title: 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.
authors.affiliation: Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden 751 23.
authors.forename: Nima
authors.initials: N
authors.lastname: Rafati
authors.affiliation: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07.
authors.forename: Lisa S
authors.initials: LS
authors.lastname: Andersson
authors.affiliation: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07.
authors.forename: Sofia
authors.initials: S
authors.lastname: Mikko
authors.affiliation: Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden 751 23.
authors.forename: Chungang
authors.initials: C
authors.lastname: Feng
authors.affiliation: Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845.
authors.forename: Terje
authors.initials: T
authors.lastname: Raudsepp
authors.affiliation: Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden 751 23.
authors.forename: Jessica
authors.initials: J
authors.lastname: Pettersson
authors.affiliation: Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845.
authors.forename: Jan
authors.initials: J
authors.lastname: Janecka
authors.affiliation: Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07.
authors.forename: Ove
authors.initials: O
authors.lastname: Wattle
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden 751 23.
authors.forename: Adam
authors.initials: A
authors.lastname: Ameur
authors.affiliation: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07.
authors.forename: Gunilla
authors.initials: G
authors.lastname: Thyreen
authors.affiliation: Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky 40546.
authors.forename: John
authors.initials: J
authors.lastname: Eberth
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98105 Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195.
authors.forename: John
authors.initials: J
authors.lastname: Huddleston
authors.affiliation: Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195.
authors.forename: Maika
authors.initials: M
authors.lastname: Malig
authors.affiliation: Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky 40546.
authors.forename: Ernest
authors.initials: E
authors.lastname: Bailey
authors.affiliation: Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195.
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
authors.affiliation: Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07.
authors.forename: Göran
authors.initials: G
authors.lastname: Dalin
authors.affiliation: New Research Complex, Qatar University, Doha, Qatar 2713.
authors.forename: Bhanu
authors.initials: B
authors.lastname: Chowdary
authors.affiliation: 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.
authors.forename: Leif
authors.initials: L
authors.lastname: Andersson
authors.affiliation: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden 750 07.
authors.forename: Gabriella
authors.initials: G
authors.lastname: Lindgren
authors.affiliation: Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden 751 23 carl-johan.rubin@imbim.uu.se.
authors.forename: Carl-Johan
authors.initials: CJ
authors.lastname: Rubin
mesh_terms: D000818:Animals; D001483:Base Sequence; D001842:Bone and Bones / Q000002:abnormalities / Q000378:metabolism*; D002874:Chromosome Mapping; D005260:Female; D056426:Genetic Loci; D016678:Genome; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D018398:Homeodomain Proteins / Q000235:genetics* / Q000378:metabolism; D006720:Homozygote; D006736:Horses / Q000235:genetics*; D008297:Male; D000071439:Pseudoautosomal Regions / Q000737:chemistry* / Q000378:metabolism; D018121:Receptors, Cytokine / Q000235:genetics / Q000378:metabolism; D017384:Sequence Deletion
chemical_list: D018398:Homeodomain Proteins; D018121:Receptors, Cytokine
keywords: PAR; SHOX; SMRT sequencing; skeletal atavism