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#116908 - 11/09/17 04:00 PM Re: Journal papers online - reference list [Re: KazJaps]
Wieslaw Online   content
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Sex Reversal and Comparative Data Undermine the W Chromosome and Support Z-linked DMRT1 as the Regulator of Gonadal Sex Differentiation in Birds.

https://www.ncbi.nlm.nih.gov/pubmed/28911174

Abstract

The exact genetic mechanism regulating avian gonadal sex differentiation has not been completely resolved. The most likely scenario involves a dosage mechanism, whereby the Z-linked DMRT1 gene triggers testis development. However, the possibility still exists that the female-specific W chromosome may harbor an ovarian determining factor. In this study, we provide evidence that the universal gene regulating gonadal sex differentiation in birds is Z-linked DMRT1 and not a W-linked (ovarian) factor. Three candidate W-linked ovarian determinants are HINTW, female-expressed transcript 1 (FET1), and female-associated factor (FAF). To test the association of these genes with ovarian differentiation in the chicken, we examined their expression following experimentally induced female-to-male sex reversal using the aromatase inhibitor fadrozole (FAD). Administration of FAD on day 3 of embryogenesis induced a significant loss of aromatase enzyme activity in female gonads and masculinization. However, expression levels of HINTW, FAF, and FET1 were unaltered after experimental masculinization. Furthermore, comparative analysis showed that FAF and FET1 expression could not be detected in zebra finch gonads. Additionally, an antibody raised against the predicted HINTW protein failed to detect it endogenously. These data do not support a universal role for these genes or for the W sex chromosome in ovarian development in birds. We found that DMRT1 (but not the recently identified Z-linked HEMGN gene) is male upregulated in embryonic zebra finch and emu gonads, as in the chicken. As chicken, zebra finch, and emu exemplify the major evolutionary clades of birds, we propose that Z-linked DMRT1, and not the W sex chromosome, regulates gonadal sex differentiation in birds.

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#116919 - 11/21/17 12:30 AM Re: Journal papers online - reference list [Re: KazJaps]
Redcap Offline
Ruler of the Roost

Registered: 08/14/06
Posts: 957
Loc: Germany
Kimball, E. (1953). Genetics of Buttercup Plumage Pattern in the Fowl, Poultry Science, Volume 32, Issue 4, 1 July 1953, Pages 683–692.
http://documents.kippenjungle.nl/#post50
Kimball, E. (1960). Differential Penciled Phenotypes & Genetic Origin of Penciled Pattern. Volume 39, Issue 1, 1 January 1960, Pages 232-234.
http://documents.kippenjungle.nl/#post49
_________________________

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#116953 - 12/10/17 05:40 PM Re: Journal papers online - reference list [Re: Redcap]
KazJaps Offline
Classroom Professor

Registered: 08/30/02
Posts: 2819
Loc: Australia
Posting again for easier reference to papers, abstracts & summaries...

To mutations that increase size - ie larger than Red Jungle Fowl.

Kerje et al. 2003.The twofold difference in adult size between the red junglefowl and White Leghorn chickens is largely explained by a limited number of QTLs. Anim Genet. 2003 Aug;34(4):264-74. -Abstract here
Quote:
The QTL analysis of growth traits revealed 13 loci that showed genome-wide significance. The four major growth QTLs explained 50 and 80% of the difference in adult body weight between the founder populations for females and males, respectively. A major QTL for growth, located on chromosome 1 appears to have pleiotropic effects on feed consumption, egg production and behaviour. There was a strong positive correlation between adult body weight and average egg weight. However, three QTLs affecting average egg weight but not body weight were identified. An interesting observation was that the estimated effects for the four major growth QTLs all indicated a codominant inheritance.


In summary:
* 13 loci affected growth (in these White Leghorns)
* 4 of which affected major growth, 50% in females, 80% in males.
* Of these 4 loci, all indicated codominant inheritance.

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

Further research 2009:
Wahlberg et al. 2009.Genetic analysis of an F2 intercross between two chicken lines divergently selected for body-weight. BMC Genomics. 2009; 10: 248. Full report
This time they refined the research, & included epistatic interactions. Eg, apparently chromosome 7, 'Growth9' QTL is important for expression for other growth loci alleles (including on other autosomal chromosomes).
Quote:
Nine of the 15 unique epistatic pairs involved interaction with the major QTL on chromosome 7 (Growth9)....

