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Animals : an open access journal from MDPI2022; 12(24); 3501; doi: 10.3390/ani12243501

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

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 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.
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Publication Date: 2022-12-12 PubMed ID: 36552421PubMed Central: PMC9774267DOI: 10.3390/ani12243501Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article investigates the genome-wide identification of copy number variations (CNVs) in four horse populations in South Korea, revealing interesting findings about genetic diversity, shared CNVs, unique CNVs, and the potential implications for functions such as olfactory pathways and the nervous system.

Copy Number Variations (CNVs) in Horse Populations

  • The researchers studied genetic variations in 469 horses from four horse populations in South Korea: Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses. The variations identified are known as Copy Number Variations (CNVs), which is a type of structural alteration in the DNA where a specific region of the genome is present in varying copy number in comparison with a reference genome.
  • The team identified a total of 843 CNVs distributed across all autosomes, with the different horse populations having specific numbers: 281 CNVs in Jeju horses, 30 in Thoroughbreds, 301 in Jeju riding horses, and 310 in Hanla horses.

Variation Characteristics

  • Overall, the most common type of CNVR (CNV region) detected was loss (48.99%), followed by gains (41.04%) and mixed CNVRs (9.96%).
  • The length of these CNVRs ranged from 0.39 kilo bases (kb) to 2.8 mega bases (Mb), covering roughly 7.2% of the reference horse genome assembly.

Comparison of CNVRs Among Populations

  • The research identified a significant number of overlapping CNVRs among the four horse populations, constituting 30.13% of the total CNVRs. Specifically, the highest number of shared CNVRs were observed between the Hanla horses and Jeju riding horses.
  • Comparing these CNVRs with those identified in previous studies, it was found that 26.8% of the CNVRs detected in this study were unique, implying distinct genetic characteristics or alterations in these horse populations.

Distribution and Functional Analysis of CNVRs

  • The study found that these CNVRs were not randomly distributed across the genome. A particular autosome (ECA) 7 held the largest proportion (16.3%) of total CNVRs, while ECA 24 had the smallest proportion (0.7%).
  • Functional analysis revealed that some of the CNVRs overlapped with genes (known as genic-CNVRs). These regions might potentially be involved with the olfactory pathway and the nervous system, highlighting their potential biological significance.
  • A QTL influencing racing performance was identified, present in a CNVR of Thoroughbreds, Jeju riding horses, and Hanla horses, with variable copy numbers across these breeds.

Cite This Article

APA
Kim YM, Ha SJ, Seong HS, Choi JY, Baek HJ, Yang BC, Choi JW, Kim NY. (2022). Identification of Copy Number Variations in Four Horse Breed Populations in South Korea. Animals (Basel), 12(24), 3501. https://doi.org/10.3390/ani12243501

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 12
Issue: 24
PII: 3501

Researcher Affiliations

Kim, Yong-Min
  • Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Republic of Korea.
Ha, Seok-Joo
  • Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea.
Seong, Ha-Seung
  • Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Republic of Korea.
Choi, Jae-Young
  • Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Republic of Korea.
Baek, Hee-Jung
  • Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea.
Yang, Byoung-Chul
  • Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Republic of Korea.
Choi, Jung-Woo
  • Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea.
Kim, Nam-Young
  • Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Republic of Korea.

Conflict of Interest Statement

The authors declare no conflict of interest.

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