Abstract
Recent studies have found that copy number variations (CNVs) are widespread in human and animal genomes. CNVs are a significant source of genetic variation, and have been shown to be associated with phenotypic diversity. However, the effect of CNVs on genetic variation in horses is not well understood. In the present study, CNVs in 6 different breeds of mare horses, Mongolia horse, Abaga horse, Hequ horse and Kazakh horse (all plateau breeds) and Debao pony and Thoroughbred, were determined using aCGH. In total, seven hundred CNVs were identified ranging in size from 6.1 Kb to 0.57 Mb across all autosomes, with an average size of 43.08 Kb and a median size of 15.11 Kb. By merging overlapping CNVs, we found a total of three hundred and fifty-three CNV regions (CNVRs). The length of the CNVRs ranged from 6.1 Kb to 1.45 Mb with average and median sizes of 38.49 Kb and 13.1 Kb. Collectively, 13.59 Mb of copy number variation was identified among the horses investigated and accounted for approximately 0.61% of the horse genome sequence. Five hundred and eighteen annotated genes were affected by CNVs, which corresponded to about 2.26% of all horse genes. Through the gene ontology (GO), genetic pathway analysis and comparison of CNV genes among different breeds, we found evidence that CNVs involving 7 genes may be related to the adaptation to severe environment of these plateau horses. This study is the first report of copy number variations in Chinese horses, which indicates that CNVs are ubiquitous in the horse genome and influence many biological processes of the horse. These results will be helpful not only in mapping the horse whole-genome CNVs, but also to further research for the adaption to the high altitude severe environment for plateau horses.
Highlights
Previous genomic research has suggested that single nucleotide polymorphisms (SNPs) are the main form of genome structure change [1,2,3]
Through the gene ontology (GO), genetic pathway analysis and comparison of copy number variations (CNVs) genes among different breeds, we found evidence that CNVs involving 7 genes may be related to the adaptation to severe environment of these plateau horses
In the comparison with the results of Metzger, only 15 overlapped CNV regions (CNVRs) were found, we proposed that the difference could be due to the different research platforms, or the application of more stringent quality criteria and combination of three detection algorithms in Metzger’s research
Summary
Previous genomic research has suggested that single nucleotide polymorphisms (SNPs) are the main form of genome structure change [1,2,3]. This notion changed in 2004 when two groups of scientists published the first whole-genome maps of copy number variations in seemingly healthy individuals [4,5]. CNV exists in the human genome [11,12,13], and widely in other mammals (pig [14,15], cattle [16,17,18], sheep [19,20], mice [21,22]) and plants [23,24]
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