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#116595 - 04/27/17 11:11 PM Re: Journal papers online - reference list [Re: Hen-Gen]
Redcap Offline
Ruler of the Roost

Registered: 08/14/06
Posts: 954
Loc: Germany
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
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#116611 - 05/04/17 08:30 PM Re: Journal papers online - reference list [Re: Wieslaw]
KazJaps Offline
Classroom Professor

Registered: 08/30/02
Posts: 2807
Loc: Australia
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

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* 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

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#116656 - 06/06/17 09:46 PM Re: Journal papers online - reference list [Re: KazJaps]
KazJaps Offline
Classroom Professor

Registered: 08/30/02
Posts: 2807
Loc: Australia
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

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#116688 - 06/23/17 12:40 PM Re: Journal papers online - reference list [Re: KazJaps]
Wieslaw Offline
Moderator
Classroom Professor

Registered: 09/18/09
Posts: 3769
Loc: Denmark
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.


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#116750 - 07/17/17 01:11 AM Re: Journal papers online - reference list [Re: Wieslaw]
Wieslaw Offline
Moderator
Classroom Professor

Registered: 09/18/09
Posts: 3769
Loc: Denmark

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

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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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#116822 - 09/19/17 06:06 AM Re: Journal papers online - reference list [Re: Wieslaw]
KazJaps Offline
Classroom Professor

Registered: 08/30/02
Posts: 2807
Loc: Australia
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/

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#116823 - 09/19/17 06:35 AM Re: Journal papers online - reference list [Re: KazJaps]
KazJaps Offline
Classroom Professor

Registered: 08/30/02
Posts: 2807
Loc: Australia
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/


Edited by KazJaps (09/19/17 09:59 PM)
Edit Reason: added link -thanks RedCap

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#116824 - 09/19/17 11:47 AM Re: Journal papers online - reference list [Re: KazJaps]
Redcap Offline
Ruler of the Roost

Registered: 08/14/06
Posts: 954
Loc: Germany
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
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#116891 - 11/01/17 12:53 AM Re: Journal papers online - reference list [Re: Redcap]
KazJaps Offline
Classroom Professor

Registered: 08/30/02
Posts: 2807
Loc: Australia
Further research on Polydactyly in Beijing You chickens:

Qin Chu, Zhixun Yan, Jian Zhang, Tahir Usman, Yao Zhang, Hui Liu, Haihong Wang, Ailian Geng, Huagui Liu
Association of SNP rs80659072 in the ZRS with polydactyly in Beijing You chickens.

PLoS One. 2017; 12(10): e0185953.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5633194/

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#116892 - 11/01/17 01:14 AM Re: Journal papers online - reference list [Re: KazJaps]
KazJaps Offline
Classroom Professor

Registered: 08/30/02
Posts: 2807
Loc: Australia
The NCBI chicken genome map viewer website is not being updated anymore.

But a new NCBI website chicken genome browser has been made available, & will be continually updated:
https://www.ncbi.nlm.nih.gov/genome/gdv/?org=gallus-gallus

Eg, it has the old Linkage Group E22C19W28 genes now placed on Microchromosome 33 (this includes loci: Fray, Crest, Dominant White, Frizzle, etc).

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