrik-Jan Megens, Huanmin Zhang, Ron Okimoto, Addie Vereijken, Annemieke Jungerius, Gerard A.A. Albers, Cindy Taylor Lawley, Mary E. Delany, Sean MacEachern and Hans H. Cheng
PNAS November 11, 2008 vol. 105 no. 4 17312–17317
full paper

Analysis of mtDNA sequences shows Japanese native chickens have multiple origins.
T. Oka1, Y. Ino, K. Nomura, S. Kawashima, T. Kuwayama, H. Hanada, T. Amano, M. Takada, N. Takahata, Y. Hayashi, F. Akishinonomiya
Animal Genetics.Volume 38, Issue 3, pages 287–293, June 2007
abstract paper

Multiple maternal origins of chickens: Out of the Asian jungles.
Yi-Ping Liua, Gui-Sheng Wua, Yong-Gang Yao, Yong-Wang Miao, Gordon Luikarte, Mumtaz Baig, Albano Beja-Pereirae Zhao-Li Ding, Malliya Gounder Palanichamy and Ya-Ping Zhan.
Molecular Phylogenetics and Evolution. Volume 38, Issue 1, January 2006, Pages 12-19
abstract paper

Conservation of red junglefowl Gallus gallus in India.
Merwyn Fernandes, Mukesh, S. Sathyakumar, Rahul Kaul, Rajiv S. Kalsi And Deepak Sharma.
2009 World Pheasant Association. International Journal of Galliformes Conservation, 1, 94–101
full paper

Genetic diversity studies of red junglefowl across its distribution range in Northern India.
Mukesh, R.S. Kalsi, R.P. Mandhan and S. Sathyakumar,
2011. Asian J. Biotechnol., 3: 293-301.
html_full paper
pdf_full paper

Genetic Diversity in Five Iranian Native Chicken Populations Estimated by Microsatellite Markers
Saleh Shahbazi, Seyed Z. Mirhosseini and Michael N. Romanov
2007. Biochemical Genetics. Volume 45, Numbers 1-2, 63-75.
abstract paper

Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken.
Sriramana Kanginakudru, Muralidhar Metta, RD Jakati and J Nagaraj
BMC Evolutionary Biology 2008, 8:17
full paper

Playing chicken with red junglefowl: identifying phenotypic markers of genetic purity in Gallus gallus.
I. L. Brisbin Jr. & A. T. Peterson
Animal Conservation 10 (2007) 429–43
full paper

In Situ Characterization Of Local Chicken Eco-Type For Functional Traits And Production System In Fogera Woreda, Amhara Rgional State.
Bogale Kibret. 2008.
full paper

Phenotypic and genetic characterization of indigenous chicken populations in Northwest Ethiopia.
Halima Hassen Mogess. 2007.
full paper

Linkage Analysis of Endogenous Viral Element 1, Blue Eggshell, and Pea Comb Loci in Chickens.
J. R. Bartlett, C. P. Jones, and Smith.
Journal of Heredity 1996:87(1)
full paper

Sequence analysis of a pea comb locus on chicken chromosome 1.
S. Sato, T. Otake, C. Suzuki, Y. Uemoto, J. Saburi, H. Hashimoto, E. Kobayashi
Animal Genetics. Volume 41, Issue 6, pages 659–661, December 2010.
abstract paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/26/11 08:45 PM

Genotype at the PMEL17 locus affects social and explorative behaviour in chickens.
Karlsson AC, Kerje S, Andersson L, Jensen P.
Br Poult Sci. 2010 Apr;51(2):170-7.
abstract paper

Role of Mitf in differentiation and transdifferentiation of chicken pigmented epithelial cell.
Mochii M, Mazaki Y, Mizuno N, Hayashi H, Eguchi G.
Dev Biol. 1998 Jan 1;193(1):47-62.
abstract paper

Physiological studies on the sex-linked dwarfism of the fowl: a review on the search for the gene's primary effect.
M Tixier-Boichard, LM Huybrechts, E Kühn, E Decuypere, J Charrier, and P Mongin
Genet Sel Evol. 1989; 21(2): 217–234.
full paper

Fifteen years of observations on the dwarf gene in the domestic fowl.
Paul E Bernier and George H Arscott.
Genetics Selection Evolution 1972, 4:183-215
full paper

Sex linked dwarf gene (dw) in White Leghorn laying hens under normal or hot temperature.
A.K. Banerjee A. Bordas P. Mérat
Ann. Genet. Sel. anim., 1982, 14 (2), 135-160.
full paper

BREEDING AND GENETICS. An Autosomal Dwarfism in the Domestic Fowl.
R. K. Cole
2000. Poultry Science 79:1507–1516
full paper

Sex-linked dwarfism in the fowl.
Hutt, F. B., 1959.
J. Hered. 50:209–221.
full paper

Genetic variants for chick biology research: from breeds to mutants.
Delany ME.
Mech Dev. 2004 Sep;121(9):1169-77.
full paper

The Phenotypic Modification of Hereditary Polydactylism of Fowl by Selection and by Insulin.
Walter Landauer
Genetics. 1948 March; 33(2): 133–157.
full paper

Inheritance Of Polydactylism in the Fowl.
D.C. Warren. 1944.
Genetics 29: 2 1 7 May 1944
full paper

The use of Tarsometatarsi in sexing and ageing domestic fowl (Gallus gallus L.), and recognising five toed breeds in archaeological material.
Peta Sadler.
Circaea 8 (1) (1991 for 1990), 41-48.
full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/26/11 08:56 PM

The Endocrine System and Plumage Types. I. Some Effects of Hypothyroidism.
A. S. Parkes and H. Selye.
Journal of Genetics Vol. 34, No. 2. 297-306. (May, 1937)
full paper
-fixed broken link & page number (p 297)

The Endocrine System and Plumage Types. II. The Effects of Thyroxin Injections to Normal, Caponized and Thyroidectomized Caponized Birds.
C. W. Emmens and A. S. Parkes
Journal of Genetics Vol. 39, No. 3. 485-492. (March, 1940)
full paper

The Endocrine System and Plumage Types. III. Further Experiments on the Relation between the Thyroid Gland and Plumage Patterns in domestic Fowls and Ducks.
J. P. Chu.
Journal of Genetics Vol. 39, No. 3. 493-502. (March, 1940)
full paper

The Endocrine System and Plumage Types. IV. Ferminization of Plumage, with especial reference to Henny Cocks and Eclipse Drakes.
C. W. Emmens and A. S. Parkes
Journal of Genetics Vol. 39, No. 3. 503-515. (March, 1940)
full paper

The Endocrine System and Plumage Types. V. The Production of Eclipse Plumage in the Mallard by Injection of Anterior Pituitary Extract and Dehydroandrosterone.
J. P. Chu.
Journal of Genetics Vol. 39, No. 3. 517-528. (March, 1940)
full paper

Reversal of the Secondary Sexual Characters in the Fowl. A Castrated Brown Leghorn Male which assumed Female Characters.
A.W. Greenwood and J.S.S. Blyth.
Journal of Genetics Vol. 26, No. 2. 199-214. (October, 1932)
full paper

Inheritance of Earlobe Color in Poultry.
Warren DC.
Genetics. 1928 Nov;13(6):470-87.
full paper

The Chromosomes of the Domestic Fowl.
M.J.D.White
Journal of Genetics Vol. 26, No. 3. 345-350. (December, 1932)
full paper

Inheritance of Spangling in the Domestic Fowl.
Lewis W. Taylor
Journal of Genetics Vol. 26, No. 3. 385-394. (December, 1932)
full paper

Studies on the Creeper Fowl. V. The Linkage of the Genes of Creeper and Single-comb.
Walter Landauer
Journal of Genetics Vol. 26, No. 2. 285-290. (October, 1932)
full paper

Studies on the Creeper Fowl. IX. Malformations occurring in the Creeper Stock. Walter Landauer
Journal of Genetics Vol. 30, No. 2. 303-320. (March, 1935)
full paper

The Genetics of the Rumpless Fowl with Evidence of a Case of Changing Dominance.
L. C. Dunn and Walter Landauer.
Journal of Genetics. Vol. 29, No. 2. 217-244. (July, 1934)
full paper

A Colour Mutation in the Rhode Island Red Fowl.
Joseph P. Quinn
Journal of Genetics. Vol. 29, No. 1. 75-83. (April, 1934)
full paper
*red splashed white mutation

Further experiments with the P Gene in the Fowl.
Joseph P. Quinn
Journal of Genetics. Vol. 30, No. 3. 477- 480. (May, 1935)
full paper
*this is red splashed white (not peacomb)

On the Left-sided Incidence of the Supernumerary Digit in Heterodactylous Fowls.
C.J. Bond
Journal of Genetics. Vol. 10, No. 1. 87-92. (July, 1920)
full paper

Further Data on a Case of Autosomal Linkage in the Domestic Fowl.
L.C. Dunn and W. Landauer.
Journal of Genetics. Vol. 22, No. 1 pp 95-102 (April, 1930)
full paper

The interpretation of autosexing.
A. G. Cock
Journal of Genetics. Vol. 51, No. 2. 421 – 433. (January, 1953)
full paper

Notes on the Genitalia of a Crowing Hen.
J. Bronte Gatenby and F.W. Rogers Brambell
Journal of Genetics. Vol. 14, No. 2. 173-184. (August, 1924)
full paper

Experiments with certain Plumage Colour and Pattern Factors in Poultry.
W.E. Agar
Journal of Genetics. Vol. 14, No. 2. 265-172. (August, 1924)
full paper

The Combination of Linkage Values, and the Calculation of Distances between the Loci of Linked Factors.
J.B.S. Haldane
Journal of Genetics. Vol. 8, No. 4. 299-309 (September, 1919)
full paper

On Certain Factors concerned in the production of Eye Colour in Birds.
C.J. Bond
Journal of Genetics. Vol. 9, No. 1. 69-82. (December, 1919)
full paper

The Genetics of the Fowl. I. The Inheritance of Frizzled Plumage.
F. B. Hutt
Journal of Genetics. Vol. 22, No. 1 pp 109-128. (April, 1930)
full paper
-fixed broken link - thanks Redcap

Genetic Studies in Poultry. II. Inheritance of Egg-Colour and Broodiness.
R.C. Punnett and Major P.G. Bailey
Journal of Genetics. Vol. 10, No. 4. 277-292. (December, 1920)
full paper

Genetic studies in poultry III. Hen-Feathered cocks.
R. C. Punnett and P. G. Bailey 1921
Journal of Genetics Volume 11, Number 1, 37-57
full paper

Genetic studies in poultry IV. On the barred plumage of certain breeds.
R. C. Punnett and M. S. Pease
Journal of Genetics Volume 11, Number 3, 235-24
full paper

Genetic studies in Poultry. VIII. On a case of sex-linkage within a breed.
R. C. Punnett and M. S. Pease
1930. Jour. Gen. 22: 395-397
full paper

Genetic Studies in Poultry. X. Linkage Data for the Sex Chromosome.
R. C. Punnett
Journal of Genetics Vol. 39, No. 2 (January, 1940)
full paper


Evolution of Avian Plumage Dichromatism from a Proximate Perspective.
Rebecca T. Kimball and J. David Ligon
vol. 154, no. 2 the american naturalist august 1999.
full paper

A suggestion as to the Nature of "Walnut" Comb in Fowls.
Bateson, W and R.C. Punnett. 1905.
Proceedings of the Cambridge Philosophical Society, 13: 165-168.
Google books preview

On asymmetric spur development in fowls.
C. J. Bond 1937
JOURNAL OF GENETICS Volume 34, Number 2, 229-235
http://www.ias.ac.in/jarch/jgenet/34/229.pdf
Posted by: Redcap

Re: Journal papers online - reference list - 02/27/11 11:08 PM

Originally Posted By: KazJaps


The Genetics of the Fowl. I. The Inheritance of Frizzled Plumage.
F. B. Hutt
Journal of Genetics. Vol. 22, No. 1 pp 109-128. (April, 1930)
full paper




Studies on the creeper fowl. III. The early development and lethal expression of homozygous creeper embryos.
Walter Landauer

JOURNAL OF GENETICS Volume 25, Number 3, 367-394, April 1932.
http://www.springerlink.com/content/n7244864r983k72m/
Available on request

Genetics of the fowl. V. The modified frizzle
F. B. Hutt

JOURNAL OF GENETICS Volume 32, Number 2, 277-285, April 1936.
http://www.springerlink.com/content/y462w41270831287/
Available on request

I can also provide the most articles from Journal of Genetics, mentioned above in an OCR-Version.
Posted by: KazJaps

Re: Journal papers online - reference list - 03/01/11 10:25 PM

The following all from the Journal of Genetics:
- Journal of Genetics - Archive (Index page - Open Access 1910 to 1994)

Studies on the Creeper Fowl. III. The Early Development and Lethal Expression of Homozygous Creeper Embryos.
Walter Landauer
Journal of Genetics Vol. 25, No. 3. 367-394. (February, 1932).
full paper

Further Observations on Polydactyly and Heterodactyly in Fowls.
C.J. Bond
Journal of Genetics Vol. 16, No. 2. 253-256. (January, 1926)
full paper

Further Data on Genetic Modification of Rumplessness in the Fowl.
L. C. Dunn and Walter Landauer
Journal of Genetics Vol. 33, No. 3. 401-406. (December, 1936)
full paper

Notes on Cross-Beak in Fowl.
Walter Landauer
Journal of Genetics Vol. 37, No. 1. 51-67. (December, 1938)
full paper

An Experimental Study on Xenia in the Domestic Fowl.
Stefan Kope
Journal of Genetics Vol. 16, No. 3 269-288 (April, 1926)
full paper

The Anomalous Appearance of Male Sexual Characters in Female Fowl.
A.S. Parkes and F.W. Rogers Brambell
Journal of Genetics Vol. 17, No. 1. 69-76. (August, 1926)
full paper

The Influence of Testis on Sexual Plumage in the Domestic Fowl.
Alan W. Greenwood and J. S. S. Blyth
Journal of Genetics. Vol. 34, No. 3. 501-508. (September, 1938)
full paper

On the Topography of the Sex-Chromosome in Fowls
A.S. Serebrovsky and E.T. Wassina
Journal of Genetics 211-216 Vol. 17, No. 2. 211-216. (October, 1926)
full paper

A Case of Leg-colour Asymmetry in the Fowl.
F.A.E.Crew
Journal of Genetics Vol. 25, No. 3. 359-366 (February, 1932)
full paper

On inheritance of weight in poultry.
R. C. Punnett and P. G. Bailey
Journal of Genetics. No. 1. 23-40. (June 1914)
full paper

Half-and half mosaics in the fowl.
A.G. Cock
Journal of Genetics. Vol. 53, No. 1. 49-80. (January, 1955)
full paper

The spread of genes by natural and artificial selection in closed poultry flock.
J.W. James and G. Macbride
Journal of Genetics. Vol. 56, No. 1. 55-62. (July, 1958)
full paper

The coefficient of inbreeding in case of repeated full-sib matings.
F.E. Binet and R.T. Leslie
Journal of Genetics. Vol. 57, No. 1. 127-130. (June, 1960)
full paper

The occurrence and possible significance of parthenogeneiss in eggs of mated turkeys.
M.W. Olse
Journal of Genetics. Vol. 58, No. 1. 1-6. (May, 1962)
full paper

Rudimentation and duplication of the radius in the duplicate mutant form of fowl. Walter Landauer
Journal of Genetics Vol. 54, No. 2. 199-218. (May, 1956)
full paper

Cyclopia and related defects as a lethal mutation of fowl.
Walter Landauer
Journal of Genetics Vol. 54, No. 2. 219-235. (May, 1956)
full paper

An application of the discriminant function for selection in poultry.
V.G. Panse
Journal of Genetics Vol. 47, No. 3. 242-248. (July, 1946)
full paper

The Production of Robin Pigment in White Leghorn Feathers by Grafts of Embryonic Robin Tissue.
Mary E. Rawles
Journal of Genetics. Vol. 38, No. 3. 517-532. (September, 1939)
full paper

On the Sterility of Hybrids between the Pheasant and the Gold Campine Fowl.
D.W. Cutler
Journal of Genetics. Vol. 7, No. 3. 155-166. (May, 1918)
full paper

Note on a pheasant showing abnormal sex-characters.
W. Bateson and Rose Haig Thomas
Journal of Genetics. No. 3. 163-164. (April 1917)
full paper

Observations on Interspecific Hybrids of the Fowl.
S. Serenbrovsky
Journal of Genetics Vol. 21, No. 3. 327-340 (December, 1929)
full paper

Sex-Ratio in Pheasant Species-crosses
Rose Haig Thomas and Julian S. Huxley
Journal of Genetics Vol. 18, No. 2. 233-246. (June, 1927)
full paper

Colour and pattern-transference in pheasant crosses.
Rose Haig Thomas
Journal of Genetics. No. 4. 243-280. (July 1916)
full paper

On the existence of Egg-laying Cycles in the Domestic Fowl.
S.C. Harland
Journal of Genetics. Vol. 18, No. 1. 55-62. (March, 1927)
full paper

Inheritance of Structural types in the Dorsosacrum of Domestic Poulty.
A.N. Promptoff
Journal of Genetics. Vol. 20, No. 1. 29-52. (July, 1928)
full paper

Note on a Sex-linked Down Character in Ducks.
R.C. Punnett.
Journal of Genetics Vol. 25, No. 2, 191-194 (February, 1932)
full paper

A Note on the Inheritance of Colour in One Breed of Pigeons-An Attempt to Demonstrate a Mendelian Type of Transmission.
J.S.W. Nuttall
Journal of Genetics. Vol. 7, No. 2. 119-124. (February, 1918)
full paper

Studies in Sexual Phenomena. VIII. "Transference" and Eclipse Plumage in Birds.
J. M. Winterbottom.
Journal of Genetics Vol. 25, No. 3. 395-406. (February, 1932).
full paper

Note on a Bronze-Bourbon Red Mosaic.
V. S. Asmundson
Journal of Genetics. Vol. 35, No. 1. 25-30 (October, 1937)
full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 06/26/11 06:18 AM

Some 2011 papers on Po - polydactyly in chickens...

The chicken polydactyly (Po) locus causes allelic imbalance and ectopic expression of Shh during limb development.
Ian C. Dunn, I. Robert Paton, Allyson K. Clelland, Sujith Sebastian, Edward J. Johnson, Lynn McTeir, Dawn Windsor, Adrian Sherman, Helen Sang, Dave W. Burt, Cheryll Tickle, Megan G. Davey.
Developmental Dynamics. Volume 240, Issue 5, pages 1163–1172, May 2011
full paper

Identification of spontaneous mutations within the long-range limb-specific Sonic hedgehog enhancer (ZRS) that alter Sonic hedgehog expression in the chicken limb mutants oligozeugodactyly and silkie breed.
Maas SA, Suzuki T, Fallon JF.
Dev Dyn. 2011 May;240(5):1212-22. doi: 10.1002/dvdy.22634.
full paper-pdf

----------------------
2009 paper....

Aberrant FGF signaling, independent of ectopic hedgehog signaling, initiates preaxial polydactyly in Dorking chickens.
Bouldin CM, Harfe BD.
Dev Biol. 2009 Oct 1;334(1):133-41. Epub 2009 Jul 17.
full paper
Posted by: Redcap

Re: Journal papers online - reference list - 10/24/11 05:19 PM

Originally Posted By: KazJaps
Duplex comb in the chicken: a multi-allelic trait.
Somes RG Jr.
J Hered. 1991 Mar-Apr;82(2):169-72.
full paper
*with B/W comb photos

Some Observations on High Cavernous Nostrils in the Chicken.
J Hered-1991-Somes-172-4
full paper
*with B/W comb photos

Creeper and single comb linkage in the fowl.
TAYLOR, L. W.
Jour. Hered. 25 :205-206. 1934
full paper

The Linkage of Polydactyly with Multiple Spurs and Duplex Comb in the Fowl.
F. B. Hutt and C. D. Mueller
The American Naturalist
Vol. 77, No. 768 (Jan. - Feb., 1943), pp. 70-78
abstract paper

GENETICS OF THE FOWL: 15. Multiple Spurs, a Mutation Linked with Duplex Comb.
F. B. HUTT
J Hered (1941) 32(10): 357-364
full paper

GENETICS OF THE FOWL:11. A FOUR-GENE AUTOSOMAL LINKAGE GROUP
F. B. HUTT
Ja 1933 Genetics: 18: 82
full paper
*posted previously

GENETICS OF THE FOWL:11 A Linkage Map for Six Chromosomes.
F. B. HUTT AND W. F. LAMOREUX
Journal of Heredity 1940 Vol. 31 pp. 231-235
full paper
*with many photos of mutations

NINE INDEPENDENTLY INHERITED AUTOSOMAL FACTORS IN THE DOMESTIC FOWL.
D. C. WARREN
GENETICS: 18: 68 Ja 1933
full paper

LINKAGE RELATIONS OF AUTOSOMAL FACTORS IN THE FOWL
D. C. WARREN
GENETICS 34: 333 May 1949
full paper

A CASE OF CLOSE AUTOSOMAL LINKAGE IN THE FOWL
A. S. SEREBROVSKY AND S. G. PETROV
J Hered (1928) 19 (7): 305-306.
full paper


No access to fullpapers at Journal of Heredity without institutional access. If required I can provide them.
Posted by: Karen T.

