Identification of copy number variants in horses

R. Doan, N. Cohen, J. Harrington, K. Veazy, R. Juras, G. Cothran, M. E. McCue, L. Skow, S. V. Dindot

Research output: Contribution to journalArticlepeer-review

45 Scopus citations


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.
Original languageEnglish (US)
Pages (from-to)899-907
Number of pages9
JournalGenome Research
Issue number5
StatePublished - Mar 1 2012
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): KUS-C1-016-04
Acknowledgements: We thank Dr. James Mickelson for critical reading of the manuscript, Dr. Charlie Love (Texas A&M University College of Veterinary Medicine and Biomedical Sciences) for DNA samples, Ted Sharpe (Broad Institute) for the horse segmental duplication map, and Drs. David Fry and Olivia Rudolphi for assistance with collecting samples. AgriLife Research, the Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, and the Link Equine Research Endowment, Texas A&M University provided funding for this study. This publication is based in part on work supported by King Abdullah University of Science and Technology (KAUST), award no. KUS-C1-016-04.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.


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