....Originally, six genome-wide significant interacting loci were reported on chromosomes 1, 2, 3, 4, 7 and 20. The loci on chromosome 1, 4, 7 and 20 are still genome-wide significant in this analysis, though the loci detected on chromosome 2 and 3 are no longer significant using the new map. On the other hand, two new loci located in a previously uncovered part of chromosome 3 as well as a locus on chromosome 24 now reach significance above the threshold level.



In short - growth factors / body weight is a polygenic trait.

- Growth factor loci were found on chromosomes 1, 2, 3, 4, 7, 20 and 24.

- 15 loci (inc. two new ones) were found to influence growth.

--------------------------------
Another one testing body weight differences between Silkie fowl & White Plymouth Rock:

Gu et al. 2011. Genome-Wide Association Study of Body Weight in Chicken F2 Resource Population PLoS ONE 6(7): e21872. https://doi.org/10.1371/journal.pone.0021872
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021872
Quote:
A chicken chromosome 4 (GGA4) region approximately 8.6 Mb in length (71.6–80.2 Mb) had a large number of significant SNP effects for late growth during weeks 7–12. The LIM domain-binding factor 2 (LDB2) gene in this region had the strongest association with body weight for weeks 7–12 and with average daily gain for weeks 6–12. This GGA4 region was previously reported to contain body weight QTL. GGA1 and GGA18 had three SNP effects on body weight with genome-wide significance.

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#116978 - 12/26/17 07:25 PM Re: Journal papers online - reference list [Re: KazJaps]
KazJaps Offline
Classroom Professor

Registered: 08/30/02
Posts: 2819
Loc: Australia
Just released Dec 2017 paper on dwarf chickens, includes research on Seramas, etc:

Wang et al., 2017.
An Evolutionary Genomic Perspective on the Breeding of Dwarf Chickens.
Molecular Biology and Evolution, Volume 34, Issue 12, 1 December 2017, Pages 3081–3088, https://doi.org/10.1093/molbev/msx227
Abstract only
Quote:
Herein, we explore the evolution of the Serama, the smallest breed of chicken. Leveraging comparative population genomics, analyses identify several genes that are potentially associated with the growth and development of bones and muscles. These genes, and in particular both POU1F1 and IGF1, are under strong positive selection. Three allopatric dwarf bantams (Serama, Yuanbao, and Daweishan) with different breeding-histories, form distinct clusters and exhibit unique population structures. Parallel genetic mechanisms underlay their variation in body size. These findings provide insights into the multiple and complex pathways, depending on genomic variation, that chicken can take in response to aviculture selection for dwarfism.

*Unfortunately only the abstract available for free.

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

Earlier 2017 paper that compares the dwarf Chinese breed Daweishan with a fast growing large breed, the Wuding chicken.

Dou T, Zhao S, Rong H, et al. 2017.
Biological mechanisms discriminating growth rate and adult body weight phenotypes in two Chinese indigenous chicken breeds.
BMC Genomics. 2017;18:469. doi:10.1186/s12864-017-3845-9.
Full Paper

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#116979 - 12/26/17 08:16 PM Re: Journal papers online - reference list [Re: KazJaps]
KazJaps Offline
Classroom Professor

Registered: 08/30/02
Posts: 2819
Loc: Australia
New 2017 Dec. paper on late feathering & ev21:

A Takenouchi, M Toshishige, N Ito, M Tsudzuki; 2017.
Endogenous viral gene ev21 is not responsible for the expression of late feathering in chickens.
Poultry Science, , pex345, https://doi.org/10.3382/ps/pex345
Abstract only
Quote:
Abstract
The late-feathering (LF) gene K on the Z chromosome is an important gene in the chicken industry, which is frequently utilized for the feather sexing, a type of autosexing, of neonatal chicks. The K gene is closely associated with the endogenous ev21 gene from an avian leukosis virus and the incomplete duplication (ID) of prolactin receptor (PRLR) and sperm flagellar protein 2 (SPEF2) genes, and ev21 has been used as a molecular marker to detect LF birds. In the present study, a comprehensive survey for the presence or absence of ev21 and ID across 1,994 birds from 52 chicken breeds, three commercial hybrid groups, and the Red Jungle Fowl revealed that almost all LF breeds have both ev21 and ID. However, only one LF breed (Ingie) has only ID and no ev21. Moreover, this study revealed that almost all early (normal)-feathering (EF) breeds lack both ev21 and ID, but only one breed (White Plymouth Rock) included EF birds with ev21 but no ID. Therefore, regarding LF expression, the results indicated that ID is responsible, but ev21 is not required. Henceforth, ID should be used as a molecular marker to detect LF birds instead of ev21. Because ev21 contains the full genome of an avian leukosis virus, there is a risk of disease development in breeds with this gene. Therefore, the Ingie breed, which has no ev21 at the K locus, represents excellent material for the establishment of new LF stocks.