Re: Journal papers online - reference list - 01/25/12 04:59 PM

William White Broomhead was widely known for his literary style in explaining the why's and how's of breeding poultry in an "everyman" style.
National poultry magazine: Volume 9, Issue 9
- Page 49 - 1911 -
http://tinyurl.com/84d7x62
Sketches of British Judges
No. 1—Mr. William White Broomhead
Written by WM. E. RICE

--------------------------------
An ultra-rare booklet by Broomhead. Unillustrated. A conversation about what a breed should look like for the novice.
The Light Sussex. (London, 1921),
by William White Broomhead

(page images at HathiTrust; US access only)
http://catalog.hathitrust.org/Record/009169678
Posted by: KazJaps

Re: Journal papers online - reference list - 01/27/12 07:53 AM

Sex-linked barring in chickens is controlled by the CDKN2A /B tumour suppressor locus.
(Pigment Cell Melanoma Res. 2010 Aug;23(4):521-30. Epub 2010 Mar 29.)
full paper

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

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

Gene Duplication of endothelin 3 is Closely Correlated with the Hyperpigmentation of the Internal Organs (Fibromelanosis) in Silky Chickens.
Shinomiya A, Kayashima Y, Kinoshita K, Mizutani M, Namikawa T, Matsuda Y, Akiyama T.
Genetics. 2011 Nov 30. [Epub ahead of print]
Full Paper

Genetics of hyperpigmentation associated with the Fibromelanosis gene (Fm) and analysis of growth and meat quality traits in crosses of native Indian Kadaknath chickens and non-indigenous breeds
G. Aroraa*, S.K. Mishraa, B. Nautiyalb, S.O. Pratapa, A. Guptaa, C.K. Beuraa & D.P. Singha
British Poultry Science Volume 52, Issue 6, 2011. pages 675-685. Available online: 06 Jan 2012
Abstract only

Interaction of fibromelanosis gene with various genetic backgrounds affecting carcass pigmentation in crossbred Kadakanath chicken.
Mishra S K;Arora G;Pratap S O;Singh D P;Raj Narayan;Beura C K.
Indian Journal of Poultry Science: 2008,43(3),267-71
Abstract only
Posted by: Spicifer

Re: Journal papers online - reference list - 02/03/12 02:22 AM

Eriksson, Jonas
A frameshift mutation in COMTD1 specifically dilutes pheomelanin pigmentation in chicken

at:
Genetic and Genomic Studies in Chicken: Assigning Function to Vertebrate Genes
Manuscript
Posted by: Wieslaw

Re: Journal papers online - reference list - 02/04/12 04:00 AM

WOW!! That is something new. Inhibitor of Gold on chromosome 6!
Posted by: Henk69

Re: Journal papers online - reference list - 02/04/12 07:32 AM

What else is on 6?
Posted by: Redcap

Re: Journal papers online - reference list - 02/04/12 08:10 AM

Is that map uptodate?
http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9031&chr=6
Posted by: KazJaps

Re: Journal papers online - reference list - 02/04/12 06:47 PM

Thank you Spicifer for posting the new research smile

Henk, I've got Chromosome 6 (Group VII) listed on the chromosome linkages web page. But none of the genes listed are pigment or other mutations commonly related to exhibition /chicken breeds that we are usually interested in here (eg genes: Ade-A, Pgm-2, Gc, Alb).

Going by the manuscript provided, it seems it is a first to find a pigment altering mutation on the COMTD1 gene (not even previously noted in mice before).

--------------------
Yes, the NCBI map has COMTD1 on chicken Chromosome 6. But you have to zoom in to the specific region on the chromosome to see the gene (not all genes are shown with initial view).

From the manuscript:
Quote:
The Inhibitor of Gold locus was mapped—by linkage analysis in a pedigree
segregating for IG—to a 3.58 megabase (Mb) region located between
the nucleotide positions 12,388,399–15,970,174 on chicken chromosome 6.


NBCI chicken master map:

Chromosome 6, region 14,389,800-14,397,800 bp (zoomed in)

Then if you click the "zoom out" blue graphic in left navigation column, it gives a good map of the whole chromosome, with position of COMTD1 on it.
Unfortunately I can't provide a direct link here on the forum as the NCBI url generated has square brackets within (messes up the code for posting).
Posted by: Poultch

Re: Journal papers online - reference list - 02/04/12 08:07 PM

Originally Posted By: Henk69
What else is on 6?



Originally Posted By: Wieslaw
I do not want to derail the discussion, but I have an extra question on barring. According to some papers, what we call 'barring gene' is actually (in the world of genetisists) synonymous with tumor suppressor gene. I have asked about it before(without getting an answer): Is B better to suppress tumors than b? If not, why bother with barring at all?



above quote taken from the B and Id thread

Suppression or necrosis?
http://www.ncbi.nlm.nih.gov/protein/NP_001186416.1
I see tumor necrosis factor is on 6 along with what seems to be a cell suicide protein
barring is now thought to cause prem death of melanocytes, rather than suppression of melanin production, is this what you mean?
Posted by: Henk69

Re: Journal papers online - reference list - 02/05/12 04:45 AM

Originally Posted By: KazJaps


NBCI chicken master map:

Chromosome 6, region 14,389,800-14,397,800 bp (zoomed in)

Then if you click the "zoom out" blue graphic in left navigation column, it gives a good map of the whole chromosome, with position of COMTD1 on it.
Unfortunately I can't provide a direct link here on the forum as the NCBI url generated has square brackets within (messes up the code for posting).



Direct link?
Posted by: KazJaps

Re: Journal papers online - reference list - 02/05/12 05:05 AM

Yes, thank you Henk wink

Must be good to have super-mod powers smile
Posted by: Henk69

Re: Journal papers online - reference list - 02/05/12 05:10 AM

Yes, the power of html. Kal (htm)el wink
Posted by: Redcap

Re: Journal papers online - reference list - 02/07/12 02:03 AM

This book could be interesting for You
Database: Cornell University Library
Author/Creator: Regnier, Victor.
Title: Hormone ovarienne et caracteres raciaux du plumage chez le coq et la poule domestiques. Etude de genetique experimentale ...
Published: Paris, Editions du Bulletin biologique de la France et de la Belgique, 1937.
Description: 1 p. l., 214 p., 7 l. illus., V pl. (3 col., 2 fold.) diagrs. 25 cm.


In Crossings of Malines <-> brown Leghorn , brown Leghorn <-> Andalusian and in a third combination cocks were injected with female hormones or ovarian were removed, to see what happens with plumage.
Similar to these studies
http://jhered.oxfordjournals.org/content/26/8/299.full.pdf
http://www.springerlink.com/content/y774275g5426p338/fulltext.pdf
Posted by: Terry

Re: Journal papers online - reference list - 02/19/12 10:46 PM

re: The "silver" Japanese quail and the MITF gene: causal mutation, associated traits and homology with the "blue" chicken plumage.
Do you believe that the Blue mutation is a MITF gene as this suggests or are they really equivalent to the Dun mentioned as an allele of PMEL17?
MITF interfers with melanoblast migration, therefore should alter both eumelanin and phaeomelanin, however homozygous Blue still produce normal phaeomelanin levels. This is consistent with the PMEL17 function.
What are your thoughts?
Posted by: KazJaps

Re: Journal papers online - reference list - 02/20/12 08:17 PM

Hi Terry,

That's interesting.

We know Bl - Blue gene is not on the PMEL17 locus through test breeding, as a single bird can have both Dominant White I/I (on the PMEL17 locus) plus Bl/Bl too.

Although in chickens (& many other species) the PMEL17 mutations (eg I - dominant white, I^D -dun, I^S-smoky) affect eumelanin only (mostly), there has been research that indicates that the dilution gene found in Charolais cattle (Dc) (dilutes both eumelanin and phaeomelanin) is a mutation of PMEL17 (SILV) too. Another PMEL17 dilution mutation in Highland cattle also dilutes both eumelanin and phaeomelanin:

Quote:
The pigment-specificity of mutations in the SILV gene observed in other species [22-25] is in agreement with the critical role reported for this protein in eumelanosomes but not in phaeomelanosomes [28] and the suppression of PMEL17 expression seen in murine phaeomelanosomes [29,30]. However, recent work in Highland cattle reported a 3-bp deletion in exon 1 of the bovine SILV gene associated with the dilution of both red and black pigments [16]. This finding, and the likely association of the SILV gene and the Dc locus, which affects both pigments, are intriguing and may suggest that the role of PMEL17 differs between species. This is plausible as the genuine function of the SILV gene product in pigmentation is not completely understood [14] and the biological basis of pigmentation may vary with species. Mutations in the SILV gene that have only been shown to affect eumelanin background are located in the c-terminal sequence of the SILV gene and affect the transmembrane or cytoplasmatic domains of the protein [22-25]. It is possible that mutations closer to the N-terminal end (such as exon 1, where both cattle mutations are found) could lead to more general interference with pigment production.


Ref:
Genetic effects on coat colour in cattle: dilution of eumelanin and phaeomelanin pigments in an F2-Backcross Charolais x Holstein population.
Gutiérrez-Gil B, Wiener P, Williams JL.
BMC Genet. 2007 Aug 16;8:56.
full paper

-------------------
Plus SLC45A2 (or MATP) mutation - S silver in chickens dilutes phaeomelanin only, but in other species mutations on this gene are generally albino like, dilute both eumelanin & phaeomelanin (including one in chickens - s^al sex-linked imperfect albinism).
Posted by: Terry

Re: Journal papers online - reference list - 02/21/12 12:47 AM

Hello KazJaps
In many species MITF mutations produce piedbald/spotting phenotypes because of their impact on cell migration. I was surprised and disbelieving to read that it could cause the Blue phenotype.
But with further consideration I realised that this transcription factor is responsible to initiating transcription of most of the important melanogenic enzymes (tyr, TRP1, TRP2, etc). So a missense mutation would reduce eumelanin production and at the same time maintain phaeomelanin production, or even enhance it. (You would know that Phaeomelanin is enhaced when tyrosinase is down regulated)
If you consider the homozygous Blue laced Gold Wyandotte, the phaeomelanin is richer than that produced in heterozygous Blue Laced Gold or Gold Laced.
I am still interested in the phenotypic difference between Dun and Blue. 'Blues' in different breeds seem to vary in the degree of depth of melanin colour. In some breeds Bl/+ are almost black and others quite blue, whilst Bl/Bl can be silver in some breeds and classical splashed in others.

With regards SLC45A2 (or MATP), as this protein transports enzymes into the melanosome, it is likely that the Silver allele interfers with cysteine transport into the melanosome for phaeomelanin production, as there are no enzymes specific to phaeomelanin.
In aviculture we like to call this locus the sex-linked ino locus, apart from the null mutations which produce virtual complete melanin loss, there are lots of examples of missense mutations producing different levels of melanisation. But none that effect phaeomelanin only - all reduce eumelanin equally.

Although this Silver allele is so far unique in the fowl, there are other genes well known in other species have only recently started to appear in fowl - TRP1 (the Chocolate Orpington) and Agouti. TRP1 mutations would be the most common mutation across all avian species (always sexlinked in these) and also common as the autosomal brown locus in mammals. So why has it not been established as a colour in different breeds of chickens during the hundreds of year people have bred them???
regards
Terry
Posted by: Wieslaw

Re: Journal papers online - reference list - 02/21/12 06:23 AM

Originally Posted By: Terry
So why has it not been established as a colour in different breeds of chickens during the hundreds of year people have bred them???


Up to this day the vast majority of breeders are people who breed to a standard, so mutations are usually mercilessly removed from the gene pool as oddities, you can actually get such birds for free if you're lucky and you know what you're looking for. Secondly, chocolate on many birds may not look particularly attractive (washed out black). It may also play a role.
Posted by: Terry

Re: Journal papers online - reference list - 02/21/12 05:44 PM

Maybe it is that simple with the domestic fowl, but in virtually all other domestic animals mutations of the brown locus (TRP1) (Chocolate)has been deemed highly desirable both as a single expression and in combination with other genes. Perhaps it is the extensive distribution of phaeomelanin in the fowl that helps produce colours which appear similar to brown eumelanin, thereby making the TRP1 mutations less distinct.
Terry
Posted by: KazJaps

Re: Journal papers online - reference list - 02/22/12 01:16 AM

These mutations are taking off now. I think choc is highly desirable (choc probably a TYRP1 mutation, similar to sex-linked roux in Quails, but not aware of choc been DNA sequenced). It was mainly a matter of multiplying a rare mutation, & getting the mutation into main stream European & American exhibition breeds.

Here are a couple of articles by Sigi on Dun (I^D) and Chocolate (choc) - explains a bit of the history in chickens:

*On I^D – Dun & choc

* Chocolate Chabos

It seems there have been at least two main waves of sex-linked chocolate in chickens, and both times occurring within the past 30 years or so. Once was Clive Carefoot (UK) obtaining Black Orpington eggs, & by chance these were carrying the choc gene. A second main wave in Asia (possibly multiple times?). One known Asian one was from a cross between a Red Jungle Fowl & Chabo (Japanese Bantam) hen (see the above article).

Dun I^D has been around for much longer. It probably has been in fighting Game stock for many decades / over a century maybe. But I imagine having Bl -blue in the gene pool as well didn't help its distinction. Plus possibly hidden in varieties such as Ginger Reds, and may have been the base gene for old Game brown-breasted varieties, Birchen Duckwings, Coffee-laced, etc.

The trouble with I^D is that it can look similar to a bad Bl/bl+ - dark greyish tones, only a hint of brown, and rustiness in blues is an exhibition flaw. But with certain modifiers, I^D can look as beautiful as Clive Carefoot's Chocolate Orpingtons.

Eg, variation in I^D shades:

Dun Polish (from Feathersite):

Dun Sumatra (from Backyard Chickens Forum: )


Chocolate Orpington (Clive Carefoot's line):


P.s. - looks like both choc and I^D need those enhanced green sheen modifiers (found in Sumatras and Orpingtons) to give that rich glossy chocolate brown tone.
Posted by: Terry

Re: Journal papers online - reference list - 02/23/12 01:14 AM

KazJaps said
"I think choc is highly desirable (choc probably a TYRP1 mutation, similar to sex-linked roux in Quails, but not aware of choc been DNA sequenced"

I have not seen any papers on it, but as someone with experience in other avian species, the TRP1 Brown mutation is so distinctive it cannot be missed. I would confidantly say it is almost the easiest mutation to identify to locus in birds, even if we have to wait for the scientists to confirm.

As you say Roux has been sequenced in Jap Quail, it exists as Chocolate in Muscovy and Turkeys, is present in over 20species of Parrots (Cinnamon), also Canaries, many finches (Cinnamon or Fawn) and King Quail.

Thanks for the articles on Dun and Choc
Posted by: KazJaps

Re: Journal papers online - reference list - 02/23/12 01:31 AM

Terry, have you heard of any DNA testing on pigment mutations in domesticated avian birds other than poultry? I recall reading of the zebra finch genome project, but not aware of any specific pigment mutations identified through DNA sequencing.
Posted by: Terry

Re: Journal papers online - reference list - 02/23/12 01:55 AM

KazJaps
They are quite advanced in reproducing the genome sequence, you can check it online and search for known loci. TRP1 is on the Z as expected ;-). But there has been no papers correlating mutations and specific phenoptypes to specific loci.
All the papers I have found on DNA sequences are for Chickens or Jap Quail - commercial species prevail at this point as they have a strong basis in old fashion genetics to work from.
But aviculturists are busy watching it closely and extrapolating from poultry into aviculture species.
Posted by: KazJaps

Re: Journal papers online - reference list - 02/23/12 04:21 AM

Thanks for the info Terry (explains why I haven't found the research at Pubmed).

I forgot to mention earlier. Bl - probably dilutes phaeomelanin a little. Usually Wyandottes are Blue Laced Red - added phaeomelanin intensifier(s) in the genotype. Need to compare bl+/bl+ siblings.

Depending on lines, but Dominant White when homozygous tends to partly wash out phaeomelanin too (quite significantly in a Pile Modern line I have, even though they have a red enhancer).
Posted by: Terry

Re: Journal papers online - reference list - 02/23/12 05:22 PM

KazJaps said
"Bl - probably dilutes phaeomelanin a little. Usually Wyandottes are Blue Laced Red - added phaeomelanin intensifier(s) in the genotype. Need to compare bl+/bl+ siblings. "

Actually I mentioned that I disagree with this. I have bred alot of Blue Laced Gold Wyandottes this year in both hetero and homozygous form plus lots of Gold Laced, all from the same line but four different matings. Without exeption, the Bl/Bl birds have stronger phaeo than the Bl/+ and wildtype. And I then realised that since MTIF regulates tyr transcription to some degree, a mutation that down regulates MITF would reduce tyr and this is a prerequisite for phaeomelanin production.
Without exception, these Bl/Bl birds also have narrower lacing than their siblings, it appears without the normal tyrosinase levels, the phaeo can spread wider on the feather.
Posted by: KazJaps

Re: Journal papers online - reference list - 02/23/12 07:34 PM

In the following thread The Coop: White tailed Reds - see Jereon's comments, eg:

Quote:
About the diluted pheomelanine which is several times visible by blue :

One of our friends have Mille Fleurs and Blue Mille Fleurs Belgian d'Uccle. When they have blue they mostly show a very light ground colour. He has sometimes some Buff Columbian and Blue Buff Columbian birds in his offspring. When they have the Bl-gene they are mostly very pale.
When I look at Blue Quail d'Anvers at shows, I mostly see the colour of the breast is much lighter than the colour by normal Quail birds.

But the strange thing is : it isn't always so.

Later he posted examples.
Blue Buff Columbian and Buff Columbian:


There is also gold diluted varieties in Belgian bantams. They have ig (or similar) phaeomelanin diluter in the Belgian gene pool - this explaining some varieties as Lemon Millefleur, White Lemon Quail, etc. But a conversion I had with a European d'Anver breeder some years back, indicated that in his line he was getting the White Lemon Quail phenotype from Bl/Bl alone (& no I - Dom. White in the gene pool). The bl+/bl+ segregates were a normal Quail phaeomelanin shade, ie not Lemon Quail (no ig in there).

I've noticed similar slight phaeomelanin dilution happening in my Bl Belgians too, but it was hard to work out specifics as I had very mixed lines, both phaeomelanin intensifiers and phaeomelanin diluters segregating, plus there are differences with Db and Co base phaeomelanin shades too (both these segregating also). But I had wondered, & thought it an interesting project to see if any correlations with shade of blue to the shade of phaeomelanin. Eg, do dark blues correlate with any phaeomelanin dilution, is it only light blues that correlate with some phaeomelanin dilution, & so on....
I.e. try to pin-point the following by Jeroen: "But the strange thing is : it isn't always so".

----------------
*Another observation. It was harder to get clean mottled eumelanin banding in Bl/bl+ Blue Millefleur than with their bl+/bl+ siblings. Bl/bl+ tends to wash out the edges of the eumelanin with the mo/mo white tip:

*But once again - not always.

A bl+/bl+ version for comparison:


(sorry - blurry. Lol I wonder if I had reading glasses when I edited the last photo).
Posted by: Terry

Re: Journal papers online - reference list - 03/03/12 06:01 AM

KazJaps
The photo below illustrates very well my opinion that when homozygous Blue, then MITF is downregulated, reducing tyr and causing an increase in phaeomelanin. The heterozygous phenotype does not vary consistently from GLW but may be slightly paler in phaeomelanin on average

The birds in the photo are siblings from the same mating pen
Posted by: KazJaps

Re: Journal papers online - reference list - 03/03/12 07:01 PM

Thank you for the photo.

Interesting that the Bl/bl+ appears slightly lighter gold ground colour than the average bl+/bl+ Aust. Gold Laced black line, yet the left Bl/Bl splash bird is darker than the average Aust. G.L. bl+/bl+ line. The left Bl/Bl bird is a darker eumelanin (eg blue head/upper neck) than the right. The Bl/bl+ a mid blue, maybe slightly lighter than average.

Any chance the line descended from breeders in the process of introducing/setting phaeomelanin intensifiers, ie possible het. red enhancers segregating in the line?
Posted by: Spicifer

Re: Journal papers online - reference list - 04/19/12 01:19 AM

WOW!
Finally,
compliments to the researchers!

The Crest Phenotype in Chicken Is Associated with Ectopic Expression of HOXC8 in Cranial Skin

Full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 04/29/12 05:30 PM

Thanks Spicifer for the interesting paper.

