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Animals : an open access journal from MDPI2025; 15(10); 1458; doi: 10.3390/ani15101458

Whole-Genome Resequencing Analysis of Copy Number Variations Associated with Athletic Performance in Grassland-Thoroughbred.

Abstract: Copy number variation (CNV) is an important source of genetic variation. However, studies utilizing whole-genome sequencing to investigate CNVs in horse populations and their effects on traits remain relatively limited. This study aims to address the lack of research on the impact of copy number variation (CNV) on racing performance in horse populations, providing new insights for locally bred racing breeds. We analyzed 60 offspring derived from the crossbreeding of Thoroughbred horses and Xilingol horses. These horses were temporarily named "Grassland-Thoroughbred" and were divided into two groups: 30 racing horses and 30 non-racing horses. A total of 89,527 CNVs were identified. After merging overlapping CNVs, 982 copy number variation regions (CNVRs) were recognized, among which the racing horse group (RH) had 29 unique CNVRs, while the non-racing horse group (NR) had 4 unique CNVRs. In addition, a total of 195 genes overlapping with CNVRs were identified. Transcriptomic analysis revealed 120 differentially expressed genes, with expressed in both CNVR-overlapping genes and mRNA. Both CNVR-overlapping genes and differentially expressed genes were enriched in the MAPK signaling pathway; CNV may affect gene expression through gene dosage effects or regulatory mechanisms. Using Vst statistical analysis, we further screened candidate CNVRs in autosomes that exceeded the 95% differentiation threshold between the RH and NR populations. Several key genes associated with energy metabolism and muscle function were identified, including , , , , , and . These findings provide new insights into the genetic structural variation in racing performance and adaptability, fill the gap in CNV studies in the genomics of Grassland-Thoroughbred horses, and offer valuable genomic data for optimizing breeding strategies in native racing horse populations.
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Publication Date: 2025-05-18 PubMed ID: 40427335PubMed Central: PMC12108297DOI: 10.3390/ani15101458Google 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 discloses a comprehensive analysis of genetic variations, specifically copy number variations (CNVs), present in a unique group of horses, referred to as “Grassland-Thoroughbred,” and their potential impact on racing performance.

Copy Number Variations and Their Impact

  • The researchers structured their investigation around a phenomenon known as copy number variation (CNV). CNVs are segments of the genome where variations in the number of copies of DNA sections occur. These variations can significantly influence genetic diversity and contribute to different traits or characteristics within a species.
  • Though wide-ranging in potential, studies focusing on the impact of CNVs in horse populations, specifically relating to traits like racing performance, have been relatively minimal. This study is designed to bridge that gap.

Study Design and Findings

  • The study examined 60 offspring that resulted from crossbreeding Thoroughbred horses with Xilingol horses. The resultant group, temporarily named “Grassland-Thoroughbred,” was split into two sub-groups: a racing group of 30 horses and a non-racing group, also consisting of 30 horses.
  • Through their investigation, the researchers identified 89,527 CNVs. These were consolidated into 982 unique copy number variation regions (CNVRs), of which 29 were unique to the racing horse group, and four were unique to the non-racing group.
  • Further analysis identified a total of 195 genes overlapping with the CNVRs and 120 differentially expressed genes. Interestingly, these genes were found to mostly enrich in the MAPK signaling pathway – a critical biochemical pathway involved in many cellular processes including proliferation, differentiation, and migration.

Implication and Application of Findings

  • The study hypothesizes that CNVs might influence gene expressions either through gene dosage effects or through certain regulatory mechanisms, which could possibly affect a horse’s racing performance.
  • Moreover, some genes connected with energy metabolism and muscle function were recognized. Thus, findings from this study may be harnessed towards optimizing breeding strategies to improve the physical performance of native racing horse populations.
  • The discovered genetic variations and their associations with racing performance effectively enrich the understanding of genomics in Grassland-Thoroughbred horses and could help pave the way for targeted genetic enhancements in the future.

Cite This Article

APA
Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D. (2025). Whole-Genome Resequencing Analysis of Copy Number Variations Associated with Athletic Performance in Grassland-Thoroughbred. Animals (Basel), 15(10), 1458. https://doi.org/10.3390/ani15101458

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 15
Issue: 10
PII: 1458

Researcher Affiliations

Ding, Wenqi
  • Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
Gong, Wendian
  • Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
Bou, Tugeqin
  • Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
Shi, Lin
  • Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
Lin, Yanan
  • Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
Shi, Xiaoyuan
  • Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
Li, Zheng
  • Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
Wu, Huize
  • Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
Dugarjaviin, Manglai
  • Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
Bai, Dongyi
  • Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China.
  • Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.

Grant Funding

  • U23A20224 / the National Natural Science Foundation of China
  • BR22-11-03 / the Basic Research Operating Expenses of Colleges and Universities Project of the Department of Education of the Inner Mongolia Autonomous Region
  • 2020ZD0004 / the construction projects of the Inner Mongolia Science and Technology Department
  • RK2400002235 / the Agricultural and Animal Husbandry Characteristic Seed Industry Project

Conflict of Interest Statement

The authors declare no conflicts of interest.

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