Handle URI:
http://hdl.handle.net/10754/598546
Title:
Identification of copy number variants in horses
Authors:
Doan, R.; Cohen, N.; Harrington, J.; Veazy, K.; Juras, R.; Cothran, G.; McCue, M. E.; Skow, L.; Dindot, S. V.
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.
Citation:
Doan R, Cohen N, Harrington J, Veazy K, Juras R, et al. (2012) Identification of copy number variants in horses. Genome Research 22: 899–907. Available: http://dx.doi.org/10.1101/gr.128991.111.
Publisher:
Cold Spring Harbor Laboratory Press
Journal:
Genome Research
KAUST Grant Number:
KUS-C1-016-04
Issue Date:
1-Mar-2012
DOI:
10.1101/gr.128991.111
PubMed ID:
22383489
PubMed Central ID:
PMC3337435
Type:
Article
ISSN:
1088-9051
Sponsors:
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.
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Full metadata record

DC FieldValue Language
dc.contributor.authorDoan, R.en
dc.contributor.authorCohen, N.en
dc.contributor.authorHarrington, J.en
dc.contributor.authorVeazy, K.en
dc.contributor.authorJuras, R.en
dc.contributor.authorCothran, G.en
dc.contributor.authorMcCue, M. E.en
dc.contributor.authorSkow, L.en
dc.contributor.authorDindot, S. V.en
dc.date.accessioned2016-02-25T13:31:56Zen
dc.date.available2016-02-25T13:31:56Zen
dc.date.issued2012-03-01en
dc.identifier.citationDoan R, Cohen N, Harrington J, Veazy K, Juras R, et al. (2012) Identification of copy number variants in horses. Genome Research 22: 899–907. Available: http://dx.doi.org/10.1101/gr.128991.111.en
dc.identifier.issn1088-9051en
dc.identifier.pmid22383489en
dc.identifier.doi10.1101/gr.128991.111en
dc.identifier.urihttp://hdl.handle.net/10754/598546en
dc.description.abstractCopy 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.en
dc.description.sponsorshipWe 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.en
dc.publisherCold Spring Harbor Laboratory Pressen
dc.subject.meshDNA Copy Number Variationsen
dc.titleIdentification of copy number variants in horsesen
dc.typeArticleen
dc.identifier.journalGenome Researchen
dc.identifier.pmcidPMC3337435en
dc.contributor.institutionTexas A and M University, College Station, United Statesen
dc.contributor.institutionUniversity of Minnesota College of Veterinary Medicine, Minneapolis, United Statesen
dc.contributor.institutionTexas A&M Health Science Center, College of Medicine, College Station, United Statesen
kaust.grant.numberKUS-C1-016-04en

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