We constructed a 400K WG tiling oligoarray for the horse and applied it for the discovery of copy number variations (CNVs) in 38 normal horses of 16 diverse breeds, and the Przewalski horse. Probes on the array represented 18,763 autosomal and X-linked genes, and intergenic, sub-telomeric and chrY sequences. We identified 258 CNV regions (CNVRs) across all autosomes, chrX and chrUn, but not in chrY. CNVs comprised 1.3% of the horse genome with chr12 being most enriched. American Miniature horses had the highest and American Quarter Horses the lowest number of CNVs in relation to Thoroughbred reference. The Przewalski horse was similar to native ponies and draft breeds. The majority of CNVRs involved genes, while 20% were located in intergenic regions. Similar to previous studies in horses and other mammals, molecular functions of CNV-associated genes were predominantly in sensory perception, immunity and reproduction. The findings were integrated with previous studies to generate a composite genome-wide dataset of 1476 CNVRs. Of these, 301 CNVRs were shared between studies, while 1174 were novel and require further validation. Integrated data revealed that to date, 41 out of over 400 breeds of the domestic horse have been analyzed for CNVs, of which 11 new breeds were added in this study. Finally, the composite CNV dataset was applied in a pilot study for the discovery of CNVs in 6 horses with XY disorders of sexual development. A homozygous deletion involving AKR1C gene cluster in chr29 in two affected horses was considered possibly causative because of the known role of AKR1C genes in testicular androgen synthesis and sexual development. While the findings improve and integrate the knowledge of CNVs in horses, they also show that for effective discovery of variants of biomedical importance, more breeds and individuals need to be analyzed using comparable methodological approaches.

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Notes/Citation Information

Published in PLOS Genetics, v. 10, no. 10, article e1004712, p. 1-19.

© 2014 Ghosh et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Funding Information

TR and BPC were supported by Texas Agrilife Research, LINK Endowment and American Quarter Horse Association, DA and ZQ were supported by The University of Adelaide; ZQ was supported by a China Scholarship Council scholarship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

journal.pgen.1004712.s001.PDF (155 kB)
Figure S1. Array and aCGH quality control.

journal.pgen.1004712.s002.PDF (379 kB)
Figure S2. Homozygous deletions.

journal.pgen.1004712.s003.PDF (180 kB)
Figure S3. Validation of selected CNVRs by quantitative PCR (qPCR).

journal.pgen.1004712.s004.PDF (801 kB)
Figure S4. Validation of a copy number gain in chr1 (114.0 Mb) by FISH.

journal.pgen.1004712.s005.XLSX (11 kB)
Table S1. Horse breeds (n = 16) and individuals (n = 38) used in this study

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Table S2. Primers for quantitative and qualitative PCR to validate CNVs.

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Table S3. List of all 950 CNV calls in the study cohort.

journal.pgen.1004712.s008.XLSX (10 kB)
Table S4. Tentative breed-specific CNVRs.

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Table S5. 258 CNVRs identified in the horse genome in this study.

journal.pgen.1004712.s010.XLSX (23 kB)
Table S6. Gains and losses with high log2 alteration values.

journal.pgen.1004712.s011.XLSX (36 kB)
Table S7. Genomic locations, names, symbols and known or predicted functions of copy number variable genes.

journal.pgen.1004712.s012.XLSX (12 kB)
Table S8. Intergenic CNVRs.

journal.pgen.1004712.s013.XLSX (19 kB)
Table S9. GO analysis of equine copy number variable genes

journal.pgen.1004712.s014.XLSX (72 kB)
Table S10. Integrated dataset of 1476 CNVs/CNVRs in the horse.

journal.pgen.1004712.s015.XLSX (13 kB)
Table S11. Details of validation of 19 selected CNVRs by qPCR.

journal.pgen.1004712.s016.XLSX (14 kB)
Table S12. List of horse breeds studied for CNVs.