-----------------------
Seems I might have forgotten to add the following (can't find with a page search):

Lethal Action of the Gene for Extension of Black Pigment in the Fowl
F. B. HUTT
Genetics. 1951 May; 36(3): 213–234.
Full Paper
Posted by: KazJaps

Re: Journal papers online - reference list - 06/12/12 11:27 PM

The following web pages - books on Sussex fowl history:
The Sussex fowl (1920)
by Sharpe.
download webpage

History of the Sussex fowl containing the English and American standard of perfection. (1911)
by Bratt.
download web page
Posted by: Spicifer

Re: Journal papers online - reference list - 06/18/12 08:29 AM

The Langshan fowl; its history and characteristics with some comments on its early opponents
by Croad, A. C

download from the web page
Posted by: KazJaps

Re: Journal papers online - reference list - 07/18/12 10:25 AM

Elaborate color patterns of individual chicken feathers may be formed by the agouti signaling protein.
Yoshihara C, Fukao A, Ando K, Tashiro Y, Taniuchi S, Takahashi S, Takeuchi S.
Gen Comp Endocrinol. 2012 Feb 1;175(3):495-9. Epub 2011 Dec 19.
Pubmed abstract
abstract & illustrations


Conserved distal promoter of the agouti signaling protein (ASIP) gene controls sexual dichromatism in chickens.
Oribe E, Fukao A, Yoshihara C, Mendori M, Rosal KG, Takahashi S, Takeuchi S.
Gen Comp Endocrinol. 2012 Jun 1;177(2):231-7. Epub 2012 Apr 23.
Pubmed abstract
abstract & illustrations
Figure 2: large image
Posted by: mdenham

Re: Journal papers online - reference list - 07/19/12 12:51 AM

Hi KazJaps,
Are these publications free/paying? There are some articles which interest me.
Thanks in advance,
Posted by: KazJaps

Re: Journal papers online - reference list - 07/19/12 04:17 AM

All the ones with "abstract/first page preview" links are not free access for the full paper. But this can change as sometimes there is a deal with the publisher where full paper access is released after a limited period (eg after a year or so). So sometimes it pays to check back later.

All the ones I've posted with "full paper" links means that I was able to download these for free, at the time of the post. But unfortunately access rights can change, & now alot of the jhered (Journal of Hereditary) ones are not accessible for free. You will find out soon enough when clicking on the links.

If access has changed, the link will re-divert to a login/payment page. They are quite expensive buying from the publisher, although there is a new web company "DeepDyve" with cheap 24hr access (read-only).
Posted by: mdenham

Re: Journal papers online - reference list - 07/19/12 04:41 AM

Thank you
Posted by: KazJaps

Re: Journal papers online - reference list - 07/19/12 04:54 AM

Some more historical poultry books from http://www.archive.org
* Note, you can do a search at the above link (in the "Media Type" drop-down box, select Texts to bring up books only).

The Poultry Book (1903) Volume 1
by Harrison Weir
http://archive.org/details/poultrybook01weir
*webpage with download links

The Poultry Book (1903) Volume 2
by Harrison Weir
http://archive.org/details/poultrybook02weir
*webpage with download links

The Poultry Book (1904) Volume 1
by Harrison Weir
http://archive.org/details/cu31924001090186
*webpage with download links
---------------------------------
Game fowl books:

The old English game fowl; its history, description, management, breeding and feeding (1891)
by HERBERT ATKINSON.
http://archive.org/details/cu31924003689167
*webpage with download links

The book of the Games (1886)
by H.H. Stoddard
http://archive.org/details/bookofgames00stod
*webpage with download links
-An American book on breeding varieties of Games.

The game fowl (Old English and modern) to which is added a reprint of The Cocker, by W. Sketchley, First published in 1814 (1903),
by Proad & Sketchley.
http://archive.org/details/cu31924003119744
*webpage with download links
-An English book on OEG & Modern Games. Discusses varieties, the Standards, etc.

Cocker's manual, devoted to the game fowl, their origin and breeding, rules for feeding, heeling, handling, etc., description of the different breeds, diseases and their treatment. (1878),
by Gray.
http://archive.org/details/cockersmanualdev00gray
*webpage with download links
- An American book, discusses history, & strains such as Claibourne etc, the Standards, etc. But a warning, also heavy on cockfighting topics.
Posted by: KazJaps

Re: Journal papers online - reference list - 08/12/12 09:59 AM

The Frizzle gene has been sequenced....

The Chicken Frizzle Feather Is Due to an a-Keratin (KRT75) Mutation That Causes a Defective Rachis.
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.
PLoS Genet. 2012 Jul;8(7):e1002748. Epub 2012 Jul 19.
Full Paper - html
Full Paper - pdf (7.7 MB)

* F - frizzle is on linkage group E22C19W28, & is about 17cM from I locus - Dominant White (PMEL17 gene) & I is about 12.5cM from Cr - crest locus (HOXC8 gene).

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

- rumpless (Rp), mapped to IRX1 and IRX2 region (Iroquois homeobox genes)(NCBI lists IRX1 on Chromosome 2)
- ear-tufted (Et)= TBX1 (T-box 1)gene (NCBI lists TBX1 on Chromosome 15)
Posted by: KazJaps

Re: Journal papers online - reference list - 08/12/12 10:38 AM

Rosecomb has been sequenced....

The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility.
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.
PLoS Genet. 2012 Jun;8(6):e1002775. Epub 2012 Jun 28.
Full paper -pdf
Quote:
Here we show that Rose-comb is caused by a 7.4 Mb inversion on chromosome 7 and that a second Rose-comb allele arose by unequal crossing over between a Rose-comb and wild-type chromosome. The comb phenotype is caused by the relocalization of the MNR2 homeodomain protein gene leading to transient ectopic expression of MNR2 during comb development.


Quote:
Rose-comb has pleiotropic effects, as homozygosity in males has been associated with poor sperm motility. We postulate that this is caused by the disruption of the CCDC108 gene located at one of the inversion breakpoints. CCDC108 is a poorly characterized protein, but it contains a MSP (major sperm protein) domain and is expressed in testis.
Posted by: Wieslaw

Re: Journal papers online - reference list - 08/12/12 07:15 PM

The whole text is extremely interesting, but the existence of another rose comb allele R2 which does not reduce fertility, beats it all! Out with R1 ! Replace it with R2!
Posted by: KazJaps

Re: Journal papers online - reference list - 08/16/12 03:09 AM

Some more research (2012) on polydactyly:

The expression of preaxial polydactyly is influenced by modifying genetic elements and is not maintained by chromosomal inversion in an avian biomedical model.
Robb EA, Delany ME.
Cytogenet Genome Res. 2012;136(1):50-68. Epub 2012 Jan 25.
abstract
Posted by: KazJaps

Re: Journal papers online - reference list - 08/16/12 03:19 AM

Indirect Genetic Effects for Survival in Domestic Chickens (Gallus gallus) are Magnified in Crossbred Genotypes and Show a Parent-of-origin effect.
Peeters K, Eppink TT, Ellen ED, Visscher J, Bijma P.
Genetics. 2012 Jul 30. [Epub ahead of print]
full paper-pdf

*An unusual example of outbreeding depression (ie cross-breds did worse than pure-breds).
Posted by: KazJaps

Re: Journal papers online - reference list - 08/16/12 04:23 AM

Some older studies on reduced fertility with R/R:

Identification of a sperm cell attribute responsible for subfertility of roosters homozygous for the rose comb allele.
McLean DJ, Froman DP.
Biol Reprod. 1996 Jan;54(1):168-72.
Full Paper -pdf

Reduced glucose transport in sperm from roosters (Gallus domesticus) with heritable subfertility.
McLean DJ, Jones LG Jr, Froman DP.
Biol Reprod. 1997 Oct;57(4):791-5.
Full Paper -pdf
Posted by: KazJaps

Re: Journal papers online - reference list - 08/20/12 10:38 PM

The genetic basis of a domestication trait in the chicken: mapping quantitative trait loci for plumage colour.
by Md. Nazmul Huq (Masters Thesis)
LiTH-IFM- Ex--12/2626--SE, Linköping University (2012).
Full Paper

This was a QTL mapping study on "red" plumage & "metallic green sheen" plumage, from crossing a Red Jungle Fowl male with 3 White Leghorn hens. 572 of the F8 were analysed.

Table 2:
Trait||| Chromosome
Red ....||| 2 (165 cM)
Red ....||| 2 (540 cM)
Red ....||| 11 (24 cM)
Red ....||| 14 (203 cM)
Green ..||| 2 (399 cM)
Green ..||| 3 (247 cM)
* In brackets - position on the chromosome.
* No sex chromosomes were sequenced.
Posted by: Michel

Re: Journal papers online - reference list - 08/22/12 05:38 PM

Originally Posted By: KazJaps
The genetic basis of a domestication trait in the chicken: mapping quantitative trait loci for plumage colour.
by Md. Nazmul Huq (Masters Thesis)
LiTH-IFM- Ex--12/2626--SE, Linköping University (2012).

[...]

This was a QTL mapping study on "red" plumage & "metallic green sheen" plumage, from crossing a Red Jungle Fowl male with 3 White Leghorn hens. 572 of the F8 were analysed.

[...]




Thanks for the link, KazJaps, I found it an interesting read, although at the moment it seems to raise more questions for me than answers. Can't seem to get my head around it. I hope someone will be able to shed some more light on this topic for me.

The first question I have is why someone, the researcher in question, would use a dominant white Leghorn strain to research 'red'? (I'm ignoring the green sheen results completely since n=9.)

Which 'red' are they actually testing here? Am I safe to assume that part of what is meassured here is of what is generally referred to as autosomal red? Does this paper tell us that stating autosomal red as a single gene is oversimplifying and is actually incorrect, and that autosomal red is a QTL, of which a couple of them are found here (a copuple from RJF and a couple found in White Leghorns in Sweden Universities)?

In the abstract it says on line 15:
Quote:
[...]The identified four QTLs together can explain approximately 36% of the phenotypic variance in this trait.[...]
Meaning the 4 QTLs concerning 'red'.
Would I be right to translate 'phenotypic variance in this trait' into pheomelanin expression? But excluding sex linked gold as Z was not included in the marker regions for the QTLs? 36% of what?

This leaves me wondering what 'red' they are meassuring in this study...
Is all the pheomelanin 'leaking' through an I/I or I/i+ specimen autosomal red? Or could there be s+ in there aswell? Because they do meassure the intensity of all? 'red' in Photoshop, but leave one of the suppliers (s+) out of the equation when setting marker regions? And not all F8 offspring seem to have been I/I or I/i+, so they must have been showing sex linked pheomelanin, right?

Or am I missing the point here? whistle

Posted by: Wieslaw

Re: Journal papers online - reference list - 11/11/12 04:28 PM

Michel , thank you for expressing my thoughts, I could not put it better. Perhaps they did not know themselves.

For those who are interested in history of the 'big' people and their discoveries, here is an interesting reading on Serebrovsky

http://www.summagallicana.it/Volume3/Serebrovsky.pdf

Posted by: KazJaps

Re: Journal papers online - reference list - 12/02/12 07:53 PM

Some papers I've missed adding previously...

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

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

Embryonic Infection with the Endogenous Avian Leukosis Virus
Rous-Associated Virus-O Alters Responses to Exogenous Avian
Leukosis Virus Infection.

L. B. CRITTENDEN, S. McMAHON, M. S. HALPERN, AND A. M. FADLY
JOURNAL OF VIROLOGY, Mar. 1987, p. 722-725
Full Paper - pdf

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

-----------------------
Studies on Dominance and Pleiotropy Using Segregating Inbred Lines of Fowl.
Smith LT, Nordskog AW.
Genetics. 1963 Sep;48(9):1141-52.
Poultry Science Department, Iowa State University, Ames, Iowa.
Full paper-pdf
Posted by: KazJaps

Re: Journal papers online - reference list - 12/10/12 04:46 AM

A new one...

Inheritance and developmental pattern of cerebral hernia in the crested polish chicken.
Yoshimura K, Kinoshita K, Mizutani M, Matsuda Y, Saito N.
J Exp Zool B Mol Dev Evol. 2012 Dec;318(8):613-20. doi: 10.1002/jez.b.22464. Epub 2012 Aug 21.
Abstract

Quote:
The present study is aimed to analyze the inheritance and ontogenic process of cerebral hernia in the crested Polish chicken. Firstly, we constructed the resource family with the Polish chicken and PNP inbred strain. Genetic analysis of this family revealed that cerebral hernia is controlled by a single autosomal recessive gene and is closely associated with crest formation.
Posted by: KazJaps

Re: Journal papers online - reference list - 12/16/12 06:28 PM

The following about Na - Naked Neck (BMP12/GDF7, Chromosome 3)

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
Full Paper

Kira Heller. (2011) How Bird Necks Get Naked. PLoS Biol. 2011 March; 9(3): e1001029.
Full Paper

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.
Full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 12/16/12 07:49 PM

FMO3 gene on Chromosome 8:

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.
abstract

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 Full Paper
Posted by: Black Feather

Re: Journal papers online - reference list - 12/27/12 07:52 AM

Scaleless mutation in FGF20 :

Wells KL, Hadad Y, Ben-Avraham D, Hillel J, Cahaner A, Headon DJ. Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of featherless chickens. BMC Genomics. 13:257, 2012 Full paper


Araucana traits (Ear-tufts and rumpless) :

Noorai RE, Freese NH, Wright LM, Chapman SC, Clark LA. Genome-wide association mapping and identification of candidate genes for the rumpless and ear-tufted traits of the Araucana chicken. PLoS One. 7:e40974, 2012 Full paper


Molecular mechanism of pea-comb :

Boije H, Harun-Or-Rashid M, Lee YJ, Imsland F, Bruneau N, Vieaud A, Gourichon D, Tixier-Boichard M, Bed'hom B, Andersson L, Hallböök F. Sonic Hedgehog-signalling patterns the developing chicken comb as revealed by exploration of the Pea-comb mutation. PLoS One. 7:e50890, 2012 Full paper


Mutation for Frizzle in KRT75 :

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. The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis. PLoS Genet. 8:e1002748, 2012 Full paper

Posted by: Wieslaw

Re: Journal papers online - reference list - 02/01/13 06:57 PM

Mutation for blue egg

abstract:

http://www.ncbi.nlm.nih.gov/pubmed/23359636
Posted by: Henk69

Re: Journal papers online - reference list - 02/02/13 01:41 AM

The picture suggests incomplete dominance...
Posted by: KazJaps

Re: Journal papers online - reference list - 02/14/13 09:08 AM

Some more historical poultry books from archive.org :

The China fowl : Shanghae, Cochin, and "Brahma." (1874), by Burnham, George. P.
download page

The Wyandotte fowl; its general characteristics and advice on rearing, mating and breeding with a chapter on judging of exhibition birds (1884), by Albany, Ferris Pub. Co.
download page

The bantam fowl; a description of all standard breeds and varieties of bantams, and of new breeds that are becoming popular .. (1899), by McGrew, Thomas Fletcher
download page

The standard-bred Cornish fowl; a practical treatise on their standard requirements--mating and breeding--rearing--housing--training and conditioning for exhibition--judging and utility values--genetics and mendelism outlined, etc. (1922), by Bohrer, Fred H
download page

A turken talk; the origin and value of the new Spencer turken fowl (1922), by Spencer, Z. T
download page
*A peculiar one. The author outlines that the "Spencer" turken (phenotype naked neck) was developed from a cross between a turkey & chicken.

Fowls; a treatise on the principal breeds. With which is repr. the 3rd ed. of The Dorking fowl (1860), by John Baily.
download page

A practical guide to the breeding, feeding, rearing & general management, for domestic use and exhibition, of the Houdan fowl (1874), by Lee, Charles.
download page

Fowls for the times. The history and development of the Orpington fowl (1896), by William Cook
download page
*Discusses what breeds went into the making of Black, White & Buff Orpingtons.

The Brahma fowl (1870), by Lewis Wright.
download page

The Minorca fowl (1893), by Harrison T.H.
download page
Posted by: KazJaps

Re: Journal papers online - reference list - 05/18/13 09:14 AM

Preliminary Studies on Genetic Diversity of Selected Polish Local Chicken Varieties.
ANTOS, P., ANDRES, K., KAPKOWSKA, E.
Journal of Central European Agriculture, 2013, 14(1), p.11-22
Full paper


Topology of Feather Melanocyte Progenitor Niche Allows Complex Pigment Patterns to Emerge.
S. J. Lin, J. Foley, T. X. Jiang, C. Y. Yeh, P. Wu, A. Foley, C. M. Yen, Y. C. Huang, H. C. Cheng, C. F. Chen, B. Reeder, S. H. Jee, R. B. Widelitz, C. M. Chuong.
Science DOI: 10.1126/science.1230374. Published Online April 25 2013
Abstract
Full Paper

The biology of feather follicles.
Mingke Yu, Zhicao Yue, Ping Wu, Da-Yu Wu, Julie-Ann Mayer, Marcus Medina, Randall B Widelitz, Ting-Xin Jiang and Cheng-Ming Chuong
Int J Dev Biol. 2004;48(2-3):181-91.
Full -Pdf download link


The pigment cell system in the Light Sussex fowl.
COHEN J.
J Embryol Exp Morphol. 1959 Sep;7:361-74.
full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 08/20/13 09:28 PM

*Another new research paper on blue eggshell:

Wragg D, Mwacharo JM, Alcalde JA, Wang C, Han J-L, et al. (2013)
Endogenous Retrovirus EAV-HP Linked to Blue Egg Phenotype in Mapuche Fowl.

PLoS ONE 8(8): e71393. doi:10.1371/journal.pone.0071393
Full Paper
Posted by: KazJaps

Re: Journal papers online - reference list - 09/08/13 05:00 AM

Okumura, Y., Ohtake, T., Uemoto, Y., Sato, S., Sato, S. and Kobayashi, E. (2013), Fine mapping of the chicken congenital loco locus on chromosome 12.
Animal Genetics. doi: 10.1111/age.12065
Abstract

Knowlton, Frank L. (1929) Congenital loco in chicks
Oregon Agri. Exp. Station Bulletin, Volume 253
Full Paper
Posted by: KazJaps

Re: Journal papers online - reference list - 02/07/14 02:41 AM

New 2014 paper....

Mottled mo has been sequenced on EDNRB2 locus, plus a new white mutation discovered mo^w (found in White Minohiki long-tail fowl).

Kinoshita K, Akiyama T, Mizutani M, Shinomiya A, Ishikawa A, et al. (2014) Endothelin Receptor B2 (EDNRB2) Is Responsible for the Tyrosinase-Independent Recessive White (mow) and Mottled (mo) Plumage Phenotypes in the Chicken. PLoS ONE 9(1): e86361. doi:10.1371/journal.pone.0086361
Full Paper

* EDNRB2 (mo) locus is found on Chromosome 4.
* mo/mo^w F1 (mottled x white) phenotype is very similar to Exchequer pattern.
Posted by: Henk69

Re: Journal papers online - reference list - 02/07/14 07:22 AM

How common is that mo^w?
Exchequer explained? wink
Posted by: KazJaps

Re: Journal papers online - reference list - 02/07/14 05:46 PM

mow white is not that common, mainly in white Japanese long-tail fowl. So it is in Asia, but would also be found in the USA in white long-tail stock.

Unfortunately Exchequer Leghorns weren't DNA tested. But mow White crossed with mo Black Mottled produced typical Exchequer phenotype.
------------------------
Here is Somes', 1980 mo paper:

RALPH G. SOMES, JR.
The Mottling Gene, the Basis of Six Plumage Color Patterns in the Domestic Fowl.
Poultry Science (1980) 59 (7): 1370-1374 doi:10.3382/ps.0591370
Full Paper
Posted by: Piet

Re: Journal papers online - reference list - 02/11/14 04:00 AM

Exchequer x Exchequer does not give white so this can't be the explanation....
Posted by: Henk69

Re: Journal papers online - reference list - 02/11/14 04:05 AM

It does not give white, but maybe whiter than average? wink
Posted by: KazJaps

Re: Journal papers online - reference list - 02/11/14 10:19 AM

No, but it means that mow and mo were alleles of the same locus. Both alleles were recessive to wild-type Mo+, but when crossed together (heterozygous mow/mo) they produced an intermediate phenotype (very similar to Exchequer). Ie, mow and mo are incomplete recessives to each other.

Reminds me of dogs & white spotting alleles.

Need to wait until an Exchequer phenotype is DNA tested.
Posted by: KazJaps

Re: Journal papers online - reference list - 02/26/14 06:57 AM

Pigeons:

Domyan et al. (2014) Epistatic and Combinatorial Effects of Pigmentary Gene Mutations in the Domestic Pigeon.
Current Biology, 2014; DOI: 10.1016/j.cub.2014.01.020
Full Paper

*Mutations found on SOX10 (e recessive red), SLC45A2 (d dilute) & TYRP1 (B^A Ash Red, b Brown).
GENE---||Chickens ||Pigeons .||
Slc45a2..|| S locus. || d locus ||
Tyrp1....|| choc.....|| B^A, b ||
Sox10....|| Db locus || e locus ||
,
-----------------

Mainly MC1R (E locus in chickens) papers:

Pigeons:

Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene (MC1R).
Derelle R, Kondrashov FA, Arkhipov VY, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E.
BMC Res Notes. 2013 Aug 5;6(1):310.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3750627/pdf/1756-0500-6-310.pdf

Guernsey MW, Ritscher L, Miller MA, Smith DA, Schöneberg T, et al. (2013) A Val85Met Mutation in Melanocortin-1 Receptor Is Associated with Reductions in Eumelanic Pigmentation and Cell Surface Expression in Domestic Rock Pigeons (Columba livia). PLoS ONE 8(8): e74475. doi:10.1371/journal.pone.0074475
Full Paper

------------------------------

Evolutionarily conserved telomeric location of BBC1 and MC1R on a microchromosome questions the identity of MC1R and a pigmentation locus on chromosome 1 in chicken.
Alexei Sazanov, Julio Masabanda, Dagmar Ewald, Sakae Takeuchi, Micheale Tixier-Boichard, Johannes Buitkamp & Ruedi Fries
Chromosome Research Vol 6 1998 651-654.
http://cdn.scipeople.com/materials/7733/BBC1_MCR1.pdf

-----------------------
Study on Association of Melanocortin 1-Receptor (MC1R ) Mutations with Melanin Trait in Chinese Domestic Chickens.
Z.Q. Yang,Z.R. Zhang,M. Xu,Q. Zhu
Research Journal of Animal Sciences. 2(2): 45-49 2008
http://docsdrive.com/pdfs/medwelljournals/rjnasci/2008/45-49.pdf

-----------------------
Investigation of MC1R SNPs and Their Relationships with Plumage Colors in Korean Native Chicken
Hoque, M.R.; Jin, S.; Heo, K.N.; Kang, B.S.; Jo, C.; Lee, J.H.
Asian-Australasian Journal of Animal Sciences: Volume 26, Issue ,5, 2013, pp.625-629
Full Paper

Genetic Variations of Chicken MC1R Gene and Associations with Feather Color of Korean Native Chicken (KNC) ‘Woorimatdag
Park et al.
Korean Journal of Poultry Science: Volume 40, Issue ,2, 2013, pp.139-145
Abstract & photo descriptions in English
----------------------------
Genome-wide Association Study of Chicken Plumage Pigmentation
Park et al.
Asian Australas. J. Anim. Sci. Vol. 26, No. 11 : 1523-1528 November 2013
http://www.ajas.info/Editor/manuscript/upload/26-188.pdf
Posted by: KazJaps

Re: Journal papers online - reference list - 02/26/14 07:04 AM

The following researchers were looking at the SOBP gene as a candidate for hookless - silky feathers.

