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Animals : an open access journal from MDPI2025; 15(14); 2068; doi: 10.3390/ani15142068

Analysis of ROH Characteristics Across Generations in Grassland-Thoroughbred Horses and Identification of Loci Associated with Athletic Traits.

Abstract: The core objective of racehorse breeding is to enhance the speed and endurance of the horses. The Grassland-Thoroughbred is an emerging horse breed developed in northern China in recent years, characterized by excellent speed performance, enduring stamina, and strong environmental adaptability. However, research on the genetic characteristics within this breed and the genes associated with athletic performance remains relatively limited. We conducted whole-genome resequencing of Grassland-Thoroughbred F1, F2, F3, and the crossbred population (CY) and obtained a total of 4056.23 Gb of high-quality data after quality control. The single nucleotide polymorphisms (SNPs) were primarily distributed in intergenic regions, followed by intronic regions. Principal component analysis (PCA) and STRUCTURE revealed clear distinctions among the generations, with a notable overlap between CY and F3. Using the SNP dataset, we analyzed the number and length distribution patterns of runs of homozygosity (ROHs) in the genomes of different generational groups of Grassland-Thoroughbreds. Short ROHs ranging from 0.5 to 2 Mb were the most abundant, with the following distribution: F1 (85.15%) > F2 (82.92%) > CY (78.75%) > F3 (77.51%). Medium-length ROHs (2-8 Mb) and long ROHs (>8 Mb) together exhibited a similar but opposite trend. The average length of ROHs was 1.57 Mb. The inbreeding coefficients (F_ROH) among different generational groups of Grassland-Thoroughbreds were as follows: F1 (0.0942) < F2 (0.1197) < CY (0.1435) < F3 (0.1497). Through ROH island analysis, 10 high-frequency ROH regions were identified and annotated with 120 genes. Genomic regions and candidate genes associated with athletic traits-, , , , , , , and -were identified. These genes may play important roles in regulating muscle performance, mitochondrial energy supply, and learning and memory processes in horses and are closely associated with the athletic ability of the Grassland-Thoroughbred population. This study is the first to systematically characterize the genomic diversity and inbreeding dynamics of the Grassland-Thoroughbred during the breeding process. It identifies candidate genes that may influence athletic performance, thereby providing an important molecular foundation and theoretical basis for the genetic improvement and performance-based selection of this emerging breed.
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Publication Date: 2025-07-13 PubMed ID: 40723531PubMed Central: PMC12291906DOI: 10.3390/ani15142068Google Scholar: Lookup
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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). Analysis of ROH Characteristics Across Generations in Grassland-Thoroughbred Horses and Identification of Loci Associated with Athletic Traits. Animals (Basel), 15(14), 2068. https://doi.org/10.3390/ani15142068

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 15
Issue: 14
PII: 2068

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

  • 2020ZD0004 / construction projects of the Inner Mongolia Science and Technology Department
  • RK2400002235 / the Agricultural and Animal Husbandry Characteristic Seed Industry 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 / Inner Mongolia Autonomous Region Science and Technology Program Project

Conflict of Interest Statement

The authors declare no conflicts of interest.

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