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Large Deletions at ...
Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies
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- Rafati, Nima (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi
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- Andersson, Lisa (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.
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- Mikko, Sofia (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.
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- Feng, Chungang (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi
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- Raudsepp, Terje (author)
- Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77845 USA.
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- Pettersson, Jessica (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi
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- Janecka, Jan (author)
- Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77845 USA.
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- Wattle, Ove (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för kliniska vetenskaper (KV),Department of Clinical Sciences,Swedish Univ Agr Sci, Dept Clin Sci, S-75007 Uppsala, Sweden.
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- Ameur, Adam (author)
- Uppsala universitet,Institutionen för immunologi, genetik och patologi
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- Thyreen, Gunilla (author)
- Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.
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- Eberth, John (author)
- Univ Kentucky, Gluck Equine Res Ctr, Dept Vet Sci, Lexington, KY 40546 USA.
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- Huddleston, John (author)
- Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98105 USA.;Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA.
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- Malig, Maika (author)
- Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA.
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- Bailey, Ernest (author)
- Univ Kentucky, Gluck Equine Res Ctr, Dept Vet Sci, Lexington, KY 40546 USA.
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- Eichler, Evan E. (author)
- Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA.
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- Dalin, Göran (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för anatomi, fysiologi och biokemi,Department of Anatomy, Physiology and Biochemistry (AFB),Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, S-75007 Uppsala, Sweden.
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- Chowdary, Bhanu (author)
- Qatar Univ, New Res Complex, Doha 2713, Qatar.
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- Andersson, Leif (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.;Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77845 USA.,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Uppsala University,Texas A&M University
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- Lindgren, Gabriella (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.
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- Rubin, Carl-Johan (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi
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(creator_code:org_t)
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- 2016-07-01
- 2016
- English.
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In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 6:7, s. 2213-2223
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Abstract
Subject headings
Close
- Skeletal atavism in Shetland ponies is a heritable disorder characterized by abnormal growth of the ulna and fibula that extend the carpal and tarsal joints, respectively. This causes abnormal skeletal structure and impaired movements, and affected foals are usually killed. In order to identify the causal mutation we subjected six confirmed Swedish cases and a DNA pool consisting of 21 control individuals to whole genome resequencing. We screened for polymorphisms where the cases and the control pool were fixed for opposite alleles and observed this signature for only 25 SNPs, most of which were scattered on genome assembly unassigned scaffolds. Read depth analysis at these loci revealed homozygosity or compound heterozygosity for two partially overlapping large deletions in the pseudoautosomal region (PAR) of chromosome X/Y in cases but not in the control pool. One of these deletions removes the entire coding region of the SHOX gene and both deletions remove parts of the CRLF2 gene located downstream of SHOX. The horse reference assembly of the PAR is highly fragmented, and in order to characterize this region we sequenced bacterial artificial chromosome (BAC) clones by single-molecule real-time (SMRT) sequencing technology. This considerably improved the assembly and enabled size estimations of the two deletions to 1602180 kb and 60280 kb, respectively. Complete association between the presence of these deletions and disease status was verified in eight other affected horses. The result of the present study is consistent with previous studies in humans showing crucial importance of SHOX for normal skeletal development.
Subject headings
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
- LANTBRUKSVETENSKAPER -- Bioteknologi med applikationer på växter och djur -- Genetik och förädling inom lantbruksvetenskap (hsv//swe)
- AGRICULTURAL SCIENCES -- Agricultural Biotechnology -- Genetics and Breeding in Agricultural Sciences (hsv//eng)
Keyword
- SMRT sequencing
- skeletal atavism
- SHOX
- PAR
Publication and Content Type
- ref (subject category)
- art (subject category)
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G3
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To the university's database
- By the author/editor
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Rafati, Nima
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Andersson, Lisa
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Mikko, Sofia
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Feng, Chungang
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Raudsepp, Terje
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Pettersson, Jess ...
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show more...
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Janecka, Jan
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Wattle, Ove
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Ameur, Adam
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Thyreen, Gunilla
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Eberth, John
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Huddleston, John
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Malig, Maika
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Bailey, Ernest
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Eichler, Evan E.
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Dalin, Göran
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Chowdary, Bhanu
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Andersson, Leif
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Lindgren, Gabrie ...
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Rubin, Carl-Joha ...
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Genetics
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- AGRICULTURAL SCIENCES
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AGRICULTURAL SCI ...
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and Agricultural Bio ...
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and Genetics and Bre ...
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G3
- By the university
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Uppsala University
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Swedish University of Agricultural Sciences