Chicken sine oculis binding protein homolog (sobp), a novel gene that may regulate feather development
W. Liu and N. Li
Poultry Science (2012) 91 (8): 1950-1955 doi:10.3382/ps.2011-02114
Full Paper

* SOBP is on Chromosome 3.
* Dorshorst et al 2010 thought that hookless might be on Chromosome 3 too.
http://jhered.oxfordjournals.org/content/early/2010/01/11/jhered.esp120.full.pdf
Posted by: Redcap

Re: Journal papers online - reference list - 03/22/14 05:08 PM

A multiple allelic series affecting feather color in the domestic fowl.
Smyth, J. R., Jr., and B. B. Bohren,
Poultry Sci. 1949. 28: 782. [Abstract]

Crosses between chickens having extended black, New Hampshire (Columbian), Dark Cornish, and Dark Brown Leghorn color patterns showed that each pattern differed from the others by a single autosomal gene. Crosses in which three or four of these characters were involved simultaneously also segregated in a manner indicating the existence of an allelic series consisting of three and possibly four genes. Black (E) is dominant to the black-red (ep) pattern as in the Cornish and Brown Leghorn and is incompletely dominant to Columbian (e).
The Columbian pattern (e) is almost completely dominant to Cornish but is less completely dominant to the Brown Leghorn pattern. The data are insufficient at this time to determine the relationship of the Cornish and Brown Leghorn patterns. The data suggest that these patterns are produced by two alleles at the E locus thus giving a four allele series. It is possible, however, that further investigation may show these two patterns to be produced by a single allele at this locus and that the differences between them is caused by genes modifying the basic black-red pattern and resulting in a three allele series.
Posted by: KazJaps

Re: Journal papers online - reference list - 01/06/15 12:03 AM

* Getting close to identifying Id locus...

A genome-wide association study identifies novel single nucleotide polymorphisms associated with dermal shank pigmentation in chickens.
Li G, Li D, Yang N, Qu L, Hou Z, Zheng J, Xu G, Chen S.
Poult Sci. 2014 Dec;93(12):2983-7. doi: 10.3382/ps.2014-04164. Epub 2014 Sep 26.
Abstract

----------------------------------

Forgot to add this Spanish E locus (MC1R) paper earlier:

Association between polymorphism in the melanocortin 1 receptor gene and E locus plumage color phenotype.
Dávila SG, Gil MG, Resino-Talaván P, Campo JL.
Poult Sci. 2014 May;93(5):1089-96. doi: 10.3382/ps.2013-03611.
abstract

------------------------
Flink LG, et al. Establishing the validity of domestication genes using DNA from ancient chickens.
Proc Natl Acad Sci USA. 2014;111:6184–6189.
Full Paper-html
pdf:
http://www.pnas.org/content/111/17/6184.full.pdf

*Includes research on BCDO2 - yellow skin allele in ancient European chickens. Although some ancient specimens were heterozygous for yellow skin allele, the researchers believed that yellow skin only became widespread in the last 500 years in European chickens.
Article:
http://www.sciencedaily.com/releases/2014/04/140418141123.htm
Posted by: KazJaps

Re: Journal papers online - reference list - 01/06/15 12:13 AM

Hookless - silky feather mutation found on PDSS2 gene....

Feng, C., Gao, Y., Dorshorst, B., Song, C., Gu, X., Li, Q., … Li, N. (2014).
A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens.
PLoS Genetics, 10(8), e1004576. doi:10.1371/journal.pgen.1004576
Full paper
Posted by: KazJaps

Re: Journal papers online - reference list - 01/06/15 04:34 AM


Identification of genes related to beak deformity of chickens using digital gene expression profiling.
Bai H, Zhu J, Sun Y, Liu R, Liu N, Li D, Wen J, Chen J.
PLoS One. 2014 Sep 8;9(9):e107050. doi: 10.1371/journal.pone.0107050. eCollection 2014.
Full Paper
Posted by: Redcap

Re: Journal papers online - reference list - 01/07/15 06:17 PM

Originally Posted By: Redcap
A multiple allelic series affecting feather color in the domestic fowl.
Smyth, J. R., Jr., and B. B. Bohren,
Poultry Sci. 1949. 28: 782. [Abstract]

Crosses between chickens having extended black, New Hampshire (Columbian), Dark Cornish, and Dark Brown Leghorn color patterns showed that each pattern differed from the others by a single autosomal gene. Crosses in which three or four of these characters were involved simultaneously also segregated in a manner indicating the existence of an allelic series consisting of three and possibly four genes. Black (E) is dominant to the black-red (ep) pattern as in the Cornish and Brown Leghorn and is incompletely dominant to Columbian (e).
The Columbian pattern (e) is almost completely dominant to Cornish but is less completely dominant to the Brown Leghorn pattern. The data are insufficient at this time to determine the relationship of the Cornish and Brown Leghorn patterns. The data suggest that these patterns are produced by two alleles at the E locus thus giving a four allele series. It is possible, however, that further investigation may show these two patterns to be produced by a single allele at this locus and that the differences between them is caused by genes modifying the basic black-red pattern and resulting in a three allele series.

http://documents.kippenjungle.nl/#post26
Posted by: KazJaps

Re: Journal papers online - reference list - 01/14/15 04:23 PM

A study of the genetic control of black-red pigment patterns in the fowl
by Brumbaugh, 1963
Iowa State University
http://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=3373&context=rtd

Citation:
Brumbaugh, John Albert, "A study of the genetic control of black-red pigment patterns in the fowl " (1963). Retrospective Theses and Dissertations. Paper 2374.

* Includes Buff Minorca research: Di, Cb, Mh etc.
Posted by: KazJaps

Re: Journal papers online - reference list - 01/30/15 03:32 PM

Brumbaugh, John Albert, "A study of the genetic control of black-red pigment patterns in the fowl" (1963).
Retrospective Theses and Dissertations. Paper 2374.

The following link has all the above paper's colour photos, listed as supplemental files (for download)
http://lib.dr.iastate.edu/rtd/2374

The scanning quality is great!

Thank you kindly to the Digital Repository team at Iowa State University! smile
Posted by: Redcap

Re: Journal papers online - reference list - 01/31/15 11:29 AM

Originally Posted By: KazJaps
Brumbaugh, John Albert, "A study of the genetic control of black-red pigment patterns in the fowl" (1963).
Retrospective Theses and Dissertations. Paper 2374.

The following link has all the above paper's colour photos, listed as supplemental files (for download)
http://lib.dr.iastate.edu/rtd/2374

The scanning quality is great!

Thank you kindly to the Digital Repository team at Iowa State University! smile

Color pictures are integrated now
http://documents.kippenjungle.nl/#post27
Better text resolution with 9 MB
http://documents.kippenjungle.nl/#post28
I can offer a 35 MB and 18 MB version aswell
Posted by: Henk69

Re: Journal papers online - reference list - 02/01/15 02:13 AM

Good work team!
Posted by: SilverSilkie

Re: Journal papers online - reference list - 02/23/15 03:17 AM

Originally Posted By: Henk69
It does not give white, but maybe whiter than average? wink


https://www.youtube.com/watch?v=JgIXsVnfJ9o
Posted by: Redcap

Re: Journal papers online - reference list - 04/14/15 12:17 PM

A nanostructural basis for gloss of avian eggshells
Branislav Igic , Daphne Fecheyr-Lippens , Ming Xiao , Andrew Chan , Daniel Hanley , Patricia R. L. Brennan , Tomas Grim , Geoffrey I. N. Waterhouse , Mark E. Hauber , Matthew D. Shawkey
DOI: 10.1098/rsif.2014.1210 Published 10 December 2014

Abstract

The role of pigments in generating the colour and maculation of birds' eggs is well characterized, whereas the effects of the eggshell's nanostructure on the visual appearance of eggs are little studied. Here, we examined the nanostructural basis of glossiness of tinamou eggs. Tinamou eggs are well known for their glossy appearance, but the underlying mechanism responsible for this optical effect is unclear. Using experimental manipulations in conjunction with angle-resolved spectrophotometry, scanning electron microscopy, atomic force microscopy and chemical analyses, we show that the glossy appearance of tinamou eggshells is produced by an extremely smooth cuticle, composed of calcium carbonate, calcium phosphate and, potentially, organic compounds such as proteins and pigments. Optical calculations corroborate surface smoothness as the main factor producing gloss. Furthermore, we reveal the presence of weak iridescence on eggs of the great tinamou (Tinamus major), an optical effect never previously documented for bird eggs. These data highlight the need for further exploration into the nanostructural mechanisms for the production of colour and other optical effects of avian eggshells.

http://rsif.royalsocietypublishing.org/content/12/103/20141210
Posted by: Wieslaw

Re: Journal papers online - reference list - 06/04/15 04:19 PM

Runting and Stunting Syndrome (full text)

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127342
Posted by: KazJaps

Re: Journal papers online - reference list - 06/21/15 05:55 PM

Archived Poultry Science journal full papers are available with free access at the moment (this might be temporary).
http://ps.oxfordjournals.org/content/by/year

-----------------------------
Eg, some for those interested in autosexing:

MacArthur, J. W., and J. J. Macllraith, 1946. Color sexing of day-old Brown Leghorns. Poultry Sci. 25: 180-183.

R. George Jaap Sex Identification in Baby Chicks of “Red” Varieties. Poultry Science (1946) 25 (2): 185-186

Jerome, F. N., 1939. Auto-sex linkage in the Barred Plymouth Rock. Poultry Sci. 18: 437-440.

Ralph G. Somes, Jr. Buff Brahma, an Autosexing Breed of Chicken. Poultry Science (1971) 50 (6): 1798-1801 doi:10.3382/ps.0501798
Full Paper

------------------
To find each paper on the Poultry Science archives website, click on the year (eg 1946), then click the month with the relevant page range numbers (eg for 180-183, select "March 1946; 25 (2) : 99 - 191" link), then the relevant paper.
Posted by: KazJaps

Re: Journal papers online - reference list - 07/23/15 04:57 PM

Just updating this list (posted recently in other threads)...

New 2015 paper on Duplex comb:

A Genomic Duplication is Associated with Ectopic Eomesodermin Expression in the Embryonic Chicken Comb and Two Duplex-comb Phenotypes
Ben Dorshorst, Mohammad Harun-Or-Rashid, Alireza Jian Bagherpoor, Carl-Johan Rubin, Chris Ashwell, David Gourichon, Michèle Tixier-Boichard, Finn Hallböök, Leif Andersson
PLoS Genet. 2015 March; 11(3): e1004947. Published online 2015 March 19. doi: 10.1371/journal.pgen.1004947
Full Paper

-------------------------------------------
Another paper on chicken combs:

Morphological Mutations: Lessons from the Cockscomb
by Denis Headon
PLoS Genet. 2015 Mar; 11(3): e1004979.
Full Paper

-------------------------------------------
Another 2015 research paper on Pea combs:

Quantitative Effect of a CNV on a Morphological Trait in Chickens.
Moro et al.
PLoS One. 2015; 10(3): e0118706.
Full Paper

-----------------------------------------

The identification of loci for polydactyly in chickens using a genome-wide association study.
Sheng X, Chen Y, Jia Y, Qi X, Feng Y, Huang Z, Guo Y.
Gene. 2015 Sep 1;568(2):176-80. doi: 10.1016/j.gene.2015.05.049. Epub 2015 May 21.
Abstract
Posted by: KazJaps

Re: Journal papers online - reference list - 07/23/15 08:41 PM

Other 2015 papers:

Molecular phylogenetic analysis of Chinese indigenous blue-shelled chickens inferred from whole genomic region of the SLCO1B3 gene.
Dalirsefat SB, Dong X, Deng X.
Poult Sci. 2015 Aug 1;94(8):1776-1786. Epub 2015 Jun 11.
Full Paper

-------------------------------
Mort, R. L., Jackson, I. J., & Patton, E. E. (2015). The melanocyte lineage in development and disease. Development (Cambridge, England), 142(4), 620–632. doi:10.1242/dev.106567
Full Paper

-----------------------------------------------------

Abebe, A. S., Mikko, S., & Johansson, A. M. (2015). Genetic Diversity of Five Local Swedish Chicken Breeds Detected by Microsatellite Markers. PLoS ONE, 10(4), e0120580. doi:10.1371/journal.pone.0120580
Full Paper

Johansson, A. M., & Nelson, R. M. (2015). Characterization of genetic diversity and gene mapping in two Swedish local chicken breeds. Frontiers in Genetics, 6, 44. doi:10.3389/fgene.2015.00044
Full Paper

*Note - in the last Swedish study they researched Swedish local chicken breeds Bohuslän-Dals svarthöna (with black plumage) and Hedemorahöna. Both breed populations have Fm segregating, the same Fm sequence as in Silkies (less Fm individuals found in the Hedemorahöna). Fm is on Chromosome 20, & Fm was correlated to the darkest combs, fm+ to red comb. But they also found comb colour variation due to modifier(s) on Chromosome 21 (this not E locus - Chr. 11, nor mo Chr. 4, etc).

They cite the following 2013 paper (good on leg colour genetics):
Siwek, M., Wragg, D., Slawinska, A., Malek, M., Hanotte, O., & Mwacharo, J. (2013). Insights into the genetic history of Green-legged Partridgelike fowl: mtDNA and genome-wide SNP analysis. Animal Genetics, 44(5), 522–532. doi:10.1111/age.12046
Full Paper


Plus they cite the following 2014 paper, full version now available online:

A genome-wide association study identifies novel single nucleotide polymorphisms associated with dermal shank pigmentation in chickens.
Li G, Li D, Yang N, Qu L, Hou Z, Zheng J, Xu G, Chen S.
Poult Sci. 2014 Dec;93(12):2983-7. doi: 10.3382/ps.2014-04164. Epub 2014 Sep 26.
Full Paper

The following another 2014 paper on Swedish chickens:

Englund, T., Strömstedt, L. and Johansson, A. M. (2014), Relatedness and diversity of nine Swedish local chicken breeds as indicated by the mtDNA D-loop. Hereditas, 151: 229–233. doi: 10.1111/hrd2.00064
Full Paper
Posted by: KazJaps

Re: Journal papers online - reference list - 07/28/15 09:35 PM

Punnett's 1923 book "Heredity in Poultry" (with colour plates):
Download page

The link is of an online page viewer but on the bottom left is a download button where you can select to download the whole pdf.

-------------------------------

Eggshell colour genetics:

Inheritance of Tinted Eggshell Colors in White-Shell Stocks
R. WEI, J. J. BITGOOD, and M. R. DENTINE
Poultry Science (1992) 71 (3): 406-418 doi:10.3382/ps.0710406
Full Paper

----------------------

The Effect of a Protoporphyrin Mutant on Some Economic Traits of the Chicken
R. N. SHOFFNER, R. SHUMAN, J. S. OTIS, J. J. BITGOOD, V. GARWOOD, and P. LOWE
Poultry Science (1982) 61 (5): 817-820 doi:10.3382/ps.0610817
Full Paper
---------------------------------

Genetic Studies in Poultry. II. Inheritance of Egg-Colour and Broodiness.
R.C. Punnett and Major P.G. Bailey
Journal of Genetics. Vol. 10, No. 4. 277-292. (December, 1920)
full paper

*posted previously
------------------

Egg Shell Color in Crosses Between White- and Brown-Egg Breeds
G. O. Hall
Poultry Science (1944) 23 (4): 259-265 doi:10.3382/ps.0230259
Full Paper
Posted by: Robbie

Re: Journal papers online - reference list - 07/29/15 07:01 PM

Thanks for posting these pages of links!! smile Very useful. I can't believe I've missed this thread, there are quite a few papers in here that I can't wait to read.
Posted by: Berend

Re: Journal papers online - reference list - 09/15/15 04:58 AM

Genetic diversity of Hungarian Indigenous Chicken Breeds
by Nóra Bodzsár 2012
Szent István University

http://www.szie.hu/file/tti/archivum/Bodzsar_Nora_thezis.pdf
Posted by: Redcap

Re: Journal papers online - reference list - 09/22/15 05:49 PM

On Monday I found an interesting sex-linked mutation in Stevens, L. (1991). Genetics and Evolution of the Domestic Fowl. Cambridge University Press.
https://books.google.de/books?id=S-DXqQ9...p;q&f=false
https://books.google.de/books?id=S-DXqQ9UOmAC&pg=PA280#v=onepage&q&f=false


Elkin RG, Bauer R, Schneider WJ. (2012). The restricted ovulator chicken strain: an oviparous vertebrate model of reproductive dysfunction caused by a gene defect affecting an oocyte-specific receptor.Anim Reprod Sci. 2012 Dec;136(1-2):1-13.

Abstract

Quote:
A unique non-laying strain of chickens with heritable hyperlipidemia and aortic atherosclerosis was first described in 1974. Subsequent work established that the phenotype results from a naturally occurring point mutation in the gene specifying the very low density lipoprotein (VLDL) receptor, a 95-kDa membrane protein which normally mediates the massive uptake of the main circulating hepatically-synthesized yolk precursors, VLDL and vitellogenin. As a result, hens of the mutant strain termed "restricted ovulator" (R/O) have approximately 5-fold elevations in circulating cholesterol and triglyceride concentrations compared with normal layers, and hepatic lipogenesis and cholesterogenesis are markedly attenuated due to feedback inhibition. R/O hens also exhibit hyperestrogenemia, hypoprogesteronemia, elevated circulating gonadotropins, and up-regulated pituitary progesterone receptor mRNA and isoforms. The ovaries of R/O hens are abnormal in that they lack a follicular hierarchy and contain many small preovulatory follicles of various colors, shapes, and sizes. However, since R/O hens occasionally lay eggs, it is possible that endocytic receptors other than the VLDL receptor may be able to facilitate oocyte growth and/or that yolk precursor uptake can occur via a nonspecific bulk process. A mammalian model of impaired fecundity with abnormal lipoprotein metabolism also has been described, but different mechanisms are likely responsible for its reproductive dysfunction. Nevertheless, as our understanding of the molecular physiology and biochemistry of avian oocyte growth continues to expand, in part due to studies of the R/O model, new analogies may emerge between avian and mammalian systems, which ultimately could help to answer important questions in reproductive biology.


Plus excerpt of the introduction
Quote:
A unique strain of hyperlipidemic female White Leghorn chickens that failed to lay eggs was initially discovered at DeKalb Agricultural Research, Inc. (DeKalb,IL)in the early 1970s. All of the hens were the daughters of a single rooster thought to carry a mutation responsible for the non-laying condition. The existence of this non-laying strain was first reported in the literature by Ho et al.(1974). As compared with wild-type (WT) hens, non-laying hens had approximately 5-fold higher serum levels of cholesterol and triglycerides, a slower daily turnover of cholesterol, attenuated endogenous cholesterol biosynthesis, developed aortic atherosclerosis, and
exhibited abnormal ovarian morphology (Ho et al.,1974).In each of two separate matings of the original mutant DeKalb rooster with WT females, approximately one-half of the offspring hens failed to lay eggs upon reaching sexual maturity. Thus, the condition was heritable and it appeared that the rooster simply carried a mutation causing the abnormal female phenotype since his reproductive functions, secondary sex characteristics, and serum lipid levels were normal (discussed in Section 3). Hence, Ho et al. (1974) referred to the original rooster and those of subsequent generations as “carrier roosters”. Jones et al. (1975) coined the term “restricted ovulator” (R/O) to describe females possessing the mutant gene. Two years later, McGibbon (1977) provided evidence that the sterile condition associated with spontaneous follicular involution was sex-linked and resulted from a single gene defect at a locus (ro) on the sex chromosome Z.


C. R. GRAU and T. E. ROUDYBUSH & W. H. McGIBBON (1979). Mineral Composition of Yolk Fractions and Whole Yolk from Eggs of Restricted Ovulator Hens. Poultry Science (1979), 58 (5): 1143-1148.

Abstract

Quote:
Yolks of eggs laid by hens with the sex-linked restricted ovulator gene (ro) contained less iron and copper and more sodium and potassium than control yolks. Phosphorus levels were not different. The granule fraction of RO yolks contained less iron and manganese than controls; the supernatant contained more sodium, potassium, magnesium, zinc, and iron than controls.

