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#116518 - 03/17/17 04:01 PM Re: Journal papers online - reference list [Re: KazJaps]
Wieslaw Offline
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Registered: 09/18/09
Posts: 3757
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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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



Edited by Wieslaw (03/21/17 10:57 AM)

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#116523 - 03/19/17 07:05 AM Re: Journal papers online - reference list [Re: Wieslaw]
Wieslaw Offline
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Classroom Professor

Registered: 09/18/09
Posts: 3757
Loc: Denmark
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.




Edited by Wieslaw (03/19/17 12:31 PM)
Edit Reason: added link

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#116524 - 03/19/17 12:36 PM Re: Journal papers online - reference list [Re: Wieslaw]
Wieslaw Offline
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Registered: 09/18/09
Posts: 3757
Loc: Denmark
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

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#116557 - 03/28/17 04:50 PM Re: Journal papers online - reference list [Re: KazJaps]
SKGray21 Offline
Feather

Registered: 09/01/16
Posts: 36
Loc: Kauai, HI, USA
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: 21122124. 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.


Edited by SKGray21 (03/28/17 04:52 PM)
Edit Reason: Added abstract

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#116583 - 04/16/17 05:04 PM Re: Journal papers online - reference list [Re: SKGray21]
Wieslaw Offline
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Classroom Professor

Registered: 09/18/09
Posts: 3757
Loc: Denmark

Bird Integumentary Melanins: Biosynthesis, Forms, Function and Evolution.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848976/pdf/ijms-17-00520.pdf

Whole document

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#116587 - 04/24/17 01:29 AM Re: Journal papers online - reference list [Re: Wieslaw]
Wieslaw Offline
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Classroom Professor

Registered: 09/18/09
Posts: 3757
Loc: Denmark
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.


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#116588 - 04/24/17 05:52 PM Re: Journal papers online - reference list [Re: Wieslaw]
Redcap Online   content
Ruler of the Roost

Registered: 08/14/06
Posts: 952
Loc: Germany
On the right sight, there is mentioned a follow-up study exclusivly about chicken.
https://www.ncbi.nlm.nih.gov/pubmed/12873211
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#116589 - 04/25/17 07:29 PM Re: Journal papers online - reference list [Re: Redcap]
KazJaps Offline
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Registered: 08/30/02
Posts: 2799
Loc: Australia
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), 779785.
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).

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#116590 - 04/26/17 12:38 AM Re: Journal papers online - reference list [Re: KazJaps]
Redcap Online   content
Ruler of the Roost

Registered: 08/14/06
Posts: 952
Loc: Germany
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.
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#116591 - 04/26/17 01:55 AM Re: Journal papers online - reference list [Re: Redcap]
Hen-Gen Online   content
Ruler of the Roost

Registered: 10/01/05
Posts: 1141
Loc: Island of Fetlar, Shetland
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!


Edited by Hen-Gen (04/26/17 01:57 AM)
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