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Home / Equine Research Bank / G3 (Bethesda) / Large Deletions at the SHOX Locus in the Pseudoautosomal Reg...
G3 (Bethesda, Md.)2016; 6(7); 2213-2223; doi: 10.1534/g3.116.029645

Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies.

Abstract: 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 160-180 kb and 60-80 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.
Copyright © 2016 Rafati et al.
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Publication Date: 2016-07-07 PubMed ID: 27207956PubMed Central: PMC4938674DOI: 10.1534/g3.116.029645Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article discusses a study that has linked large deletions in the SHOX locus of the pseudoautosomal region on the X/Y chromosome to skeletal atavism in Shetland ponies, a hereditary disorder that disrupts normal bone growth and movement.

Introduction and Aim of the Study

  • Skeletal atavism in Shetland ponies is a hereditary disorder. It leads to abnormal growth of the ulna and fibula, resulting in extended carpal and tarsal joints. This condition distorts the skeletal structure of these ponies, impairs their movements, and often results in the euthanasia of affected foals.
  • The researchers aimed to identify the genetic mutation causing this disorder.

Research Methodology

  • To identify the causal mutation, researchers conducted whole-genome resequencing on six confirmed Swedish cases and a DNA pool consisting of 21 control individuals.
  • The team screened for polymorphisms where the cases and control pool had opposite alleles. This process revealed a signature for only 25 SNPs, most of which were on genome assembly unassigned scaffolds.
  • The researchers also deployed read depth analysis at these loci, which unveiled homozygosity or compound heterozygosity for two large deletions in the pseudoautosomal region of chromosome X/Y in the cases, but not in the control pool.

Results

  • One deletion found in the affected cases removes the entire coding region of the SHOX gene whereas both deletions remove parts of the CRLF2 gene located downstream of SHOX.
  • The reference assembly of the pseudoautosomal region in the horse’s genome have been fragmented, making it hard to analyze this region. To overcome this, researchers sequenced bacterial artificial chromosome (BAC) clones using single-molecule real-time (SMRT) sequencing technology.
  • This approach improved assembly and allowed size estimations of the two deletions to 160-180 kb and 60-80 kb, respectively.
  • A complete association between the presence of these deletions and the disease status was verified after testing eight other affected horses.

Conclusion

  • The findings support the idea that the SHOX gene is crucial for normal skeletal development, a fact already established in human studies.
  • This study sheds light on the genetic underpinnings of skeletal atavism in Shetland ponies, bringing researchers one step closer to potentially developing effective treatment or preventive strategies in the future.

Cite This Article

APA
Rafati N, Andersson LS, Mikko S, Feng C, Raudsepp T, Pettersson J, Janecka J, Wattle O, Ameur A, Thyreen G, Eberth J, Huddleston J, Malig M, Bailey E, Eichler EE, Dalin G, Chowdary B, Andersson L, Lindgren G, Rubin CJ. (2016). Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies. G3 (Bethesda), 6(7), 2213-2223. https://doi.org/10.1534/g3.116.029645

Publication

G3 (Bethesda, Md.)
ISSN: 2160-1836
NlmUniqueID: 101566598
Country: England
Language: English
Volume: 6
Issue: 7
Pages: 2213-2223

Researcher Affiliations

Rafati, Nima
  • Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden 751 23.
Andersson, Lisa S
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07.
Mikko, Sofia
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07.
Feng, Chungang
  • Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden 751 23.
Raudsepp, Terje
  • Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845.
Pettersson, Jessica
  • Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden 751 23.
Janecka, Jan
  • Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845.
Wattle, Ove
  • Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07.
Ameur, Adam
  • Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden 751 23.
Thyreen, Gunilla
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07.
Eberth, John
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky 40546.
Huddleston, John
  • Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98105 Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195.
Malig, Maika
  • Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195.
Bailey, Ernest
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky 40546.
Eichler, Evan E
  • Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195.
Dalin, Göran
  • Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07.
Chowdary, Bhanu
  • New Research Complex, Qatar University, Doha, Qatar 2713.
Andersson, Leif
  • Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden 751 23 Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07 Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845.
Lindgren, Gabriella
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07.
Rubin, Carl-Johan
  • Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden 751 23 carl-johan.rubin@imbim.uu.se.

MeSH Terms

  • Animals
  • Base Sequence
  • Bone and Bones / abnormalities
  • Bone and Bones / metabolism
  • Chromosome Mapping
  • Female
  • Genetic Loci
  • Genome
  • Heterozygote
  • High-Throughput Nucleotide Sequencing
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / metabolism
  • Homozygote
  • Horses / genetics
  • Male
  • Pseudoautosomal Regions / chemistry
  • Pseudoautosomal Regions / metabolism
  • Receptors, Cytokine / genetics
  • Receptors, Cytokine / metabolism
  • Sequence Deletion

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