RT Journal
A1 Doan, Ryan
A1 Cohen, Noah
A1 Harrington, Jessica
A1 Veazy, Kylee
A1 Juras, Rytis
A1 Cothran, Gus
A1 McCue, Molly E.
A1 Skow, Loren
A1 Dindot, Scott V.
T1 Identification of copy number variants in horses
JF Genome Research 
JO Genome Research 
YR 2012 
FD May 01 
VO 22 
IS 5 
SP 899 
OP 907 
DO 10.1101/gr.128991.111 
UL http://genome.cshlp.org/content/22/5/899.abstract 
AB 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.