title: Identification of copy number variants in horses.
abstract: Copy number variants (CNVs) represent a substantial source of genetic variation in mammals. However, the occurrence of CNVs in horses and their subsequent impact on phenotypic variation is unknown. We performed a study to identify CNVs in 16 horses representing 15 distinct breeds (Equus caballus) and an individual gray donkey (Equus asinus) using a whole-exome tiling array and the array comparative genomic hybridization methodology. We identified 2368 CNVs ranging in size from 197 bp to 3.5 Mb. Merging identical CNVs from each animal yielded 775 CNV regions (CNVRs), involving 1707 protein- and RNA-coding genes. The number of CNVs per animal ranged from 55 to 347, with median and mean sizes of CNVs of 5.3 kb and 99.4 kb, respectively. Approximately 6% of the genes investigated were affected by a CNV. Biological process enrichment analysis indicated CNVs primarily affected genes involved in sensory perception, signal transduction, and metabolism. CNVs also were identified in genes regulating blood group antigens, coat color, fecundity, lactation, keratin formation, neuronal homeostasis, and height in other species. Collectively, these data are the first report of copy number variation in horses and suggest that CNVs are common in the horse genome and may modulate biological processes underlying different traits observed among horses and horse breeds.
authors.affiliation: Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
authors.forename: Ryan
authors.initials: R
authors.lastname: Doan
authors.forename: Noah
authors.initials: N
authors.lastname: Cohen
authors.forename: Jessica
authors.initials: J
authors.lastname: Harrington
authors.forename: Kylee
authors.initials: K
authors.lastname: Veazey
authors.forename: Kylee
authors.initials: K
authors.lastname: Veazy
authors.forename: Rytis
authors.initials: R
authors.lastname: Juras
authors.forename: Gus
authors.initials: G
authors.lastname: Cothran
authors.forename: Molly E
authors.initials: ME
authors.lastname: McCue
authors.forename: Loren
authors.initials: L
authors.lastname: Skow
authors.forename: Scott V
authors.initials: SV
authors.lastname: Dindot
mesh_terms: D000818:Animals; D001483:Base Sequence; D052005:Bone Morphogenetic Protein Receptors, Type I / Q000235:genetics; D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D059472:Exome; D016678:Genome; D006736:Horses / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010641:Phenotype; D058951:gp100 Melanoma Antigen / Q000235:genetics
chemical_list: D058951:gp100 Melanoma Antigen; D052005:Bone Morphogenetic Protein Receptors, Type I