Copy Number Variation in the Horse Genome

Authors

Sharmila Ghosh, Texas A&M University
Zhipeng Qu, University of Adelaide, Australia
Pranab J. Das, Texas A&M University
Erica Fang, Texas A&M University
Rytis Juras, Texas A&M University
E. Gus Cothran, Texas A&M University
Sue McDonell, University of Pennsylvania
Daniel G. Kenney, University of Guelph, Canada
Teri L. Lear, University of KentuckyFollow
David L. Adelson, University of Adelaide, Australia
Bhanu P. Chowdhary, Qatar University, Qatar
Terje Raudsepp, Texas A&M University

Abstract

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.

Document Type

Article

Publication Date

10-23-2014

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.

Digital Object Identifier (DOI)

http://dx.doi.org/10.1371/journal.pgen.1004712

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.

Repository Citation

Ghosh, Sharmila; Qu, Zhipeng; Das, Pranab J.; Fang, Erica; Juras, Rytis; Cothran, E. Gus; McDonell, Sue; Kenney, Daniel G.; Lear, Teri L.; Adelson, David L.; Chowdhary, Bhanu P.; and Raudsepp, Terje, "Copy Number Variation in the Horse Genome" (2014). Maxwell H. Gluck Equine Research Center Faculty Publications. 5.
https://uknowledge.uky.edu/gerc_facpub/5