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Animals : an open access journal from MDPI2025; 15(10); doi: 10.3390/ani15101462

Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome Resequencing.

Abstract: Speed and endurance are the primary goals in racehorse breeding. The Grassland-Thoroughbred is a newly developed breed in northern China that combines speed, endurance, and environmental adaptability. However, current research on the genetic background of this breed and the genes associated with athletic performance remains limited. We conducted whole-genome resequencing on Mongolian (MG), Thoroughbred (TB), Xilingol (XL), and Grassland-Thoroughbred (CY) horses, generating 3813.74 Gb of clean data after quality control. The number of transitions was significantly higher than that of transversions. The SNPs were mainly located in intergenic regions, followed by intronic regions. Principal component analysis, population structure analysis, and phylogenetic tree results indicated that the CYs had a distinct genetic background from MGs, TBs, and XLs, but based on PCA and phylogenetic clustering, they showed greater genetic similarity to Thoroughbreds. Using fixation index (Fst) and nucleotide diversity ratio (π ratio) analyses between CYs and the other three horse populations, 70, 76, and 80 candidate genes were identified from the intersection of the two methods, respectively. A total of 179 candidate genes were obtained from the union of the three groups. Candidate genes associated with athletic performance (ATF2, NDUFS7, PRKG1, IGFN1, MTOR, TTN) and growth and development (MTOR, IGFN1, COL21A1, NEDD4, PIEZO1) were screened. These genes are related to athletic ability and developmental processes in the CY population. Our study reveals genomic information associated with important traits in Grassland-Thoroughbreds and identifies valuable candidate genes, laying a foundation for future breeding and trait association studies.
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Publication Date: 2025-05-19 PubMed ID: 40427339PubMed Central: PMC12108167DOI: 10.3390/ani15101462Google Scholar: Lookup
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  • Journal Article

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.

This research was focused on studying an emerging horse breed in northern China, named the Grassland-Thoroughbred. This breed is gaining popularity for its speed, stamina, and ability to adapt to various environments. The researchers undertook genome sequencing studies on this breed along with three other established horse breeds to identify unique genetic characteristics associated with performance and development. They also identified specific candidate genes linked with these traits, providing a basis for future genetics-based breeding programs.

Background

  • The study, focused on the Grassland-Thoroughbred horse breed in northern China, analyzed its genetic structure with the goal of understanding its traits of speed, endurance, and environmental adaptability. Along with the Grassland-Thoroughbred (CY), three other horse breeds – the Mongolian (MG), Thoroughbred (TB), and Xilingol (XL) were also studied.
  • Existing, pertinent research on this breed is reportedly limited in scope, deepening the relevance of this study to breeders interested in understanding the genetic bases of athletic performance and adaptability.

Methodology

  • The researchers conducted whole-genome resequencing on representatives of four horse breeds. From the collected data, they filtered out the clean data totaling 3813.74 Gb after running quality control measures.
  • Genes of interest or “candidate genes” were identified, and the locations of these genes were tracked chiefly in intergenic regions, followed by intronic zones. These regions define the presence, type, and operation of genes in an organism.

Findings

  • The Grassland-Thoroughbred horses had a unique genetic makeup distinct from the other three breeds, but they showed some similarity with Thoroughbreds according to tests like principal component analysis, population structure analysis, and the construction of a phylogenetic tree.
  • Applying the fixation index (Fst) and nucleotide diversity ratio (π ratio) analyses, the researchers identified groups of candidate genes linked with athletic performance and growth development that could potentially be attributed to the Grassland-Thoroughbreds’ desirable traits.
  • A total of 179 candidate genes were isolated, helping to provide a possible genetic explanation for athleticism and adaptability in the Grassland-Thoroughbred breed.

Conclusion

  • This study generated valuable information on the genetic structure of the Grassland-Thoroughbreds, specifically identifying genes that could be associated with desirable athletic performance and adaptability.
  • The accomplished research sets a solid groundwork for future examination of trait association and can influence directions taken in breeding programs, thereby optimizing the exceptional traits of this breed.

Cite This Article

APA
Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D, Zhao Y. (2025). Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome Resequencing. Animals (Basel), 15(10). https://doi.org/10.3390/ani15101462

Publication

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

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.
Zhao, Yiping
  • 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 / 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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