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Animals : an open access journal from MDPI2025; 15(8); doi: 10.3390/ani15081123

Pilot Study on the Profiling and Functional Analysis of mRNA, miRNA, and lncRNA in the Skeletal Muscle of Mongolian Horses, Xilingol Horses, and Grassland-Thoroughbreds.

Abstract: Muscle fibers, as the fundamental units of muscle tissue, play a crucial role in determining skeletal muscle function through their growth, development, and composition. To investigate changes in muscle fiber types and their regulatory mechanisms in Mongolian horses (MG), Xilingol horses (XL), and Grassland-Thoroughbreds (CY), we conducted histological and bioinformatic analyses on the gluteus medius muscle of these three horse breeds. Immunofluorescence analysis revealed that Grassland-Thoroughbreds had the highest proportion of fast-twitch muscle fibers at 78.63%, while Mongolian horses had the lowest proportion at 57.54%. Whole-transcriptome analysis identified 105 differentially expressed genes (DEGs) in the CY vs. MG comparison and 104 DEGs in the CY vs. XL comparison. Time-series expression profiling grouped the DEGs into eight gene sets, with three sets showing significantly up-regulated or down-regulated expression patterns (p < 0.05). Additionally, 280 differentially expressed long non-coding RNAs (DELs) were identified in CY vs. MG, and 213 DELs were identified in CY vs. XL. A total of 32 differentially expressed microRNAs (DEMIRs) were identified in CY vs. MG, while 44 DEMIRs were found in CY vs. XL. Functional enrichment analysis indicated that the DEGs were significantly enriched in essential biological processes, such as actin filament organization, muscle contraction, and protein phosphorylation. KEGG pathway analysis showed their involvement in key signaling pathways, including the mTOR signaling pathway, FoxO signaling pathway, and HIF-1 signaling pathway. Furthermore, functional variation-based analyses revealed associations between non-coding RNAs and mRNAs, with some non-coding RNAs targeting genes potentially related to muscle function regulation. These findings provide valuable insights into the molecular basis for the environmental adaptability, athletic performance, and muscle characteristics in horses, offering new perspectives for the breeding of Grassland-Thoroughbreds.
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Publication Date: 2025-04-13 PubMed ID: 40281957PubMed Central: PMC12024394DOI: 10.3390/ani15081123Google Scholar: Lookup
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Summary

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The study investigates the differences in muscle fiber types and their regulatory mechanisms among Mongolian, Xilingol, and Grassland-Thoroughbred horses, revealing disparities in their muscle composition. The findings facilitate comprehension of the molecular basis for environmental adaptability, athletic performance, and muscle traits in horses, offering novel insights for Grassland-Thoroughbred horse breeding.

Analyses and Findings

  • The research utilized histological and bioinformatic examinations on the gluteus medius muscle of these three horse breeds to understand the differences in their muscle fiber types and governing mechanisms.
  • Immunofluorescence analysis disclosed that Grassland-Thoroughbreds harbored the greatest ratio of fast-twitch muscle fibers at 78.63% whereas Mongolian horses had the least concentration at 57.54%.
  • Through whole-transcriptome analysis, the study identified differentially expressed genes (DEGs) in the comparisons between Grassland-Thoroughbreds and the other two breeds.
  • The DEGs were grouped into eight gene sets through time-series expression profiling, with three sets demonstrating significantly up- or down-regulated expression patterns.

Non-Coding RNAs and their Functional Roles

  • In addition to DEGs, the study recognized differentially expressed long non-coding RNAs (DELs) and microRNAs (particular subset of RNA).
  • The identified DELs and DEMIRs were significantly numerous in the comparisons between Grassland-Thoroughbreds and the other two breeds.
  • The study indicated associations between the non-coding RNAs and mRNAs, suggesting that some non-coding RNAs may target genes potentially linked to muscle function regulation.

Implications of the Findings

  • Functional enrichment analysis suggested that the DEGs were noticeably enriched in essential biological operations, such as actin filament organization, muscle contraction, and protein phosphorylation.
  • The DEGs engaged in several vital signaling pathways, including the mTOR signaling pathway, FoxO signaling path, and HIF-1 signaling route.
  • Therefore, the obtained results provide crucial insights into the molecular foundation for the environmental adaptability, athletic performance, and muscle features in horses.
  • These findings offer fresh viewpoints for the breeding of Grassland-Thoroughbreds.

Cite This Article

APA
Ding W, Gong W, Bou T, Shi L, Lin Y, Wu H, Dugarjaviin M, Bai D. (2025). Pilot Study on the Profiling and Functional Analysis of mRNA, miRNA, and lncRNA in the Skeletal Muscle of Mongolian Horses, Xilingol Horses, and Grassland-Thoroughbreds. Animals (Basel), 15(8). https://doi.org/10.3390/ani15081123

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 15
Issue: 8

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.
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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Citations

This article has been cited 2 times.
  1. Ma S, Ren W, Li Z, Li L, Wang R, Su Y, Huang Q, Dehaxi S, Wang J. Comparative analysis of miRNA expression in Yili horses pre- and post-5000-m race. Front Genet 2025;16:1676558.
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  2. Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D, Zhao Y. Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome Resequencing. Animals (Basel) 2025 May 19;15(10).
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