Identification of Copy Number Variations in Four Horse Breed Populations in South Korea

SIMPLE SUMMARY: The objective of this study is to detect copy number variations (CNVs) in four horse populations (Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses) in South Korea. We found a total of 843 CNV regions (CNVRs) (164.3 Mb), which coincided with 7.2% of the reference horse genome. Overall, copy number losses were found more than gains and mixed CNVRs. A comparison of the CNVRs among the populations showed that a substantial number of CNVRs overlapped each other, while some CNVRs were found specifically in each population. We retrieved parts of CNVRs that overlapped with genes; these overlapping areas are potentially associated with traits of interest in horses. The Thoroughbred and crossbred populations had shared CNVRs overlapping with QTLs (Quantitative trait loci) that were associated with withers height and racing performance. Using gene ontology (GO) analysis, a total of 1884 functional genes were identified within the 577 CNVRs. GO analysis further showed that several of the genes are involved in the olfactory pathway and the nervous system. ABSTRACT: In this study, genome-wide CNVs were identified using a total of 469 horses from four horse populations (Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses). We detected a total of 843 CNVRs throughout all autosomes: 281, 30, 301, and 310 CNVRs for Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses, respectively. Of the total CNVRs, copy number losses were found to be the most abundant (48.99%), while gains and mixed CNVRs accounted for 41.04% and 9.96% of the total CNVRs, respectively. The length of the CNVRs ranged from 0.39 kb to 2.8 Mb, while approximately 7.2% of the reference horse genome assembly was covered by the total CNVRs. By comparing the CNVRs among the populations, we found a significant portion of the CNVRs (30.13%) overlapped; the highest number of shared CNVRs was between Hanla horses and Jeju riding horses. When compared with the horse CNVRs of previous studies, 26.8% of CNVRs were found to be uniquely detected in this study. The CNVRs were not randomly distributed throughout the genome; in particular, the Equus caballus autosome (ECA) 7 comprised the largest proportion of its genome (16.3%), while ECA 24 comprised the smallest (0.7%). Furthermore, functional analysis was applied to CNVRs that overlapped with genes (genic-CNVRs); these overlapping areas may be potentially associated with the olfactory pathway and nervous system. A racing performance QTL was detected in a CNVR of Thoroughbreds, Jeju riding horses, and Hanla horses, and the CNVR value was mixed for three breeds.