It is suggested that a relationship exists between the effects of the ro gene on iron metabolism and the known hyperlipemia of RO hens.

The yolk ring structure of laid RO eggs was completely disrupted, but rings were found in follicular yolk.
Posted by: Redcap

Re: Journal papers online - reference list - 10/04/15 06:05 AM

Domestication/Taming has been proven as a pleiotropic effect to body size and laying performance.

B. Agnvall, A. Ali, S. Olby and P. Jensen (2014). Red Junglefowl (Gallus gallus) selected for low fear of humans are larger, more dominant and produce larger offspring. animal, 8, pp 1498-1505.
http://liu.diva-portal.org/smash/get/diva2:739276/FULLTEXT01.pdf

B Agnvall, R Katajamaa, J Altimiras & P Jensen. Is domestication driven by reduced fear of humans? Boldness, metabolism and serotonin levels in divergently selected red junglefowl (Gallus gallus). Biology Letters, September 2015
http://rsbl.royalsocietypublishing.org/content/11/9/20150509.long
https://www.liu.se/forskning/forskningsnyheter/1.649515?l=en
Abstract only - so far.
Full text after September 2016
Posted by: KazJaps

Re: Journal papers online - reference list - 10/04/15 08:34 PM

Karlsson A-C et al.(2015)
The Effect of a Mutation in the Thyroid Stimulating Hormone Receptor (TSHR) on Development, Behaviour and TH Levels in Domesticated Chickens.
PLoS ONE 10(6): e0129040
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460094/pdf/pone.0129040.pdf

----------------------------
Gheyas et al. 2015
Functional classification of 15 million SNPs detected from diverse chicken populations.
DNA Res (2015) 22 (3): 205-217.
http://dnaresearch.oxfordjournals.org/content/22/3/205.full.pdf
Quote:
....goal to predict variants with potential functional implications (pfVars) from both coding and non-coding regions.

*cites the below Flink et al. paper & further researches the TSHR and BCD02 (yellow skin) genes, plus many others.
-----------------------------
Flink et al. 2014
Establishing the validity of domestication genes using DNA from ancient chickens
Proc Natl Acad Sci U S A. 2014 Apr 29; 111(17): 6184–6189.
http://www.pnas.org/content/111/17/6184.full.pdf?with-ds=yes

Quote:
We extracted DNA from 80 ancient chickens excavated from 12 European archaeological sites, dated from &#8764;280 B.C. to the 18th century A.D. We targeted three unlinked genetic loci: the mitochondrial control region, a gene associated with yellow skin color (&#946;-carotene dioxygenase 2), and a putative domestication gene thought to be linked to photoperiod and reproduction (thyroid-stimulating hormone receptor, TSHR). Our results reveal significant variability in both nuclear genes, suggesting that the commonality of yellow skin in Western breeds and the near fixation of TSHR in all modern chickens took place only in the past 500 y.


--------------------------------
Plus your earlier ref. RedCap:

Van Rooijen, J. (2014). Examples of overlooking common sense solutions: the domestication gene and selection against mortality. Frontiers in Genetics, 5, 266.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124454/pdf/fgene-05-00266.pdf

--------------------------
Forgot to list this one earlier....

The domestic chicken: Causes and consequences of an egg a day.
P. A. Johnson, C. S. Stephens, and J. R. Giles
Poultry Science (April 2015) 94 (4): 816-820
Full Paper

Quote:
growth differentiation factor 9 (GDF9) (Microchromosome 13)
bone morphogenetic factor 15 (BMP15) (Chromosome 4)


----------------------------------------
Posted by: KazJaps

Re: Journal papers online - reference list - 10/04/15 08:46 PM

Natt et al. 2014
Large Sex Differences in Chicken Behavior and Brain Gene Expression Coincide with Few Differences in Promoter DNA-Methylation
PLoS One. 2014; 9(4): e96376.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004567/pdf/pone.0096376.pdf
Posted by: Redcap

Re: Journal papers online - reference list - 10/05/15 04:49 PM

P. MÉRAT, A. BORDAS, G. Coquerelle, L. Durand. GÈNES A EFFET VISIBLE ET COLORATION OU ÉPAISSEUR DES COQUILLES D'OEUFS. Annales de génétique et de sélection
animale, 1970, 2 (3), pp.263-267. <hal-00892399>
HAL Id: hal-00892399
https://hal.archives-ouvertes.fr/hal-00892399
Quote:
SUMMARY
GENES WITH VISIBLE EFFECT AND THICKNESS
OR EXTERNAL PIGMENTATION OF EGGSHELLS
Among 12 loci studied in one population, two, concerned with plumage color, show an association with thickness and external pigmentation of eggshells : Pullets with extended black compared with restricted black plumage (E locus) and pullets with colored (ii) vs non-black plumage (Ii) lay eggs with significantly thicker and more intensely pigmented shells. A similar but less marked tendency seems to be associated, for shell thickness, with two other plumage color loci (C and S).


P. MÉRAT, G. Coquerelle, L. Durand. GÈNES A EFFET VISIBLE : RELATION AVEC LA PONTE, LE POIDS DES OEUFS ET LE POIDS DES POULES ADULTES (1). Annales de
génétique et de sélection animale, 1972, 4 (4), pp.555-560. <hal-00892553>
HAL Id: hal-00892553
https://hal.archives-ouvertes.fr/hal-00892553
Quote:
SUMMARY
GENES WITH VISIBLE EFFECT :
ASSOCIATION WITH EGG LAYING, EGG WEIGHT AND ADULT HEN WEIGHT
Among 1 5 loci studied in one population, one of them, concerning plumage color (C), shows a highly significant association with adult weight of hens and egg weight, white hens (cc) having for these two traits a mean value inferior to colored ones (Cc or CC). The body weight difference appears to be increased in cages vs. on floor, and a parallel result, although not significant, appears for other color genes (I, E, S). For age at first egg and number of eggs laid till about 10 months, no unquestionable effect is associated to the studied loci.


P. MÉRAT, L. Durand. GÈNE Hi ET PRODUCTION D'OEUFS CHEZ LA POULE : INTENSITÈ DE PONTE ET " PAUSES ". Annales de génétique et de sélection animale, 1976, 8 (1),
pp.1-7. <hal-00892709>
HAL Id: hal-00892709
https://hal.archives-ouvertes.fr/hal-00892709
Quote:
SUMMARY
HI GENE AND EGG PRODUCTION IN THE FOWL: LAYING INTENSITY AND « PAUSES »
Additional data (see DURAND and MÉRAT, 1971, MÉRAT and DURAND 1973) are presented concerning quantitative effects associated to the antigenic-determining Hi gene in three experimental populations.
In the « Jouy » Strain, the overall laying percentage was found higher for the Hihi genotype than for the two homozygotes, as for egg number. « Pause » days defined as cessations of laying for more than 2 consecutive days are less for this genotype. On the contrary, laying percentage excluding « pauses » (highly correlated with mean clutch length) does not differ appreciably between Hihi and hihi hens, although it may be somewhat lower for HiHi ones. Results are given in table I (comparison between Hihi and hihi on pairs of full sisters ; comparison between HiHi and Hihi deduced from average performance of phenotypically Hi daughters in families with different expected proportion of the HiHi and Hihi genotypes). Table 2 includes a variance analysis on family means for the second comparison.
In the «L22» and «M55» strains of the Poultry Research Station at Nouzilly, the present results confirm and extend previous ones, showing a less variable age at first egg and higher egg number till the ages 30, 40 and 50 weeks for the Hihi genotype as compared to hihi, and probably also in a comparison with HiHi made the same way as for the « Jouy » population. On the other hand, egg weight at 30 weeks of age does not differ between genotypes (as observed in the « Jouy »
strain) but at 60 weeks genotype Hihi has the lowest average egg weight.
The possibility of a pleiotropic effect at the Hi locus (as opposed to linkage) is not excluded.
A parallel is suggested with results of SCHEINBERG (1971) on the possible effect of the gene on the distribution of an oestrogen-binding protein. Anyway, it is interesting to isolate a gene (or chromosomal region) with a special effect on «pauses», as little knowledge is available on their genetic and even physiological determination.


P. MÉRAT. Effets associées au gène Na (Cou Nu) sur le poids corporel et le poids des oeufs chez des poules " Normales " et " Naines ". Annales de génétique et de séelection animale, 1979, 11
(2), pp.127-131. <hal-00893113>
HAL Id: hal-00893113
https://hal.archives-ouvertes.fr/hal-00893113
Quote:
Summary
Effects associated with the Na (Naked neck) gene on body weight and egg weight in normal-sized and dwarf hens
The heterozygous genotype at locus Na (Naked neck) in the Fowl has been found associated with a slight reduction of 8-week weight of cockerels, and a slight but highly significant increase of mean egg weight, in normal-sized (Dw) and dwarf (dw) hens.


P. MÉRAT, A. BORDAS. Corrélations entre production d'oeufs et variables liées à la consommation alimentaire chez des poules rationnées en période de ponte. Annales de génétique et de
sélection animale, 1977, 9 (4), pp.413-422. <hal-00892894>
HAL Id: hal-00892894
https://hal.archives-ouvertes.fr/hal-00892894
Quote:
Summary
Correlation between egg production and variables associated with ,feed consumption among feed-restricted hens during the laying period Laying hens from a Rhode-Island strain in individual cages were first fed ad libitum, their feed intake and production being observed, then they were restricted to a fixed daily amount of feed during two successive periods. The results were analyzed separately for the group of hens
initially heavier vs. lighter. Egg production with restricted feeding was positively correlated with production in unrestricted condition, and negatively with body weight especially for « heavier» hens), with weight gain in the corresponding period, and with « residual feed consumption in the ad lib. period (especially for « lighter » hens). These preliminary results are briefly discussed in view of possible breeding for egg laying in presence of restricted feeding.


Henri Banga-Mboko, André Bordas, Francis Minvielle, Pascal Leroy. Effects of separate calcium feeding on laying hens selected for low (R-) or high (R+) residual feed consumption. Animal Research, EDP Sciences, 2001, 50 (3), pp.239-250. <10.1051/animres:2001130>. <hal-00889837>
HAL Id: hal-00889837
https://hal.archives-ouvertes.fr/hal-00889837
Quote:
Abstract —The experiment was carried out with a sample of females from the 21st generation of lines R– and R+ selected divergently for residual food intake in the laying period. After a breeding period of 18 weeks the hens of each line had been distributed among climatic rooms into two groups, one fed with a complete commercial feed (control group) and the other one with both a low calcium feed and
oyster shells given in two separate troughs (treated group). Egg production was recorded during 77 days, egg and shell traits were obtained during the third and fourth weeks of the experiment, and the voluntary consumption of feed was measured over a period of 28 days. The treatment had a significant effect for both lines on average egg weight (p < 0.05), shell weight (p < 0.01), shell thickness (p < 0.01), and albumen thickness (p < 0.05). However, the line ´ treatment interaction was significant for yolk weight (p < 0.05) and voluntary calcium consumption (p < 0.001), indicating that the under-consuming line (R–) showed a better response to separate calcium feeding with a 40% decrease of its residual feed consumption, and better egg and shell qualities. The advantage of line R– might be related to the expression of a specific calcium appetite which is masked in line R+ which ingests excess nutrients.


Posted by: KazJaps

Re: Journal papers online - reference list - 10/13/15 06:57 AM

Pigeon & dove crest genetics:

Shapiro MD, Kronenberg Z, Li C, et al. 2013.
Genomic diversity and evolution of the head crest in the rock pigeon.
Science (New York, NY). 2013;339(6123):1063-1067. doi:10.1126/science.1230422.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3778192/

Vickrey AI, Domyan ET, Horvath MP, Shapiro MD. 2015
Convergent Evolution of Head Crests in Two Domesticated Columbids Is Associated with Different Missense Mutations in EphB2.
Mol Biol Evol. 2015 Oct;32(10):2657-64. doi: 10.1093/molbev/msv140. Epub 2015 Jun 23.
Full Paper - Uni of Utah copy
*They found a crest mutation on the same EPHB2 locus in crested ringneck doves (different mutation in pigeons but same locus).

There are other pigeon papers at the following link:
http://biologylabs.utah.edu/shapiro/Shapiro_Lab/Publications.html
Posted by: Henk69

Re: Journal papers online - reference list - 11/06/15 07:57 AM

artificial surrogate eggs topic:
http://www.the-coop.org/forums/ubbthreads.php?ubb=showflat&Number=115050#Post115050
Posted by: KazJaps

Re: Journal papers online - reference list - 11/19/15 05:37 PM

Zhang, J., Liu, F., Cao, J., & Liu, X. (2015). Skin Transcriptome Profiles Associated with Skin Color in Chickens. PLoS ONE, 10(6), e0127301. http://doi.org/10.1371/journal.pone.0127301
Posted by: Wieslaw

Re: Journal papers online - reference list - 02/02/16 09:32 AM


What makes a feather shine? A nanostructural basis for glossy black colours in feathers(full text)

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107640/
Posted by: KazJaps

Re: Journal papers online - reference list - 03/04/16 04:25 PM

2016 beak deformity research by Bai et al. (follow up to their 2014 paper):

Bai, H., Sun, Y., Zhu, J., Liu, N., Li, D., Xue, F., … Chen, J. (2016). Study on LOC426217 as a candidate gene for beak deformity in chicken. BMC Genetics, 17, 44. http://doi.org/10.1186/s12863-016-0353-x
Full Paper
Posted by: KazJaps

Re: Journal papers online - reference list - 03/04/16 06:59 PM

These papers are on Michrochromosome 16, MHC genes & disease resistance (eg Mareks Disease) etc:

Miller MM, Taylor JR. (2016) Brief review of the chicken major histocompatibility complex—the genes, their distribution on chromosome 16 and their contributions to disease resistance. Poult Sci. 2016. doi:10.3382/ps/pev379.
Full Paper

Fulton, J. E., McCarron, A. M., Lund, A. R., Pinegar, K. N., Wolc, A., Chazara, O., … Miller, M. M. (2016). A high-density SNP panel reveals extensive diversity, frequent recombination and multiple recombination hotspots within the chicken major histocompatibility complex B region between BG2 and CD1A1. Genetics, Selection, Evolution&#8239;: GSE, 48, 1. http://doi.org/10.1186/s12711-015-0181-x
Full Paper

Miller MM, Robinson CM, Abernathy J, Goto RM, Hamilton MK, Zhou H, et al. (2014) Mapping genes to chicken microchromosome 16 and discovery of olfactory and scavenger receptor genes near the major histocompatibility complex. J Hered. 2014;105(2):203–15. doi: 10.1093/jhered/est091.
Full Paper

Miller, M. M., Goto, R. M., Taylor, R. L., Zoorob, R., Auffray, C., Briles, R. W., … Bloom, S. E. (1996). Assignment of Rfp-Y to the chicken major histocompatibility complex/NOR microchromosome and evidence for high-frequency recombination associated with the nucleolar organizer region. Proceedings of the National Academy of Sciences of the United States of America, 93(9), 3958–3962.
Full Paper
Posted by: KazJaps

Re: Journal papers online - reference list - 03/04/16 08:35 PM

Further evidence that there are two different Polydactyly Po genes. Chinese breeds (Beijing-You, Silkie, Jiningbairi) & Sultans with one Po gene, and European group: Houdan, Dorkings & Faverolles with another Po gene, possibly on a different locus (no confirmation on exact loci/gene for both Po genes). Although both Po genes are located on the same chromosome (2) & in close proximity.

Zhang, Z., Nie, C., Jia, Y., Jiang, R., Xia, H., Lv, X., … Qu, L. (2016). Parallel Evolution of Polydactyly Traits in Chinese and European Chickens. PLoS ONE, 11(2), e0149010. http://doi.org/10.1371/journal.pone.0149010
Full Paper
Posted by: KazJaps

Re: Journal papers online - reference list - 03/04/16 08:50 PM

The following was a genetic comparison in maternal behaviorial traits between Silkies and White Leghorns.

Basheer, A., Haley, C. S., Law, A., Windsor, D., Morrice, D., Talbot, R., … Dunn, I. C. (2015). Genetic loci inherited from hens lacking maternal behaviour both inhibit and paradoxically promote this behaviour. Genetics, Selection, Evolution&#8239;: GSE, 47, 100. http://doi.org/10.1186/s12711-015-0180-y
Full Paper
Posted by: Redcap

Re: Journal papers online - reference list - 03/04/16 10:01 PM

There was a study before 2004, which has investigated broodiness of White Leghorn x Polish Green-Legged Partridge Fowl and vice versa.
WL rooster over PGLPF hens brought F1 hens which showed no broodiness. But PGLPF rooster over WL hens brought F1 hens which showed 80 % broodiness.
http://www.europastandard.com/odc/_9_tipps_zur_huehnerzucht.html

So the paradox could lay in the sex-linked nature of the heredity.
I try to find the mentioned paper ...

Until then, I can refer to this
https://books.google.de/books?id=08gXl-a...ked&f=false
http://ajas.info/upload/pdf/14-248.pdf
https://kar.kent.ac.uk/37572/
Posted by: Wieslaw

Re: Journal papers online - reference list - 03/25/16 05:36 PM

I'm not sure it has been posted before(will check it tomorrow)

Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of featherless chickens

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464622/


The effect of the scaleless gene, sc, on growth performance and carcass composition of broilers.(abstract)

http://www.ncbi.nlm.nih.gov/pubmed/7088797



Posted by: Wieslaw

Re: Journal papers online - reference list - 03/25/16 05:41 PM

Terrifying:

Detection and characterization of avian leukosis virus in Marek's disease vaccines.

http://www.ncbi.nlm.nih.gov/pubmed/16863069

Posted by: Robbie

Re: Journal papers online - reference list - 03/26/16 05:46 AM

That's from 2006, I wonder if it's still an issue?
Posted by: KazJaps

Re: Journal papers online - reference list - 03/26/16 06:16 PM

Yes, still an issue.

Peng Zhao, Xuan Dong, and Zhizhong Cui
2014. Isolation, identification, and gp85 characterization of a subgroup A avian leukosis virus from a contaminated live Newcastle Disease virus vaccine, first report in China.
Poultry Science (September 2014) 93 (9): 2168-2174
http://www.ncbi.nlm.nih.gov/pubmed/25002550
----------------------------------
Ever heard of Egg Drop Syndrome in chickens? Apparently the virus came about in chickens from contaminated vaccines (developed using duck embryos):

Merck Vet Manual, EDSV:
Quote:
It is thought that the virus was introduced to chickens through a vaccine that had been grown in contaminated duck-embryo fibroblasts. The virus became established in chickens, causing substantial problems with egg shell quality and loss of eggs.
Posted by: Redcap

Re: Journal papers online - reference list - 03/26/16 07:43 PM

Yes, in the german poultry forum there is an user, who made experience with EDS - as far as I know in show breeds. She has a mixed flock of different breeds and don't hatch, so it came into her flock by a purchase. She vaccinates against EDS since then.
Posted by: KazJaps

Re: Journal papers online - reference list - 03/26/16 07:45 PM

I suppose this following paper is somewhat reassuring:

Schat KA, Erb HN. 2014 Lack of evidence that avian oncogenic viruses are infectious for humans: a review. Avian Dis. 2014 Sep;58(3):345-58.
http://www.ncbi.nlm.nih.gov/pubmed/25518427

The paper is mostly about chicken meat processing workers (whether any human risks from avian viruses such as Mareks, Avian Leukosis, REV). It also touches on the history of human vaccine contaminants (from chicken embryo developed vaccines):

Quote:
Moreover, humans vaccinated with exogenous or endogenous ALV-contaminated vaccines against yellow fever, measles, and mumps did not become antibody- or virus-positive for ALV. The risks for human infection with REV are similarly limited......


And about the Marek's virus (MDV)
Quote:

....MDV is typically associated with infection of chickens, and almost all experimental data show that MDV cannot infect mammalian cells or animals, including nonhuman primates. One study reports the presence of MDV gD DNA in human sera, but this finding could not be confirmed by another group.
Posted by: Redcap

Re: Journal papers online - reference list - 03/26/16 08:19 PM

There are contradictionary results.

Particularly Herpes Viruses should be considered with caution
A few months ago I have found only two studies about this topic (both from 1973) - and with contradictionary claims.



Quote:
These data supported earlier findings and provided additional circumstantial evidence that MDV and HVT do not constitute a public health hazard.

http://jnci.oxfordjournals.org/content/51/4/1123.abstract

Quote:
Common antigenicity has been discovered between glycoprotein antigens obtained from leukotic lesions of chickens with Marek’s disease and antigens obtained from a variety of human cancers. This suggests that Marek’s disease herpesvirus is a possible etiological agent in human cancer.

https://www.karger.com/Article/Pdf/224813

So - if the Marek virus can be considered as possible reason of human cancer it should prick up your ears because in the last 40 years the virulence has multiplied - by the vaccines itself. Nevertheless vaccination is still considered as the best way for food safety:

http://www.pbs.org/newshour/updates/tthis-chicken-vaccine-makes-virus-dangerous
Quote:
“Food chain security and everything rests on vaccines. They are the most successful and cheapest public health interventions that we’ve ever had. We just need to consider the evolutionary consequences of these ones with leaky transmission.”


Who knows why there are so many cancer patients today? Meat consumption per se has been repeatedly discussed, but perhaps it is especially Marek-contaminated meat (under the vaccine coverage)?

