Identification of copy number variants in horses

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 wholeexome 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.

Genetic Susceptibility to Rhodococcus equi

“…Our laboratory conducted a CNV‐based GWAS by applying the aforementioned equine exon tilling array71 to the 72 foals studied in our SNP GWAS 48. Although similar lengths and numbers of CNVs were observed in these foals as in the previous report using this array, no CNVs were significantly associated with R. equi pneumonia in these foals.…”

“…The results of studies identifying CNVs by NGS are limited by variation in read‐depth (ie, the number of copies of sequences aligned to a specific area) across the genome and the size of the CNVs identified. Specifically, CNVs of lengths ranging from 197 bp to 3.5 Mb have been identified and confirmed using a CGH array designed to identify CNVs in genes of the equine genome 71. In a subsequent study using NGS, CNVs ranging in length from 3.74 kb to 4.84 Mb were identified 70.…”

“…Although there are discrepancies among the approaches used to identify CNVs, the studies to date have identified CNVs in genes involved in similar pathways, such as sensory perception, signal transduction, and immune‐related pathways. Results from some CNV studies of horses also have found concordant results between aCGH and NGS whole genome sequencing in which CNVs of horses have been shown to be enriched in genes relating to sensory perception, signal transduction, and immune‐related functions 71, 72…”

“…Use of aCGH also has limitations for the identification of CNVs, principally related to probe placement and density. The currently published equine arrays are a whole genome tiling array (ie, probes tiled across the whole genome) and an exon tiling array (ie, probes tiled across noncoding and coding exons of genes) 71, 72. Thus, these arrays only permit evaluation of CNVs within specific regions of the genome.…”

0309 Systematic profiling of short tandem repeats in the cattle genome

“…ksk Within these 25 STRs, we indeed found seven genes which may involve in selection signature: FAM171B, INHBB, TFCP2L1, RPRD2, KLHL1, SP2, and WRN. Three of these loci are of particular interest: INHBB has an important role of inhibin in reproduction (Chu et al 2011;Lee et al 2013); KLHL1 is involved in poor sperm motility in Holstein-Friesian bulls (Shin et al 2014;Hering et al 2014); and WRN gene is related to Werner syndrome (WS), also known as "adult progeria", a rare and autosomal recessive progeroid syndrome (PS), which was characterized by the appearance of premature aging (Doan et al 2012).…”