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Animals : an open access journal from MDPI2025; 15(15); 2323; doi: 10.3390/ani15152323

Whole-Genome Resequencing Analysis of Athletic Traits in Grassland-Thoroughbred.

Abstract: Speed is not only the primary objective of racehorse breeding but also a crucial indicator for evaluating racehorse performance. This study investigates a newly developed racehorse breed in China. Through whole-genome resequencing, we selected 60 offspring obtained from the crossbreeding of Thoroughbred horses and Xilingol horses for this study. This breed is tentatively named "Grassland-Thoroughbred", and the samples were divided into two groups based on racing ability: 30 racehorses and 30 non-racehorses. Based on whole-genome sequencing data, the study achieved an average sequencing depth of 25.63×. The analysis revealed strong selection pressure on chromosomes (Chr) 1 and 3. Selection signals were detected using methods such as the nucleotide diversity ratio (π ratio), integrated haplotype score (iHS), fixation index (Fst), and cross-population extended haplotype homozygosity (XP-EHH). Regions ranked in the top 5% by at least three methods were designated as candidate regions. This approach detected 215 candidate genes. Additionally, the Fst method was employed to detect Indels, and the top 1% regions detected were considered candidate regions, covering 661 candidate genes. Functional enrichment analysis of the candidate genes suggests that pathways related to immune regulation, neural signal transmission, muscle contraction, and energy metabolism may significantly influence differences in performance. Among these identified genes, , , , , , , , and play crucial roles in muscle function, metabolism, sensory perception, and neurobiology, indicating their key significance in shaping racehorse phenotypes. This study not only enhances understanding of the molecular mechanisms underlying racehorse speed but also provides essential theoretical and practical references for the molecular breeding of Grassland-Thoroughbreds.
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Publication Date: 2025-08-07 PubMed ID: 40805113PubMed Central: PMC12346297DOI: 10.3390/ani15152323Google 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.

Overview

  • This research analyzed the genetic basis of athletic performance in a newly developed Chinese racehorse breed called the Grassland-Thoroughbred by comparing whole-genome data from racehorses and non-racehorses.
  • The study identified specific genomic regions and genes related to traits such as muscle function, energy metabolism, neural signaling, and immune regulation that may influence racehorse speed and performance.

Introduction and Research Purpose

  • The primary goal of racehorse breeding is to enhance speed, a key measure of racehorse performance.
  • This study focused on a newly developed breed in China, the Grassland-Thoroughbred, derived from crossing Thoroughbred and Xilingol horses.
  • Understanding the genetic basis of speed and athletic traits in this breed can assist in molecular breeding to improve racehorse performance.

Sample Collection and Grouping

  • A total of 60 offspring from Grassland-Thoroughbred crosses were selected.
  • These samples were divided into two equal groups based on racing ability: 30 racehorses and 30 non-racehorses.

Whole-Genome Resequencing Methodology

  • Whole-genome resequencing was performed on all 60 horses, achieving an average sequencing depth of 25.63×, which ensures detailed and reliable genetic information.
  • Genome-wide analyses were conducted to identify signals of selection and genetic variants associated with athletic traits.

Genomic Regions Under Selection

  • Strong selection pressure was detected particularly on chromosomes 1 and 3.
  • Four statistical methods were used to identify selection signals:
    • π ratio (nucleotide diversity ratio)
    • Integrated haplotype score (iHS)
    • Fixation index (Fst)
    • Cross-population extended haplotype homozygosity (XP-EHH)
  • Regions identified in the top 5% by at least three of these methods were considered candidate regions related to racing ability, leading to the identification of 215 candidate genes.
  • Insertions and deletions (Indels) were also analyzed using the Fst method, and the top 1% regions were designated candidate regions, revealing 661 candidate genes.

Functional Enrichment and Candidate Genes

  • Candidate genes were functionally enriched to understand their biological roles and pathways.
  • Key pathways identified include:
    • Immune regulation
    • Neural signal transmission
    • Muscle contraction
    • Energy metabolism
  • The involvement of these pathways suggests they significantly influence racing performance differences.
  • Several specific genes were highlighted for their importance in muscle function, metabolism, sensory perception, and neurobiology, underscoring their role in shaping the athletic phenotype of the Grassland-Thoroughbred (the abstract noted several gene names but they were missing—these would typically include genes related to these physiological processes).

Significance of the Study

  • This research provides insights into the molecular mechanisms of horse speed and athletic ability, aiding in the understanding of performance variation at the genetic level.
  • The findings offer a valuable foundation for molecular breeding strategies aimed at improving racehorse performance in the Grassland-Thoroughbred breed.
  • Identifying candidate genes and pathways allows breeders to focus on genetic markers associated with desirable traits, facilitating precision breeding.

Conclusion

  • The whole-genome resequencing approach effectively revealed genomic regions and genes under selection related to racing ability in Grassland-Thoroughbreds.
  • The integration of multiple methods strengthened the reliability of candidate gene identification.
  • Pathways related to muscle, metabolism, neural function, and immunity appear central to the differences in racing performance, highlighting complex biological underpinnings of speed.
  • Overall, this study advances the molecular understanding of athletic traits in racehorses and supports breeding programs targeting enhanced racing capabilities.

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 Athletic Traits in Grassland-Thoroughbred. Animals (Basel), 15(15), 2323. https://doi.org/10.3390/ani15152323

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 15
Issue: 15
PII: 2323

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 / Inner Mongolia Autonomous Region Science and Technology Program Project
  • 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 / 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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