This is a newer study, which I could find finally
http://www.microbiologyresearch.org/docs...9E01B63EFB3B2DB
Posted by: KazJaps

Re: Journal papers online - reference list - 03/26/16 09:07 PM

At least the Marek's herpes virus is not transmitted vertically through hen eggs (& therefore not a human vaccine contaminant).
Posted by: Redcap

Re: Journal papers online - reference list - 03/26/16 09:34 PM

I could find the full paper of Schat
https://en.engormix.com/MA-poultry-indus...3450/165-p0.htm
Posted by: Robbie

Re: Journal papers online - reference list - 03/27/16 04:54 AM

Maybe all those people who are blaming vaccines for all kinds of illness including autism aren't so crazy? It's insane how many vaccines are given to kids these days. Here's the American recommended list:
http://www.cdc.gov/vaccines/schedules/hcp/imz/child-adolescent.html
Posted by: Redcap

Re: Journal papers online - reference list - 03/27/16 09:26 AM

But there are mainly vaccine adjuvants blamed like Thiomersal, which is ironically no longer used (in children vaccines).
Posted by: Redcap

Re: Journal papers online - reference list - 04/14/16 10:17 PM

J. Zhao, J. Yao, F. Li, Z. Yang, Z. Sun, L. Qu, K. Wang, Y. Su, A. Zhang, S. A. Montgomery, T. Geng, and H. Cui
Identification of candidate genes for chicken early- and late-feathering
Poultry Science 2016 : pew131v1-pew131.

Abstract:
Previous studies suggest that prolactin receptor (Prlr) is a potential causative gene for chicken early- (EF) and late-feathering (LF) phenotypes. In this study, we evaluated candidate genes for this trait and determined the expression of 3 genes, including Prlr, sperm flagellar protein 2 (Spef2), and their fusion gene, in the skins of one-day-old EF and LF chicks using RT­qPCR. Data indicated that Prlr expression in the skin did not show significant difference between EF and LF chicks, suggesting Prlr may not be a suitable candidate gene. In contrast, Spef2 expression in the skin displayed a significant difference between EF and LF chicks (P < 0.01), suggesting that Spef2 may be a good candidate gene for chicken feathering. Moreover, dPrlr/dSpef2, the fusion gene, was also a good candidate gene as it was expressed only in LF chicks. However, the expression of the fusion gene was much lower than that of Prlr. Additionally, using strand-specific primers, we found that the fusion gene was transcribed in 2 directions (one from dPrlr promoter, another from dSpef2 promoter), which could result in the formation of a double strand RNA. In conclusion, both Spef2 and the fusion gene are good candidate genes for chicken feathering, but Prlr is not. The research on the function and regulation of the candidate genes will help elucidate the molecular basis of the chicken feathering trait.
Posted by: Redcap

Re: Journal papers online - reference list - 04/22/16 03:58 PM

http://www.lgcgroup.com/LGCGroup/media/P...ne-app-note.pdf
Variation in the ovocalyxin–32 gene in commercial egg-laying chickens and its relationship with egg production and egg quality trait.
Posted by: Redcap

Re: Journal papers online - reference list - 05/03/16 11:34 AM

Løtvedt, P., & Jensen, P. (2014). Effects of Hatching Time on Behavior and Weight Development of Chickens. PLoS ONE, 9(7), e103040.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0103040
Posted by: Robbie

Re: Journal papers online - reference list - 05/07/16 06:09 AM


GENETIC CONTROL OF MELANIN PIGMENTATION IN THE FOWL
J. Robert Smyth, Jr. Department of Veterinary and Animal Sciences
University of Massachusetts Amherst, Massachusetts
No date but I believe it's 1976.
Some excellent drawings of chick/adult feather markings related to the genotype especially the E locus.
Posted by: Redcap

Re: Journal papers online - reference list - 05/24/16 10:14 PM

Originally Posted By: Redcap
There are contradictionary results.

Particularly Herpes Viruses should be considered with caution
A few months ago I have found only two studies about this topic (both from 1973) - and with contradictionary claims.



Quote:
These data supported earlier findings and provided additional circumstantial evidence that MDV and HVT do not constitute a public health hazard.

http://jnci.oxfordjournals.org/content/51/4/1123.abstract
J. M. Sharma, R. L. Witter, B. R. Burmester, and J. C. Landon
Public Health Implications of Marek's Disease Virus and Herpesvirus of Turkeys. Studies on Human and Subhuman Primates
JNCI J Natl Cancer Inst (1973) 51 (4): 1123-1128.
Quote:
Common antigenicity has been discovered between glycoprotein antigens obtained from leukotic lesions of chickens with Marek’s disease and antigens obtained from a variety of human cancers. This suggests that Marek’s disease herpesvirus is a possible etiological agent in human cancer.

https://www.karger.com/Article/Pdf/224813


Makari JG (1973. Association between Marek's herpesvirus and human cancer. I. Detection of cross-reacting antigens between chicken tumors and human tumors. Oncology. 1973;28(2):164-76.


So - if the Marek virus can be considered as possible reason of human cancer it should prick up your ears because in the last 40 years the virulence has multiplied - by the vaccines itself. Nevertheless vaccination is still considered as the best way for food safety:

http://www.pbs.org/newshour/updates/tthis-chicken-vaccine-makes-virus-dangerous
Quote:
“Food chain security and everything rests on vaccines. They are the most successful and cheapest public health interventions that we’ve ever had. We just need to consider the evolutionary consequences of these ones with leaky transmission.”


Who knows why there are so many cancer patients today? Meat consumption per se has been repeatedly discussed, but perhaps it is especially Marek-contaminated meat (under the vaccine coverage)?

This is a newer study, which I could find finally and Schat mentioned probably http://www.ncbi.nlm.nih.gov/pubmed/11125176
Laurent S(1), Esnault E, Dambrine G, Goudeau A, Choudat D, Rasschaert D. (2001). Detection of avian oncogenic Marek's disease herpesvirus DNA in human sera. J Gen Virol. 2001 Jan;82(Pt 1):233-40.

Link-Update plus Addition of two references

http://jcm.asm.org/content/41/6/2428.abstract
Holger Hennig, Nikolaus Osterrieder, Michael Müller-Steinhardt, Hanns-Martin Teichert, Holger Kirchner, and Klaus-Peter Wandinger (2003). Detection of Marek's Disease Virus DNA in Chicken but Not in Human Plasma. J. Clin. Microbiol. June 2003 41:6 2428-2432
http://oem.bmj.com/content/60/9/e4.abstract
L Fritschi, S Fenwick, M Bulsara (2003). Mortality and cancer incidence in a cohort of meatworkers. Occup Environ Med 2003;60:9

Posted by: KazJaps

Re: Journal papers online - reference list - 06/27/16 08:25 PM

The Mb muff/beard mutation has been determined, DNA sequenced.

They first determined the Mb sequence in some muff/beard Chinese breeds & then tested some European Mb breeds (Dutch Polish, Dutch Owl, Brabanter) & found the same sequence.

Guo Y, Gu X, Sheng Z, et al. 2016.
A Complex Structural Variation on Chromosome 27 Leads to the Ectopic Expression of HOXB8 and the Muffs and Beard Phenotype in Chickens.
Leeb T, ed. PLoS Genetics. 2016;12(6):e1006071. doi:10.1371/journal.pgen.1006071.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890787/

Note, Mb locus was found on Chromosome 27, the chromosome previously determined in the following study:

Sun Y, Liu R, Zhao G, et al. 2015.
Genome-Wide Linkage Analysis Identifies Loci for Physical Appearance Traits in Chickens.
G3: Genes|Genomes|Genetics. 2015;5(10):2037-2041. doi:10.1534/g3.115.020883.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4592986/
Posted by: KazJaps

Re: Journal papers online - reference list - 06/28/16 12:47 AM

With this research they DNA sequenced the MLPH gene in the Chinese Anyi tile-like gray chicken, & compared to the lav allele (previously sequenced by Vaez et al. 2008). They found the gray Anyi MLPH allele to be different to the lav allele in European lavenders (& both different sequence to wild-type).

Interactions of allele E of the MC1R gene with FM and mutations in the MLPH gene cause the five-gray phenotype in the Anyi tile-like gray chicken.
Xu JG, Xie MG, Zou SY, Liu XF, Li XH, Xie JF, Zhang XQ.
Genet Mol Res. 2016 Apr 26;15(2). doi: 10.4238/gmr.15027633.
http://www.funpecrp.com.br/gmr/year2016/vol15-2/pdf/gmr7633.pdf

Previous lav study:
Vaez M, Follett SA, Bed’hom B, Gourichon D, Tixier-Boichard M, Burke T.
A single point-mutation within the melanophilin gene causes the lavender plumage colour dilution phenotype in the chicken.
BMC Genetics. 2008;9:7. doi:10.1186/1471-2156-9-7.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253553/
Posted by: Redcap

Re: Journal papers online - reference list - 06/29/16 11:38 AM

Y. P. Wu , J. H. Huo , J. F. Xie , L. X. Liu , Q. P. Wei , M. G. Xie , Z. F. Kang , H. Y. Ji , Y. H. Ma (2014). Phylogeography and origin of Chinese domestic chicken. Mitochondrial DNA. Vol. 25, Iss. 2.
http://www.tandfonline.com/doi/abs/10.3109/19401736.2013.786704?journalCode=imdn20
Full text on request
Abstract
The loss of local chicken breeds as result of replacement with cosmopolitan breeds indicates the need for conservation measures to protect the future of local genetic stocks. The aim of this study is to describe the patterns of polymorphism of the hypervariable control region of mitochondrial DNA (HVR1) in domestic chicken in China’s Jiangxi province to investigate genetic diversity, genetic structure and phylo-dynamics. To this end, we sequenced the mtDNA HVR1 in 231 chickens including 22 individuals which belonged to previously published sequences. A neighbor-joining tree revealed that these samples clustered into five lineages (Lineages A, B, C, E and G). The highest haplotype diversity and nucleotide diversity were both found in Anyi tile-liked gray breed. We estimated that the most recent common ancestor of the local chicken existed approximately 16 million years ago. The mismatch distribution analysis showed two major peaks at positions 4 and 9, while the neutrality test (Tajima’s D&#8201;=&#8201;&#8722;2.19, p&#8201;<&#8201;0.05) and Fu’s F-statistics (&#8722;8.59, p&#8201;<&#8201;0.05) revealed a significant departure from the neutrality assumption. These results support the idea that domestication of chickens facilitated population increases. Results of a global AMOVA indicated that there was no obvious geographic structure among the local chicken breeds analyzed in this study. The data obtained in this study will assist future conservation management of local breeds and also reveals intriguing implications for the history of human population movements and commerce.
Posted by: Redcap

Re: Journal papers online - reference list - 06/29/16 09:29 PM

This is another interesting thesis, which could support the hypothesis that the Silkies were the progenitors of Sultan Chicken and other crested/bearded breeds - at least they seems to have a close genetic relation regarding the polydactyly.

Quote:
SHH ZRS sequencing results. Breeds in which the highly conserved ZPA regulatory sequence (ZRS) of Sonic Hedgehog was sequenced for detection of SNPs associated with the polydactyly phenotype. The White Silkie and White Sultan breeds were both found to have the T allele at the SNP ss161109890 while all other breeds, both four and five toed, had the G allele.

http://repository.lib.ncsu.edu/ir/bitstream/1840.16/6584/1/etd.pdf

So the Silkies seems to be the progenitor of all bearded and crested chickens
See history of Silkies beginning with the description of Aristotle (btw. Does anyone know in which Book/Volume Aristotle mentioned chickens with "cat hair/fur" from the Mangi/Manzi Realm?).
http://www.aviculture-europe.nl/nummers/09e06a07.pdf
Posted by: KazJaps

Re: Journal papers online - reference list - 08/09/16 06:59 PM

Some new research on white earlobe genetics (in a Rhode Island Red line). Historically believed a polygenic trait, with some evidence of sex-linked inheritance, in this new research they found further DNA evidence on the Z chromosome for the white earlobes trait.


Nie C, Zhang Z, Zheng J, Sun H, Ning Z, Xu G, Yang N, Qu L. 2016
Genome-wide association study revealed genomic regions related to white/red earlobe color trait in the Rhode Island Red chickens.
BMC Genet. 2016 Aug 5;17(1):115. doi: 10.1186/s12863-016-0422-1.
http://bmcgenet.biomedcentral.com/articles/10.1186/s12863-016-0422-1
Quote:
The study has revealed the white/red earlobe trait is polygenic and sex-linked in Rhode Island Red chickens. In the genome significant ~2.38 Mb region, twenty-three genes were found and some of them could play critical roles in the formation of white/red earlobe color, especially gene SLCO4C1

--------------------
The authors cite previous DNA research on earlobe colour by Wragg et al. 2012....

Quote:
Recently, Wragg et al. [9] identified 7 concordant significances (P < 0.05 and Z > 4) SNPs on chicken chromosomes 1, 2, 4 and Z related to white/red earlobe color by using genome-wide association (GWA) analysis, indicating that earlobe color trait is sex-linked and polygenic.


Wragg D, Mwacharo JM, Alcalde JA, Hocking PM, Hanotte O. 2012
Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens.
Heredity. 2012;109(1):6–18.
http://www.nature.com/hdy/journal/v109/n1/full/hdy20129a.html
Posted by: KazJaps

Re: Journal papers online - reference list - 08/09/16 07:30 PM

An aggression gene SORCS2 on Chromosome 4, found in a Chinese dwarf yellow meat type breed:

Li Z, Zheng M, Abdalla BA, Zhang Z, Xu Z, Ye Q, Xu H, Luo W, Nie Q, Zhang X
Genome-wide association study of aggressive behaviour in chicken.
Sci Rep. 2016 Aug 3;6:30981. doi: 10.1038/srep30981.
http://www.nature.com/articles/srep30981
Posted by: KazJaps

Re: Journal papers online - reference list - 08/09/16 08:30 PM

In the following research they looked for genes that influence comb traits (measured length, height, weight) compared between Leghorns & a Chinese breed. They determined the three genes VPS36, AR and WNT11B had significant influence on comb length, height & weight. These genes are found on Chromosomes 1 (VPS36) & 4 (WNT11B, AR).

VPS36 = vacuolar protein sorting 36
AR = Androgen Receptor
WNT11B = wingless-type MMTV integration site family, member 11B

Shen, M., Qu, L., Ma, M., Dou, T., Lu, J., Guo, J., … Yang, N. (2016).
Genome-Wide Association Studies for Comb Traits in Chickens.
PLoS ONE, 2016 11(7), e0159081. http://doi.org/10.1371/journal.pone.0159081
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4948856/
Posted by: KazJaps

Re: Journal papers online - reference list - 08/09/16 09:32 PM

The causal gene for Creeper has been determined, a deletion on IHH Indian Hedgehog gene (Chromosome 7). This gene is very close to the rosecomb gene MNR2 (ie very close linkage between Rosecomb & Creeper). They used the Chinese breed: "Chinese Xingyi bantams" for their source of the Creeper gene. The paper also has interesting images of homozygous Cp/Cp embryos (a lethal gene when homozygous).

Jin, S., Zhu, F., Wang, Y., Yi, G., Li, J., Lian, L., … Yang, N. (2016).
Deletion of Indian hedgehog gene causes dominant semi-lethal Creeper trait in chicken.
Scientific Reports, 2016, 6, 30172. http://doi.org/10.1038/srep30172
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4954956/
Posted by: dingsda

Re: Journal papers online - reference list - 08/10/16 12:31 PM

Originally Posted By: KazJaps
The causal gene for Creeper has been determined, a deletion on IHH Indian Hedgehog gene (Chromosome 7). This gene is very close to the rosecomb gene MNR2 (ie very close linkage between Rosecomb & Creeper). They used the Chinese breed: "Chinese Xingyi bantams" for their source of the Creeper gene. The paper also has interesting images of homozygous Cp/Cp embryos (a lethal gene when homozygous).

Jin, S., Zhu, F., Wang, Y., Yi, G., Li, J., Lian, L., … Yang, N. (2016).
Deletion of Indian hedgehog gene causes dominant semi-lethal Creeper trait in chicken.
Scientific Reports, 2016, 6, 30172. http://doi.org/10.1038/srep30172
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4954956/


thank you for the link. This year I had a similar Cp/Cp embryo dead in the egg from my japanese bantams, with tiny wings and no visible legs.

I wonder why some develope this far, since most embryos seem to die early. Alas, the paper does not elaborate on that.
Posted by: Wieslaw

Re: Journal papers online - reference list - 08/10/16 03:39 PM

Originally Posted By: dingsda
Originally Posted By: KazJaps
The causal gene for Creeper has been determined, a deletion on IHH Indian Hedgehog gene (Chromosome 7). This gene is very close to the rosecomb gene MNR2 (ie very close linkage between Rosecomb & Creeper). They used the Chinese breed: "Chinese Xingyi bantams" for their source of the Creeper gene. The paper also has interesting images of homozygous Cp/Cp embryos (a lethal gene when homozygous).

Jin, S., Zhu, F., Wang, Y., Yi, G., Li, J., Lian, L., … Yang, N. (2016).
Deletion of Indian hedgehog gene causes dominant semi-lethal Creeper trait in chicken.
Scientific Reports, 2016, 6, 30172. http://doi.org/10.1038/srep30172
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4954956/


thank you for the link. This year I had a similar Cp/Cp embryo dead in the egg from my japanese bantams, with tiny wings and no visible legs.

I wonder why some develope this far, since most embryos seem to die early. Alas, the paper does not elaborate on that.


There is somewhere a japanese paper on so called "mother effect" (or so) on Cp/Cp. I do not remember all details, but something in that style:" all leghorns and minorcas that were Cp/Cp died, but some chabo survived and hatched. Does anybody else remember it too?
Posted by: KazJaps

Re: Journal papers online - reference list - 08/10/16 04:45 PM

That's interesting Dingsda re. Cp/Cp embryo in Japs. I've never seen them (although I did lose interest in inspecting all dead-in-shell Jap embryos/chicks). I think in PB&G there is mention of different studies on the Creeper gene where the embryos died at different incubation periods, depending on lines/ breeds studied. I think in my Japs that most (if not all) Cp/Cp died very early, as I didn't find any of those legless or deformed embryos.

Note too that mutations on the IHH (Indian hedgehog) gene (chicken Cp creeper locus) in other species can cause Brachydactyly phenotypes (eg shortened digits).

-------------------------------

Looks like I might have forgotten to post this 2016 paper. It's mostly on pigeon foot feather mutations, candidate genes PITX1 & TBX5 (touches on chicken research):

Domyan, E. T., Kronenberg, Z., Infante, C. R., Vickrey, A. I., Stringham, S. A., Bruders, R., … Shapiro, M. D. (2016).
Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species.
eLife, 5, e12115. http://doi.org/10.7554/eLife.12115
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4805547/
Posted by: Wieslaw

Re: Journal papers online - reference list - 08/11/16 01:07 AM

I have found it. I remembered incorrectly. It was about surviving of the embryos to near hatch, not hatching

MATERNAL EFFECTS ON EXPRESSION OF LETHALITY IN THE CREEPER CHICKEN

https://www.jstage.jst.go.jp/article/ggs1921/51/5/51_5_347/_article
Posted by: dingsda

Re: Journal papers online - reference list - 08/11/16 07:48 AM

Originally Posted By: Wieslaw
I have found it. I remembered incorrectly. It was about surviving of the embryos to near hatch, not hatching

MATERNAL EFFECTS ON EXPRESSION OF LETHALITY IN THE CREEPER CHICKEN

https://www.jstage.jst.go.jp/article/ggs1921/51/5/51_5_347/_article


thank you Wieslaw, much appreciated!

I checked my hatch records and the Cp/Cp embryo was actually the second egg of the hens laying period, so it corresponds to the authors results.

But still wondering what gets put in the egg for the embryos to come so far.
Posted by: Wieslaw

Re: Journal papers online - reference list - 12/21/16 04:02 PM

Green shanks and adult mortality in chickens, abstract

https://www.ncbi.nlm.nih.gov/pubmed/469223

Pay attention to the description of feathers.
Posted by: KazJaps

Re: Journal papers online - reference list - 12/22/16 11:00 PM

Thanks Wieslaw. That's interesting.

Although I've posted the full paper link previously (which usually means that I've downloaded the full paper), I haven't been able to find a full copy saved:

Green shanks and adult mortality in chicken.
(W. H. MCGIBBON)(J Hered-1979-MCGIBBON-44-6)
http://jhered.oxfordjournals.org/content/70/1/44.full.pdf
* this one not available for free now.

But I did find McGibbon's earlier 1974 Poultry Science full paper on this id^c Cornell line mutation:


A shank color mutation in Cornell random bred S.C. White Leghorns.
McGibbon WH.
Poult Sci. 1974 May;53(3):1251-3.
http://ps.oxfordjournals.org/content/53/3/1251.abstract

In the final paragraph (of full paper):
Quote:
Most of the birds with green shanks (White Leghorns) that have been reared to maturity display some color on the mandibles and a distinct surface coloration of the plumage. The males' coloration is of a grayish caste or dirty white overall, while the females display a pale golden color restricted to the neck feathers. The causative allele "idc" is suggested.
Posted by: Redcap

Re: Journal papers online - reference list - 12/23/16 03:04 PM

Could this gene IdC play a role in Marsh Daisies and the Polish Green-legged Partridge Fowl?

In this context the following study about a health-affecting gene is also interesting.

