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#116609 - 05/04/17 06:36 PM New 2017 B locus paper - 3 mutation alleles
KazJaps Offline
Classroom Professor

Registered: 08/30/02
Posts: 2792
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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#116610 - 05/04/17 07:52 PM Re: New 2017 B locus paper - 3 mutation alleles [Re: KazJaps]
KazJaps Offline
Classroom Professor

Registered: 08/30/02
Posts: 2792
Loc: Australia
One of my previous posts discussing the Hellstrom et al. 2010 B locus paper:
http://www.the-coop.org/forums/ubbthreads.php?ubb=showflat&Number=107454#Post107454

Originally Posted By: KazJaps
I forgot to mention that in the following DNA research, they noted some slight variations in sequences of B (multiple mutations), but they weren't sure at that stage whether the differences had any effect on barring phenotype.

Sex-linked barring in chickens is controlled by the CDKN2A /B tumour suppressor locus.
Hellström AR, Sundström E, Gunnarsson U, Bed'Hom B, Tixier-Boichard M, Honaker CF, Sahlqvist AS, Jensen P, Kämpe O, Siegel PB, Kerje S, Andersson L.
Pigment Cell Melanoma Res. 2010 Aug;23(4):521-30. doi: 10.1111/j.1755-148X.2010.00700.x. Epub 2010 Mar 29.
Full paper

Quote:
Here, we show that Sex-linked barring is controlled by the CDKN2A/B locus, which encodes the INK4b and ARF transcripts. We identified two non-coding mutations in CDKN2A that showed near complete association with the phenotype. In addition, two missense mutations were identified at highly conserved sites, V9D and R10C, and every bird tested with a confirmed Sex-linked barring phenotype carried one of these missense mutations. Further work is required to determine if one of these or a combined effect of two or more CDKN2A mutations is causing Sex-linked barring.


Eg, in Figure 4 they note 3 barring alleles, the first B0 allele they needed further research to substantiate that those birds were indeed B - barred phenotype (white leghorns, assumed to have B), but the other two alleles B1 & B2 they were confident as being B - barred.

The B1 allele was found in breeds /lines like:
-Barred Plymouth Rock,
-broiler lines,
-Coucou de Rennes,
-Coucou du Vercors.

The B2 allele was found in breeds / lines like:
-White Leghorn, commercial
-White Leghorn, line 13
-White Leghorn, Obese strain
-Järhöns


2017 paper substantiated the following:
  • Allele B0: Sex-linked Extreme Dilution (new mutation discovered),
  • Allele B1: B Sex-linked Barring,
  • Allele B2: B^Sd Sex-linked Dilution.


* 2017 paper Figure 1 shows photos of each (unfortunately not homozygous B0, only heterozygous/hemizygous B0 were segregated). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384658/figure/pgen.1006665.g001/

* In 2017 paper supporting file S1 Fig chick down photos. https://doi.org/10.1371/journal.pgen.1006665.s004 (download TIF file)

Quote:
Phenotype of chicks at hatch with different CDKN2A genotypes: (A) N/N, (B) B0/N and (C) B2/N allele. The arrow marks the characteristic white spot associated with Sex-linked barring.


Note, the heterozygous/hemizygous B0 sex-linked extreme dilution chick down looks very similar in pattern to the Australian Pit Game sex-linked spotty mutation on E or ER (although this pattern varies in spotty chicks), ie there is a bleached white patch on the back.

Sex-linked Spotty:

* 2 Spotty chicks top middle & right showing the white back patch.
--------------
Spotty chicks, left on E (or ER), right on e+:

* left chick showing a clear white patch back.


Edited by KazJaps (09/28/17 08:30 PM)
Edit Reason: temporary update of image links

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#116612 - 05/04/17 11:32 PM Re: New 2017 B locus paper - 3 mutation alleles [Re: KazJaps]
KazJaps Offline
Classroom Professor

Registered: 08/30/02
Posts: 2792
Loc: Australia
An article discussing the 2017 paper:

New study reveals how some chickens got striped feathers

April 7, 2017
https://m.phys.org/news/2017-04-reveals-chickens-striped-feathers.html

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#116614 - 05/05/17 03:54 PM Re: New 2017 B locus paper - 3 mutation alleles [Re: KazJaps]
KazJaps Offline
Classroom Professor

Registered: 08/30/02
Posts: 2792
Loc: Australia
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

Quote:
Abstract

Sex-linked barring is a fascinating plumage pattern in chickens recently shown to be associated with two non-coding and two missense mutations affecting the ARF transcript at the CDKN2A tumor suppressor locus. It however remained a mystery whether all four mutations are indeed causative and how they contribute to the barring phenotype.

Here, we show that Sex-linked barring is genetically heterogeneous, and that the mutations form three functionally different variant alleles. The B0 allele carries only the two non-coding changes and is associated with the most dilute barring pattern, whereas the B1 and B2 alleles carry both the two non-coding changes and one each of the two missense mutations causing the Sex-linked barring and Sex-linked dilution phenotypes, respectively.

The data are consistent with evolution of alleles where the non-coding changes occurred first followed by the two missense mutations that resulted in a phenotype more appealing to humans. We show that one or both of the non-coding changes are cis-regulatory mutations causing a higher CDKN2A expression, whereas the missense mutations reduce the ability of ARF to interact with MDM2.

Summary
- B0 sex-linked extreme dilution allele occurred first (2 non-coding mutations: SNP1 in the promoter and SNP2 in intron 1)
- B1 sex-linked barring, extra missense mutation occurred on the B0 allele (2 non-coding mutations SNP1 & SNP2, 1 missense mutation: SNP3 causes a Valine to Aspartic acid (V9D) substitution)
- B2 sex-linked dilution, extra missense mutation occurred on the B0 allele (2 non-coding mutations SNP1 & SNP2, 1 missense mutation: SNP4 causes an Arginine to Cysteine (R10C) substitution).

Quote:
All three variant alleles carry the two non-coding mutations whereas V9D and R10C are associated with the B1 and B2 allele, respectively

- B0 - extreme dilution (2 non coding mutations (SNP1 & SNP2))
- B1 - barring (2 non coding mutations + V9D substitution (SNP1, SNP2 & SNP3))
- B2 - dilution (2 non coding mutations + R10C substitution (SNP1, SNP2 & SNP4)).


Edited by KazJaps (05/05/17 05:04 PM)
Edit Reason: edited the summary

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#116616 - 05/10/17 01:57 AM Re: New 2017 B locus paper - 3 mutation alleles [Re: KazJaps]
Wieslaw Offline
Moderator
Classroom Professor

Registered: 09/18/09
Posts: 3751
Loc: Denmark
It could explain the chicks I once had

heterozygous cockerel


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