*Note, earlier research had noted that ev21 positive was not responsible for the late feathering trait, this determined with LF lines where individuals mutated back to wild-type k+ (early feathering) but still ev21 positive. Where the above 2017 research differs is in finding a K late feathering breed that is ev21 negative.

Elferink MG, Vallée AA, Jungerius AP, Crooijmans RP, Groenen MA. 2008.
Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken.
BMC Genomics. 2008;9:391. doi:10.1186/1471-2164-9-391
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2542384/

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

In the following 2016 research paper the authors believed that the SPEF2 gene & not PRLR might be more responsible for the late feathering phenotype (indicated in their gene expression research):

J. Zhao, J. Yao, F. Li, Z. Yang, Z. Sun, L. Qu, K. Wang, Y. Su, A. Zhang, S. A. Montgomery, T. Geng, H. Cui; 2016.
Identification of candidate genes for chicken early- and late-feathering.
Poultry Science, Volume 95, Issue 7, 1 July 2016, Pages 1498–1503, https://doi.org/10.3382/ps/pew131
https://academic.oup.com/ps/article/95/7/1498/2563787
Quote:
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.

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#116985 - 01/07/18 06:16 AM Re: Journal papers online - reference list [Re: KazJaps]
Wieslaw Online   content
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Registered: 09/18/09
Posts: 3776
Loc: Denmark
Evaluation of genetic resistance to Salmonella Pullorum in three chicken lines.
https://www.ncbi.nlm.nih.gov/pubmed/29294099

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#116986 - 01/07/18 11:51 AM Re: Journal papers online - reference list [Re: Wieslaw]
Wieslaw Online   content
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Classroom Professor

Registered: 09/18/09
Posts: 3776
Loc: Denmark
https://www.ncbi.nlm.nih.gov/pubmed/9395470

The chicken genome contains two functional nonallelic beta1,4-galactosyltransferase genes. Chromosomal assignment to syntenic regions tracks fate of the two gene lineages in the human genome.

Abstract
Quote:
Two distinct but related groups of cDNA clones, CKbeta4GT-I and CKbeta4GT-II, have been isolated by screening a chicken hepatoma cDNA library with a bovine beta1,4-galactosyltransferase (beta4GT) cDNA clone. CKbeta4GT-I is predicted to encode a type II transmembrane glycoprotein of 41 kDa with one consensus site for N-linked glycosylation. CKbeta4GT-II is predicted to encode a type II transmembrane glycoprotein of 43 kDa with five potential N-linked glycosylation sites. At the amino acid level, the coding regions of CKbeta4GT-I and CKbeta4GT-II are 52% identical to each other and 62 and 49% identical, respectively, to bovine beta4GT. Despite this divergence in amino acid sequence, high levels of expression of each cDNA in Trichoplusia ni insect cells demonstrate that both CKbeta4GT-I and CKbeta4GT-II encode an alpha-lactalbumin-responsive, UDP-galactose:N-acetylglucosamine beta4-galactosyltransferase. An analysis of CKbeta4GT-I and CKbeta4GT-II genomic clones established that the intron positions within the coding region are conserved when compared with each other, and these positions are identical to the mouse and human beta4GT genes. Thus CKbeta4GT-I and CKbeta4GT-II are the result of the duplication of an ancestral gene and subsequent divergence. CKbeta4GT-I maps to chicken chromosome Z in a region of conserved synteny with the centromeric region of mouse chromosome 4 and human chromosome 9p, where beta4-galactosyltransferase (EC 2.4.1.38) had previously been mapped. Consequently, during the evolution of mammals, it is the CKbeta4GT-I gene lineage that has been recruited for the biosynthesis of lactose. CKbeta4GT-II maps to a region of chicken chromosome 8 that exhibits conserved synteny with human chromosome 1p. An inspection of the current human gene map of expressed sequence tags reveals that there is a gene noted to be highly similar to beta4GT located in this syntenic region on human chromosome 1p. Because both the CKbeta4GT-I and CKbeta4GT-II gene lineages are detectable in mammals, duplication of the ancestral beta4-galactosyltransferase gene occurred over 250 million years ago in an ancestral species common to both mammals and birds.

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