Increased copy number of SOCS2 gene in Chinese gamecocks
H. Bi, G. Yi, and N. Yang
Poult Sci published 22 December 2016, 10.3382/ps/pew391

Quote:
Abstract

As a member of the suppressor of cytokine signaling (SOCS) family, the SOCS2 gene has been associated with negative regulation of the inflammatory immune response and a positive effect on growth when it is overexpressed. In our previous study, using next-generation sequencing, it was found that the Luxi Game (LX, a Chinese indigenous gamecock) had an increased copy number (CN) of the SOCS2 gene. To verify the copy number increase of the SOCS2 gene in gamecocks, we quantified the copy number value in 8 chicken breeds by quantitative PCR. The results showed that the average CN values of the SOCS2 gene were highly variable among the 8 breeds, and the highest was found in LX (CN = 5.0), almost 3.5 folds as many as the lowest in Rhode Island Red (CN = 1.43). All 4 gamecock breeds possessed significantly higher CN values than others, including broilers and commercial breeds. Thus, it is suggested that most Chinese gamecocks possess an increased copy number in the SOCS2 gene, indicating the plausible functions of the SOCS2 gene in inflammation control and increased body size.


http://ps.oxfordjournals.org/content/early/2016/12/22/ps.pew391.abstract?papetoc
Posted by: Redcap

Re: Journal papers online - reference list - 12/23/16 05:42 PM

Originally Posted By: Redcap
Could this gene IdC play a role in Marsh Daisies and the Polish Green-legged Partridge Fowl?


It can, but in this study they mention it not clear.

Siwek, M., Wragg, D., Slawinska, A., Malek, M., Hanotte, O., & Mwacharo, J. (2013). Insights into the genetic history of Green-legged Partridgelike fowl: mtDNA and genome-wide SNP analysis. Animal Genetics, 44(5), 522–532. http://doi.org/10.1111/age.12046
https://www.ncbi.nlm.nih.gov/pmc/article...m=auto,-107,666

They only say :

Quote:
The green shank colour has previously been shown to result from the interaction of the w/w and id+/id+ alleles in the Cornell random-bred White Leghorn population (McGibbon 1974, 1979).
Posted by: KazJaps

Re: Journal papers online - reference list - 01/03/17 03:33 PM

A new study on proteins that influence light/dark brown eggshell colour:

Li G, Sun C, Wu G, Shi F, Liu A, et al. (2016)
iTRAQ-Based Quantitative Proteomics Identifies Potential Regulatory Proteins Involved in Chicken Eggshell Brownness.
PLOS ONE 11(12): e0168750. doi: 10.1371/journal.pone.0168750
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168750
Posted by: Redcap

Re: Journal papers online - reference list - 01/05/17 04:55 PM

Originally Posted By: KazJaps
Thanks Wieslaw. That's interesting.

Although I've posted the full paper link previously (which usually means that I've downloaded the full paper), I haven't been able to find a full copy saved:

Green shanks and adult mortality in chicken.
(W. H. MCGIBBON)(J Hered-1979-MCGIBBON-44-6)
http://jhered.oxfordjournals.org/content/70/1/44.full.pdf
* this one not available for free now.

Full text is online.
http://documents.kippenjungle.nl/#post36
Posted by: Redcap

Re: Journal papers online - reference list - 01/08/17 03:26 PM

Btw. the most frequent tumour type Hemangioma (in idC Chicken) is mostly associated with Avian Leucosis Virus (ALV). So it seems that there is a susceptibility to ALV for Chicken with the idC trait.

I wonder why McGibbon didn't come to the conclusion, that there is a relation to ALV. Especially he didn't mentioned which line he has studied. Maybe the Cornell line S?

Quote:
In comparison to the frequency of ev6 found in the Cornell line K, the incidence of ev6 in the Cornell line S, selected in the opposite direction for susceptibility to the ‘avian leukosis complex’, which shares about 30% of its original genetic basis with the Cornell line K (R.K. Cole, 1991, personal communication), was as low as 0.28 (Kuhnlein et al. 1989b). There cannot be much doubt that the role of ev6 in disease resistance may also depend on the genetic background, when these varying results are considered.

The availability of information on the incidence of ev genes in three Leghorn strains of different origin, each with two sublines differing in their genotype for resistance to ALV infection, has increased the understanding of observed strain differences on the effects of ALV infection. However, it has also added to the complexity of the underlying problem in studies concerned with the effects of major genes in disease resistance.

http://onlinelibrary.wiley.com/doi/10.1111/j.1439-0388.1995.tb00581.x/full
Posted by: KazJaps

Re: Journal papers online - reference list - 01/16/17 05:55 AM

Note - I'm finding a lot of full papers from Journal of Heredity and Poultry Science available online for free at the moment. This probably won't last long, so grab them quickly.
Posted by: KazJaps

Re: Journal papers online - reference list - 01/16/17 08:05 AM

I haven't seen the following reference before:

Smyth, J. R., Jr., M. L. Boyle, HI, and N. Lakshmanan, 1990. Genetics of self black and birchen patterns and their effects on feather, eye and shank pigmentation in the chicken.
Poultry Sci. 69(Suppl. l):128.(Abstr.)

Only an abstract. Unfortunately I couldn't find it listed for viewing /download at the Poultry Science website. All I could find was Smyth's name listed for 1990 paper authors: Smyth, J. R., Jr., 77*. 128*
Posted by: Redcap

Re: Journal papers online - reference list - 01/16/17 03:58 PM

Originally Posted By: KazJaps

Smyth, J. R., Jr., M. L. Boyle, HI, and N. Lakshmanan, 1990. Genetics of self black and birchen patterns and their effects on feather, eye and shank pigmentation in the chicken.
Poultry Sci. 69(Suppl. l):128.(Abstr.)


Quote:
Further evidence was obtained to support the existence of separate alleles at the E-locus for self-black (E) and birchen (ER) feather color patterns. E and ER alleles were isolated from a heterogeneous population by consecutive backcrosses to wild type (e+/e+) tester stocks thus separating out the effects of segregating eumelanizing modifiers.
Dominance of E over is complete in females and nearly complete in males. E/e+ chick down is black, while adult eye and shank color is black in females and intermediate in males with no obvious dosage effects. The expression of ER is more variable with ER/ER females having black down, while male down varies from brown-faced black to dark reddish. ER/e+ chicks have varying degrees of reddish-brown down. Adult ER/ER females vary from near black to dark birchen, while males are dark birchen. Adult heterozygotes are variably birchen. Eye and shank color is reduced by ER on a dosage basis, with some ER/ER males having clear shanks. It was also shown that eumelanizing modifiers can convert ER/- birds to self black plumage without altering eye or shank melanization.

http://documents.kippenjungle.nl/#post40
Posted by: KazJaps

Re: Journal papers online - reference list - 01/16/17 06:10 PM

Thank you Redcap smile

Maybe Smyth learn't more in future years about the brown-down ones to explain the following 1994 quote, ie maybe eventually segregated out 2 different birchen alleles:

Quote:
E (self-black)>
E^R (black-downed birchen) >
E^RB (red-brown downed birchen)


Melanin Pigmentation: Its Biological Roles, Inheritance
and Expression in the Chicken

Dr. J. Robert Smyth,Jr.
1994
http://www.poultryscience.org/docs/pba/1952-2003/1994/1994%20Smyth.pdf

And it is great to see that they tried to segregate out E from additional eumelanisers, giving further evidence that there is a more melanised E locus allele - Extended Black (not possibly ER + eumelanisers).
Posted by: KazJaps

Re: Journal papers online - reference list - 01/29/17 11:46 PM

Don't think I've posted this one before....

Freese, N. H., Lam, B. A., Staton, M., Scott, A., & Chapman, S. C. (2014).
A Novel Gain-Of-Function Mutation of the Proneural IRX1 and IRX2 Genes Disrupts Axis Elongation in the Araucana Rumpless Chicken.
PLoS ONE, 9(11), e112364. http://doi.org/10.1371/journal.pone.0112364
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4221472/

---------------
Jeong, H., Kim, K., Caetano-Anollés, K., Kim, H., Kim, B., Yi, J.-K., … Oh, D. Y. (2016).
Whole genome sequencing of Gyeongbuk Araucana, a newly developed blue-egg laying chicken breed, reveals its origin and genetic characteristics.
Scientific Reports, 2016. 6, 26484. http://doi.org/10.1038/srep26484
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877703/
Posted by: Redcap

Re: Journal papers online - reference list - 01/31/17 08:23 PM

So, the ancestral background of Gyeongbuk Araucana is similar to the Cream Legbar.
http://www.creamlegbarclub.com/20-history-of-the-cream-legbar
Posted by: Wieslaw

Re: Journal papers online - reference list - 03/02/17 01:21 AM


Melanism in guinea fowl (Numida meleagris) is associated with a deletion of Phenylalanine-256 in the MC1R gene.

Vidal O1, Araguas RM, Fernández E, Heras S, Sanz N, Pla C.
Author information

https://www.ncbi.nlm.nih.gov/pubmed/20477788?log$=activity


Abstract
We have characterized a deletion in the MC1R gene causing the loss of one amino acid (p.Phe256del), which is perfectly associated with melanism in guinea fowl (Numida meleagris). Co-segregation of the p.Phe256del with melanism was confirmed in 25 offspring born from a cross of two heterozygote birds; therefore we suggest that this mutation is responsible for the black phenotype. Interestingly, this is the first case of recessive melanism linked to MC1R.





Variability of the melanocortin 1 receptor (MC1R) gene explains the segregation of the bronze locus in turkey (Meleagris gallopavo).

Vidal O1, Viñas J, Pla C.

https://www.ncbi.nlm.nih.gov/pubmed/20634512?log$=activity


Abstract
By sequencing the full coding region of the turkey melanocortin 1 receptor (MC1R) gene, we have found 4 mutations (c.96G > A, c.364A > T, c.450C > T, and c.887C > T) that are organized in 5 different haplotypes (MC1R*1 to MC1R*5). These haplotypes correlate perfectly with the 3 alleles of the bronze locus (i.e., B, b(+), and b(1)). We suggest that the dominant black phenotype, associated with the B allele, results from the constitutive activation of the receptor, an effect that might be mediated by the missense mutation c.364A > T (p.Ile122Phe). Moreover, we propose that the recessive black-winged bronze phenotype (linked to b(1)) might be produced by 2 deleterious mutations of MC1R (c.96G > A and c.887C > T). This is an unexpected finding because in mammals, MC1R deleterious polymorphisms are usually related with either red or lighter fur colors.

Inheritance of wing feather development rate in guinea fowl (Numida meleagris).

Pal SK1, Singh H.
Author information


Abstract
1. A study of primary wing feather development rate in guinea fowl revealed genetic control through a single pair of sex-linked alleles. The allele for slow feathering (K) was dominant over that for rapid feathering (k+). 2. Wing feather sexing showed 94% accuracy in 10-d-old keets. 3. Incidence of rapid feathering allele (k+) was higher in the population selected for high body weight compared to the unselected population

https://www.ncbi.nlm.nih.gov/pubmed/9280348?log$=activity

Posted by: Wieslaw

Re: Journal papers online - reference list - 03/02/17 01:35 AM

https://gsejournal.biomedcentral.com/articles/10.1186/s12711-017-0287-4

A genome-wide association study in a large F2-cross of laying hens reveals novel genomic regions associated with feather pecking and aggressive pecking behavior

Vanessa Lutz
Email author
, Patrick Stratz, Siegfried Preuß, Jens Tetens, Michael A. Grashorn, Werner Bessei and Jörn Bennewitz
Posted by: Wieslaw

Re: Journal papers online - reference list - 03/04/17 02:36 PM


Whole-genome resequencing of Xishuangbanna fighting chicken to identify signatures of selection (free file)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5000499/
Posted by: Wieslaw

Re: Journal papers online - reference list - 03/04/17 02:39 PM

Abstract

Whole-genome resequencing reveals loci under selection during chicken domestication.

https://www.ncbi.nlm.nih.gov/pubmed/20220755/

Domestic animals are excellent models for genetic studies of phenotypic evolution. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.

Whole pdf fil:

http://www.nature.com/nature/journal/v464/n7288/pdf/nature08832.pdf

Posted by: Wieslaw

Re: Journal papers online - reference list - 03/05/17 10:09 AM

Previously listed by Kazjaps as an abstract, here is the whole document. Grab it while you can:

http://onlinelibrary.wiley.com/doi/10.1111/j.1755-148X.2010.00700.x/epdf

Sex-linked barring in chickens is controlled by the CDKN2A/B tumour suppressor locus
Posted by: Wieslaw

Re: Journal papers online - reference list - 03/05/17 04:51 PM

Grab while you can

Increased copy number of SOCS2 gene in Chinese gamecocks

https://www.researchgate.net/publication...inese_gamecocks

Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken Whole document

http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-391

Posted by: Wieslaw

Re: Journal papers online - reference list - 03/09/17 11:39 AM

Previously listed as an abstract, here is the whole document

The twofold difference in adult size between the red junglefowl and White Leghorn chickens is largely explained by a limited number of QTLs.

http://www.animalgenome.org/QTLdb/references/12873214.pdf


Domestication and tameness: brain gene expression in red junglefowl selected for less fear of humans suggests effects on reproduction and immunology. Whole document


Bélteky J1, Agnvall B1, Johnsson M1, Wright D1, Jensen P1.

https://www.ncbi.nlm.nih.gov/pubmed/27853585

Abstract
The domestication of animals has generated a set of phenotypic modifications, affecting behaviour, appearance, physiology and reproduction, which are consistent across a range of species. We hypothesized that some of these phenotypes could have evolved because of genetic correlation to tameness, an essential trait for successful domestication. Starting from an outbred population of red junglefowl, ancestor of all domestic chickens, we selected birds for either high or low fear of humans for five generations. Birds from the fifth selected generation (S5) showed a divergent pattern of growth and reproduction, where low fear chickens grew larger and produced larger offspring. To examine underlying genetic mechanisms, we used microarrays to study gene expression in thalamus/hypothalamus, a brain region involved in fear and stress, in both the parental generation and the S5. While parents of the selection lines did not show any differentially expressed genes, there were a total of 33 genes with adjusted p-values below 0.1 in S5. These were mainly related to sperm-function, immunological functions, with only a few known to be relevant to behaviour. Hence, five generations of divergent selection for fear of humans produced changes in hypothalamic gene expression profiles related to pathways associated with male reproduction and to immunology. This may be linked to the effects seen on growth and size of offspring. These results support the hypothesis that domesticated phenotypes may evolve because of correlated effects related to reduced fear of humans.

Posted by: Wieslaw

Re: Journal papers online - reference list - 03/10/17 04:39 PM

Anim Sci J. 2016 Aug 17. doi: 10.1111/asj.12677. [Epub ahead of print]

Involvement of circadian clock in crowing of red jungle fowls (Gallus gallus).

Ito S1, Hori S2, Hirose M1, Iwahara M2, Yatsushiro A2, Matsumoto A3, Tanaka M4, Okamoto C1, Yayou KI5, Shimmura T6,7,8.
Author information


Abstract
The rhythmic locomotor behavior of flies and mice provides a phenotype for the identification of clock genes, and the underlying molecular mechanism is well studied. However, interestingly, when examining locomotor rhythm in the wild, several key laboratory-based assumptions on circadian behavior are not supported in natural conditions. The rooster crowing 'cock-a-doodle-doo' is a symbol of the break of dawn in many countries. Previously, we used domestic inbred roosters and showed that the timing of roosters' crowing is regulated by the circadian clock under laboratory conditions. However, it is still unknown whether the regulation of crowing by circadian clock is observed under natural conditions. Therefore, here we used red jungle fowls and first confirmed that similar crowing rhythms with domesticated chickens are observed in red jungle fowls under the laboratory conditions. Red jungle fowls show predawn crowing before light onset under 12:12 light&#8201;:&#8201;dim light conditions and the free-running rhythm of crowing under total dim light conditions. We next examined the crowing rhythms under semi-wild conditions. Although the crowing of red jungle fowls changed seasonally under semi-wild conditions, predawn crowing was observed before sunrise in all seasons. This evidence suggests that seasonally changed crowing of red jungle fowls is under the control of a circadian clock.

https://www.ncbi.nlm.nih.gov/pubmed/27530363


The highest-ranking rooster has priority to announce the break of dawn Whole article

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4512148/

Posted by: KazJaps

Re: Journal papers online - reference list - 03/12/17 10:58 PM


A Major Locus for Quantitatively Measured Shank Skin Color Traits in Korean Native Chicken.
Jin S, Lee JH, Seo DW, et al.
Asian-Australasian Journal of Animal Sciences. 2016;29(11):1555-1561. doi:10.5713/ajas.16.0183.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5088374/

------------------
Association of MC1R genotypes with shank color traits in Korean native chicken.
Jin S, Park HB, Seo DW, Cahyadi M, Choi NR, Heo KN, Jo C, Lee JH. Livest Sci. 2014;170:1–7.
http://www.docsford.com/document/5754507
Posted by: Wieslaw

Re: Journal papers online - reference list - 03/17/17 04:01 PM

Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators.

Bellott DW1,2, Skaletsky H1,3, Cho TJ1, Brown L1,3, Locke D4, Chen N5,6,7, Galkina S8, Pyntikova T1, Koutseva N1, Graves T4, Kremitzki C4, Warren WC4, Clark AG5,9, Gaginskaya E8, Wilson RK4, Page DC1,2,3.

https://www.ncbi.nlm.nih.gov/pubmed/28135246

Abstract
After birds diverged from mammals, different ancestral autosomes evolved into sex chromosomes in each lineage. In birds, females are ZW and males are ZZ, but in mammals females are XX and males are XY. We sequenced the chicken W chromosome, compared its gene content with our reconstruction of the ancestral autosomes, and followed the evolutionary trajectory of ancestral W-linked genes across birds. Avian W chromosomes evolved in parallel with mammalian Y chromosomes, preserving ancestral genes through selection to maintain the dosage of broadly expressed regulators of key cellular processes. We propose that, like the human Y chromosome, the chicken W chromosome is essential for embryonic viability of the heterogametic sex. Unlike other sequenced sex chromosomes, the chicken W chromosome did not acquire and amplify genes specifically expressed in reproductive tissues. We speculate that the pressures that drive the acquisition of reproduction-related genes on sex chromosomes may be specific to the male germ line.

----------------------------------------------------------

Convergence and divergence in sex-chromosome evolution.
Peichel CL1.


Abstract
A sequence assembly of the chicken W chromosome enables reconstruction of the gene content of the W chromosome across 14 bird species and shows striking similarities in the maintenance of broadly expressed and dosage-sensitive genes on highly degenerate sex chromosomes in both birds and mammals. However, the chicken W chromosome is not enriched for genes with expression in female-specific tissues, providing an intriguing contrast to the acquisition and amplification of genes with testis-specific expression on mammalian Y chromosomes and suggesting that the inheritance of chromosomes solely through females or males can lead to different evolutionary outcomes.

https://www.ncbi.nlm.nih.gov/pubmed/28232729

Posted by: Wieslaw

Re: Journal papers online - reference list - 03/19/17 07:05 AM

Sex and death in birds: A model of dosage compensation that predicts lethality of sex chromosome aneuploids

https://www.karger.com/Article/Abstract/74349

Abstract

Birds show female heterogamety, with ZZ males and ZW females. It is still not clear whether the W is female-determining, or whether two doses of the Z chromosomes are male-determining, or both. This question could easily be settled by the sexual phenotypes of ZZW and ZO birds, in the same way that the sexual phenotypes of XXY and XO showed that the Y is male determining in humans, but that the dosage of an X-borne gene determines sex in Drosophila. However, despite extensive searches, no ZZW or ZO diploid birds have been satisfactorily documented, so we must assume that these genotypes are embryonic lethals. Given that ZW and ZZ are viable and the W contains few genes it is not clear why this should be so. Here I propose that sex chromosome aneuploids are lethal in chicken because, to achieve dosage compensation, a locus on the W chromosome controls the upregulation of genes on the Z in ZW females. ZO birds would therefore have only half the normal dose of Z-linked gene product and ZZW would have twice the amount, both of which would undoubtedly be incompatible with life. Reports of other aneuploids and triploids are also consistent with this hypothesis.   
© 2003 S. Karger AG, Basel


Conserved synteny between the chicken Z sex chromosome and human chromosome 9 includes the male regulatory gene DMRT1: a comparative (re)view on avian sex determination

https://www.karger.com/Article/Abstract/15567

Abstract.
Sex-determination mechanisms in birds and mammals evolved independently for more than 300 million years. Unlike mammals, sex determination in birds operates through a ZZ/ZW sex chromosome system, in which the female is the heterogametic sex. However, the molecular mechanism remains to be elucidated. Comparative gene mapping revealed that several genes on human chromosome 9 (HSA 9) have homologs on the chicken Z chromosome (GGA Z), indicating the common ancestry of large parts of GGA Z and HSA 9. Based on chromosome homology maps, we isolated a Z-linked chicken ortholog of DMRT1, which has been implicated in XY sex reversal in humans. Its location on the avian Z and within the sex-reversal region on HSA 9p suggests that DMRT1 represents an ancestral dosage-sensitive gene for vertebrate sex-determination. Z dosage may be crucial for male sexual differentiation/determination in birds.   
© 2000 S. Karger AG, Basel

Enhanced Expression of Serotonin Receptor 5-Hydroxytryptamine 2C is Associated with Increased Feather Damage in Dongxiang Blue-Shelled Layers.

https://www.ncbi.nlm.nih.gov/pubmed/28275879

Abstract
The gene encoding the serotonin receptor 5-hydroxytraptamine 2C (HTR2C) has been implicated in behavioral phenotypes in a number of species. In previous studies, a mutation in the chicken HTR2C gene was found to be associated with feather condition, thereby suggesting a relationship between the gene and receiving feather pecking activity. The present study analyzed the chicken HTR2C gene at both the genomic make-up and expression level in Dongxiang blue-shelled layer. A significant association between the single nucleotide polymorphism (SNP) rs13640917 (C/T) and feather condition was confirmed in the Chinese local layer. Enhanced HTR2C gene expression (151.1-fold) that was associated with high feather damage indicated that the right cerebrum might be the critical region for HTR2C to participate in the regulation of receiving feather pecking behavior.


Posted by: Wieslaw

Re: Journal papers online - reference list - 03/19/17 12:36 PM

Novel copy number variation of the TGF&#946;3 gene is associated with TGF&#946;3 gene expression and duration of fertility traits in hens.

https://www.ncbi.nlm.nih.gov/pubmed/28301526

Abstract
Improvements in the duration of fertility (DF) could increase the interval between successive artificial inseminations, thereby decreasing the cost associated with production of hatching eggs. The molecular mechanisms involved in DF in hens remains under-explored. In this study, expression levels of the transforming growth factor-&#946; genes (TGF&#946;s: TGF&#946;1, TGF&#946;2, TGF&#946;3) were investigated in utero-vaginal junctions (UVJs) of hens with long DF (Group L, n = 10) and short DF (Group S, n = 10). TGF&#946;1 and 2 tended to exhibit higher expression levels in UVJs from Group L hens. The expression levels of TGF&#946;3 mRNA and protein were significantly increased in UVJs of hens from Group L compared to hens in Group S. Consistently, six TGF&#946;s downstream genes (DAXX, MEKK1, T-BET, GATA-3, TAK1, and FOXP3) associated with the immune response were found to be significantly differentially expressed in UVJs of Group L than Group S hens. In addition, four SNPs were identified in intron 1 of TGF&#946;3, and these SNPs were significantly associated with DF traits (P < 0.05). Furthermore, we identified multi-copy and copy number variants (CNVs) in chicken TGF&#946;3 and later determined significant associations between TGF&#946;3 CNVs and DF traits in hens. Specifically, TGF&#946;3 copy number exhibited a significant positive correlation with its expression (P < 0.05). Collectively, our results suggest that chicken DF traits may be regulated by the expression of TGF&#946;3 in UVJ. Meanwhile, the copy number variation in the TGF&#946;3 gene identified in this study seems to be one marker for DF traits.

free full text

http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0173696&type=printable
Posted by: SKGray21

Re: Journal papers online - reference list - 03/28/17 04:50 PM

Found this while browsing/searching for some of the papers listed on this thread.
grin

Mixed ancestry and admixture in Kauai's feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs

Gering, E., Johnsson, M., Willis, P., Getty, T. and Wright, D. (2015), Mol Ecol, 24: 2112–2124. doi:10.1111/mec.13096

http://onlinelibrary.wiley.com/doi/10.1111/mec.13096/full

Abstract

A major goal of invasion genetics is to determine how establishment histories shape non-native organisms' genotypes and phenotypes. While domesticated species commonly escape cultivation to invade feral habitats, few studies have examined how this process shapes feral gene pools and traits. We collected genomic and phenotypic data from feral chickens (Gallus gallus) on the Hawaiian island of Kauai to (i) ascertain their origins and (ii) measure standing variation in feral genomes, morphology and behaviour. Mitochondrial phylogenies (D-loop & whole Mt genome) revealed two divergent clades within our samples. The rare clade also contains sequences from Red Junglefowl (the domestic chicken's progenitor) and ancient DNA sequences from Kauai that predate European contact. This lineage appears to have been dispersed into the east Pacific by ancient Polynesian colonists. The more prevalent MtDNA clade occurs worldwide and includes domesticated breeds developed recently in Europe that are farmed within Hawaii. We hypothesize this lineage originates from recently feralized livestock and found supporting evidence for increased G. gallus density on Kauai within the last few decades. SNPs obtained from whole-genome sequencing were consistent with historic admixture between Kauai's divergent (G. gallus) lineages. Additionally, analyses of plumage, skin colour and vocalizations revealed that Kauai birds' behaviours and morphologies overlap with those of domestic chickens and Red Junglefowl, suggesting hybrid origins. Together, our data support the hypotheses that (i) Kauai's feral G. gallus descend from recent invasion(s) of domestic chickens into an ancient Red Junglefowl reservoir and (ii) feral chickens exhibit greater phenotypic diversity than candidate source populations. These findings complicate management objectives for Pacific feral chickens, while highlighting the potential of this and other feral systems for evolutionary studies of invasions.
Posted by: Wieslaw

Re: Journal papers online - reference list - 04/16/17 05:04 PM


Bird Integumentary Melanins: Biosynthesis, Forms, Function and Evolution.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848976/pdf/ijms-17-00520.pdf

Whole document
Posted by: Wieslaw

Re: Journal papers online - reference list - 04/24/17 01:29 AM

Here is a very interesting abstract. PAY ATTENTION to the red part. It recalls some patterns in chickens

https://www.ncbi.nlm.nih.gov/pubmed/12851331


Ann N Y Acad Sci. 2003 Jun;994:313-8.
Melanocortin receptor variants with phenotypic effects in horse, pig, and chicken.
Andersson L1.
Author information


Abstract
The melanocortin system is of considerable interest in domestic animals because their energy metabolism and pigmentation have been under strong selection. This article reviews our work on MC1R variants in horse, pig, and chicken, as well as a study on MC4R polymorphism in the pig. The chestnut coat color in horses is caused by an MC1R missense mutation (S83F). In the pig, we have described seven MC1R alleles controlling four different coat color phenotypes (wild type, dominant black, black spotting, and recessive red). The most interesting allele is the one causing black spotting because it carries two causative mutations, a frameshift and a missense mutation. The frameshift mutation is somatically unstable, and the black spots reflect somatic reversion events restoring the reading frame. Classic genetics have established eight alleles at the Extended black locus in chicken, which is assumed to correspond to the Extension locus in mammals. We have analyzed the co-segregation of alleles at MC1R and Extended black using a red jungle fowl x White Leghorn intercross and provide compelling evidence that these loci are identical. A previous study indicated that a missense mutation (D298N) in pig MC4R has an effect on fatness, growth, and feed intake. We could not confirm this association using an intercross between the wild boar and Large White domestic pigs, but it is possible that our F(2) generation was too small to detect the rather modest effect reported for this polymorphism.

Posted by: Redcap

Re: Journal papers online - reference list - 04/24/17 05:52 PM

On the right sight, there is mentioned a follow-up study exclusivly about chicken.
https://www.ncbi.nlm.nih.gov/pubmed/12873211
Posted by: KazJaps

Re: Journal papers online - reference list - 04/25/17 07:29 PM

The following paper discusses more that pig MC1R (E locus) black spotting allele E^P:

Kijas, J. M., Moller, M., Plastow, G., & Andersson, L. (2001)
A frameshift mutation in MC1R and a high frequency of somatic reversions cause black spotting in pigs.
Genetics, 158(2), 779–785.
Full paper -pdf
Abstract:
Quote:
Black spotting on a red or white background in pigs is determined by the E(P) allele at the MC1R/Extension locus. A previous comparison of partial MC1R sequences revealed that E(P) shares a missense mutation (D121N) with the E(D2) allele for dominant black color. Sequence analysis of the entire coding region now reveals a second mutation in the form of a 2-bp insertion at codon 23 (nt67insCC). This mutation expands a tract of six C nucleotides to eight and introduces a premature stop codon at position 56. This frameshift mutation is expected to cause a recessive red color, which was in fact observed in some breeds with the E(P) allele present (Tamworth and Hereford). RT-PCR analyses were conducted using skin samples taken from both spotted and background areas of spotted pigs. The background red area had transcript only from the mutant nt67insCC MC1R allele, whereas the black spot also contained a transcript without the 2-bp insertion. This indicates that black spots are due to somatic reversion events that restore the frame and MC1R function. The phenotypic expression of the E(P) allele is highly variable and the associated coat color ranges from red, red with black spots, white with black spots, to almost completely solid black. In several breeds of pigs the phenotypic manifestation of this allele has been modified by selection for or against black spots.

So it is a bizarre allele that has two mutations, one which on its own gives a dominant black phenotype, the other on its own would give a recessive red (tan) phenotype. But instead of one mutation dominating /suppressing the other, or giving an intermediate phenotype, the allele produces a patchy somatic reversion phenotype, expressing the black mutation in spots only. This is very different expression to eb & similar alleles in chickens which have both dominant black MC1R substitutions with other ameliorating substitutions (including White Prat e^bc allele).
Posted by: Redcap

Re: Journal papers online - reference list - 04/26/17 12:38 AM

An interesting fact of red pigmentation in Cows is, that red protects against sunburn and skin cancer (e.g. at the udder) - much better than in white or black animals.
Posted by: Hen-Gen

Re: Journal papers online - reference list - 04/26/17 01:55 AM

Interesting indeed, Redcap. Though my cows are black (Galloways) sunburn is unlikely to be a problem in these northern climes.
But the world wide domination of the Freisian/Holstein as a dairy animal would seem to be problematic. We could be on the cusp of the increase of Ayrshires and Shorthorns!
Posted by: Redcap

Re: Journal papers online - reference list - 04/27/17 11:11 PM

I came over this curiosity due to the research about the history of commercial Leghorn ... I could trace back all known Big Chicken lines to Wyckoff & Tancred Farm, who were the pioneres in using Trapnests.
https://books.google.com.au/books?id=nMQ...off&f=false
By this way I came over Shaver Poultry to Shaver Beef Blend (nine breeds blend) and the genetics of red coat.
http://www.shaverbeef.com/shaver-beefblend-history/

Quote:
On his father’s side, the Shaver name is from the middle-high German "schæfære" meaning shepherd. Don Shaver was descended from Hessian mercenaries. George 3rd engaged Hessian mercenaries to combat American Independence forces. In all twenty thousand troops from Hesse fought during the Revolutionary War, plus ten thousand from other German states. When they were demobilised back to England, they were given the option of settling in England; some of them did and married English women; others were offered tracts of land in Canada. Don Shaver’s ancestor was in that group and migrated in about 1840. [....] In 1959, Shaver developed a new beef breed - Shaver Beef Brand – and when talking at the cattle breeders meetings it would be as a hen breeder stepping into their world; a head wind of resistance and the cattlemen directed an attitude of neophyte at Shaver. The development of broiler products also meet with a similar, though lesser, resistance.
The Beef Brand was stabilised in 1985. Shaver cattle are the most advanced Composite beef breed available worldwide. The beef brand was renamed the Shaver Composites. The Composites were derived from nine breeds of cattle (Galloway, Highland, Red Devon, South Devon and Lincoln Red, Gelbvieh, Saler, Blonde Aquitane and Maine Anjou) and have higher levels of heterosis than composites derived from only three or four breeds. Since the composites do not contain Angus, Hereford, Friesian or Simmental genes, a greater heterosis is possible when used as a sire of these breeds (www.shaverbeef.co.nz/ 13.7.2010).

http://www.hypor.com/~/media/Files/ISA/H...td%20Canada.pdf
Posted by: KazJaps

Re: Journal papers online - reference list - 05/04/17 08:30 PM

Researchers have undertaken further research of their earlier sex-linked barring DNA sequencing 2010 study, substantiated that there are indeed 3 mutation alleles with 3 different phenotypes on the sex-linked barring B locus:

Allele B1: B Sex-linked Barring,
Allele B2: B^Sd Sex-linked Dilution,
Allele B0: Sex-linked Extreme Dilution (new mutation discovered).

References:
2017:
Schwochow Thalmann, D., Ring, H., Sundström, E., Cao, X., Larsson, M., Kerje, S., … Andersson, L. (2017).
The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes in CDKN2A.
PLoS Genetics, 13(4), e1006665. http://doi.org/10.1371/journal.pgen.1006665
- Full paper -pdf
- additional supporting files download page (download individually or all as a zip file)
* some supporting files include photos (eg heterozygous B0 chick down, etc)

2010
Hellström AR, Sundstrom E, Gunnarsson U, Bed'Hom B, Tixier-Boichard M, Honaker CF, et al.
Sex-linked barring in chickens is controlled by the CDKN2A /B tumour suppressor locus.
Pigment Cell Melanoma Res. 2010;23(4):521–30. doi: 10.1111/j.1755-148X.2010.00700.x
- Full paper -pdf
- additional supporting file - PCMR_700_sm_fS1.doc (includes Figure S1 and Table S1)

2009
Dorshorst BJ, Ashwell CM. (2009)
Genetic mapping of the sex-linked barring gene in the chicken.
Poult Sci. 2009 Sep;88(9):1811-7. doi: 10.3382/ps.2009-00134.
Full paper -pdf

-----------------------------

* Note, I've started a new thread "New 2017 B locus paper - 3 mutation alleles" on this 2017 paper for anyone who would like to discuss the topic further....

http://www.the-coop.org/forums/ubbthreads.php?ubb=showflat&Number=116609
Posted by: KazJaps

Re: Journal papers online - reference list - 06/06/17 09:46 PM

He, C., Chen, Y., Yang, K., Zhai, Z., Zhao, W., Liu, S., … Meng, H. (2017).
Genetic pattern and gene localization of polydactyly in Beijing fatty chicken.
PLoS ONE, 12(5), e0176113. http://doi.org/10.1371/journal.pone.0176113
Posted by: Wieslaw

Re: Journal papers online - reference list - 06/23/17 12:40 PM

Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators.
Bellott DW1,2, Skaletsky H1,3, Cho TJ1, Brown L1,3, Locke D4, Chen N5,6,7, Galkina S8, Pyntikova T1, Koutseva N1, Graves T4, Kremitzki C4, Warren WC4, Clark AG5,9, Gaginskaya E8, Wilson RK4, Page DC1,2,3.

https://www.ncbi.nlm.nih.gov/pubmed/28135246

Abstract
After birds diverged from mammals, different ancestral autosomes evolved into sex chromosomes in each lineage. In birds, females are ZW and males are ZZ, but in mammals females are XX and males are XY. We sequenced the chicken W chromosome, compared its gene content with our reconstruction of the ancestral autosomes, and followed the evolutionary trajectory of ancestral W-linked genes across birds. Avian W chromosomes evolved in parallel with mammalian Y chromosomes, preserving ancestral genes through selection to maintain the dosage of broadly expressed regulators of key cellular processes. We propose that, like the human Y chromosome, the chicken W chromosome is essential for embryonic viability of the heterogametic sex. Unlike other sequenced sex chromosomes, the chicken W chromosome did not acquire and amplify genes specifically expressed in reproductive tissues. We speculate that the pressures that drive the acquisition of reproduction-related genes on sex chromosomes may be specific to the male germ line.

Posted by: Wieslaw

Re: Journal papers online - reference list - 07/17/17 01:11 AM


Trends Genet. 2002 Jan;18(1):25-8.

Dosage compensation: do birds do it as well?
Ellegren H1.

Abstract
In birds males carry ZZ and females ZW sex chromosomes, and it has been proposed that there is no dosage compensation in the expression of sex-linked genes. However, recent data suggest the opposite, indicating that male and female birds might demonstrate similar levels of expression of Z-linked genes. If they do, the equalization between the sexes is probably not achieved by inactivation of one of the male Z chromosomes. Other possible mechanisms include the transcription of Z-linked genes being upregulated in females or downregulated in males, or equalization at the translation stage in either sex. A recently identified hypermethylated region on the Z chromosome, with similarities to the X inactivation centre on the mammalian X chromosome, might play a part in this process or have a role in avian sex determination.

https://www.ncbi.nlm.nih.gov/pubmed/11750697

----------------------------------------------------------

Avian sex, sex chromosomes, and dosage compensation in the age of genomics.
Graves JA1.

Abstract
Comparisons of the sex chromosome systems in birds and mammals are widening our view and deepening our understanding of vertebrate sex chromosome organization, function, and evolution. Birds have a very conserved ZW system of sex determination in which males have two copies of a large, gene-rich Z chromosome, and females have a single Z and a female-specific W chromosome. The avian ZW system is quite the reverse of the well-studied mammalian XY chromosome system, and evolved independently from different autosomal blocs. Despite the different gene content of mammal and bird sex chromosomes, there are many parallels. Genes on the bird Z and the mammal X have both undergone selection for male-advantage functions, and there has been amplification of male-advantage genes and accumulation of LINEs. The bird W and mammal Y have both undergone extensive degradation, but some birds retain early stages and some mammals terminal stages of the process, suggesting that the process is more advanced in mammals. Different sex-determining genes, DMRT1 and SRY, define the ZW and XY systems, but DMRT1 is involved in downstream events in mammals. Birds show strong cell autonomous specification of somatic sex differences in ZZ and ZW tissue, but there is growing evidence for direct X chromosome effects on sexual phenotype in mammals. Dosage compensation in birds appears to be phenotypically and molecularly quite different from X inactivation, being partial and gene-specific, but both systems use tools from the same molecular toolbox and there are some signs that galliform birds represent an early stage in the evolution of a coordinated system.

https://www.ncbi.nlm.nih.gov/pubmed/24599719
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The avian Z-linked gene DMRT1 is required for male sex determination in the chicken.
Smith CA1, Roeszler KN, Ohnesorg T, Cummins DM, Farlie PG, Doran TJ, Sinclair AH.
Author information


Abstract
Sex in birds is chromosomally based, as in mammals, but the sex chromosomes are different and the mechanism of avian sex determination has been a long-standing mystery. In the chicken and all other birds, the homogametic sex is male (ZZ) and the heterogametic sex is female (ZW). Two hypotheses have been proposed for the mechanism of avian sex determination. The W (female) chromosome may carry a dominant-acting ovary determinant. Alternatively, the dosage of a Z-linked gene may mediate sex determination, two doses being required for male development (ZZ). A strong candidate avian sex-determinant under the dosage hypothesis is the conserved Z-linked gene, DMRT1 (doublesex and mab-3-related transcription factor 1). Here we used RNA interference (RNAi) to knock down DMRT1 in early chicken embryos. Reduction of DMRT1 protein expression in ovo leads to feminization of the embryonic gonads in genetically male (ZZ) embryos. Affected males show partial sex reversal, characterized by feminization of the gonads. The feminized left gonad shows female-like histology, disorganized testis cords and a decline in the testicular marker, SOX9. The ovarian marker, aromatase, is ectopically activated. The feminized right gonad shows a more variable loss of DMRT1 and ectopic aromatase activation, suggesting differential sensitivity to DMRT1 between left and right gonads. Germ cells also show a female pattern of distribution in the feminized male gonads. These results indicate that DMRT1 is required for testis determination in the chicken. Our data support the Z dosage hypothesis for avian sex determination.

https://www.ncbi.nlm.nih.gov/pubmed/19710650

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Posted by: KazJaps

Re: Journal papers online - reference list - 09/19/17 06:06 AM

A sex-linked dominant tail-less (feathers only) mutation, in a Chinese breed:

Wang, Qiong et al. “A Novel Sex-Linked Mutant Affecting Tail Formation in Hongshan Chicken.” Scientific Reports 7 (2017): 10079. PMC. Web. 19 Sept. 2017.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5577132/

Hongshan chicken photos here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5577132/figure/Fig1/
Posted by: KazJaps

Re: Journal papers online - reference list - 09/19/17 06:35 AM

The following 2017 paper compares various mutations/phenotypes in chickens, pigeons etc (eg naked neck, frizzle, silky feathers, foot feathers (ptilopody), crests, etc

Boer EF, Van Hollebeke HF, Shapiro MD.
Genomic determinants of epidermal appendage patterning and structure in domestic birds.
Dev Biol. 2017 Sep 15;429(2):409-419. doi: 10.1016/j.ydbio.2017.03.022. Epub 2017 Mar 24.
http://www.sciencedirect.com/science/article/pii/S0012160616308673
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Another 2017 paper on pigeons:

Domyan, E. T., & Shapiro, M. D. (2017).
Pigeonetics takes flight: evolution, development, and genetics of intraspecific variation.
Developmental Biology, 2017 427(2), 241–250. http://doi.org/10.1016/j.ydbio.2016.11.008
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5521274/
Posted by: Redcap

Re: Journal papers online - reference list - 09/19/17 11:47 AM

Originally Posted By: KazJaps
The following 2017 paper compares various mutations/phenotypes in chickens, pigeons etc (eg naked neck, frizzle, silky feathers, foot feathers (ptilopody), crests, etc

Boer EF, Van Hollebeke HF, Shapiro MD.
Genomic determinants of epidermal appendage patterning and structure in domestic birds.
Dev Biol. 2017 Sep 15;429(2):409-419. doi: 10.1016/j.ydbio.2017.03.022. Epub 2017 Mar 24.
http://www.sciencedirect.com/science/article/pii/S0012160616308673
--------------------
Another 2017 paper on pigeons:

Domyan, E. T., & Shapiro, M. D. (2017).
Pigeonetics takes flight: evolution, development, and genetics of intraspecific variation.
Developmental Biology, 2017 427(2), 241–250. http://doi.org/10.1016/j.ydbio.2016.11.008
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5521274/


Added paper link