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. 2025 Feb 4;16(2):197.
doi: 10.3390/genes16020197.

Effects of Combined Transcriptome and Metabolome Analysis Training on Athletic Performance of 2-Year-Old Trot-Type Yili Horses

Liping Yang  1 , Pengcheng Li  1 , Xinxin Huang  1 , Chuankun Wang  1 , Yaqi Zeng  1   2   3 , Jianwen Wang  1   2   3 , Xinkui Yao  1   2   3 , Jun Meng  1   2   3
Affiliations

Effects of Combined Transcriptome and Metabolome Analysis Training on Athletic Performance of 2-Year-Old Trot-Type Yili Horses

Liping Yang et al. Genes (Basel). .

Abstract

Objectives: Training is essential for enhancing equine athletic performance, but the genetic mechanisms that regulate athletic performance are unknown. Therefore, this paper aims to identify candidate genes and metabolic pathways for the effects of training on equine athletic performance through multi-omics analyses.

Methods: The experiment selected 12 untrained trot-type Yili horses, which underwent a 12-week professional training program. Blood samples were collected at rest before training (BT) and after training (AT). Based on their race performance, whole blood and serum samples from 4 horses were chosen for transcriptomic and metabolomic analyses.

Results: The race performance of the horses is dramatically improved in the AT period compared to the BT (p < 0.01) period. The transcriptome analysis identified a total of 57 differentially expressed genes, which were significantly enriched in pathways related to circadian entrainment, steroid hormone biosynthesis, chemokine signaling, and cholinergic synapses (p < 0.05). Additionally, metabolomic analysis revealed 121 differentially identified metabolites, primarily enriched in metabolic pathways such as histidine metabolism, purine metabolism, and the PI3K-Akt signaling pathway. The integration of transcriptomic and metabolomic analyses uncovered five shared pathways, and further combined pathway analyses identified eight differentially expressed genes that correlate with 19 differentially identified metabolites.

Conclusions: The current findings will contribute to establishing a theoretical framework for investigating the molecular mechanisms of genes associated with the impact of training on equine athletic performance. Additionally, these results will serve as a foundation for enhancing the athletic capabilities of trot-type Yili horses.

Keywords: Yili horses; athletic performance; metabolomics; transcriptomics; trot.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Transcriptome analysis of equine blood in AT versus BT. (A) The number of up- and down-regulated differentially expressed genes (DEGs). (B) Volcano plot for differential genes expression (n = 4).
Figure 2
Figure 2
Analysis of differential genes enrichment in AT versus BT. (A) GO enrichment analysis of up-regulated genes. (B) GO enrichment analysis of down-regulated genes. (C) KEGG enrichment analysis of up-regulated genes. (D) KEGG enrichment analysis of down-regulated genes.
Figure 3
Figure 3
Interaction analysis of AT and BT differential genes protein networks. (A) Differential genes protein network interaction map. (B) Map of core genes significantly associated with the athletic performance of the trot-type Yili horses.
Figure 4
Figure 4
Quality control analysis of equine plasma in AT versus BT. (A) PCA score plot of the metabolome. (B) PLS-DA score plot of the metabolome. (C) PLS-DA model test of the metabolome. (D) Pearson correlation between samples.
Figure 5
Figure 5
Metabolome analysis of equine plasma in AT versus BT. (A) The number of up- and down-regulated differentially expressed metabolites. (B) Volcano plot for differential metabolites expression (n = 4).
Figure 6
Figure 6
Analysis of differential metabolites enrichment in AT versus BT.
Figure 7
Figure 7
Integrated analysis of metabolomic and transcriptomic profiling of AT and BT. (A) Venn diagram of shared KEGG terms among transcriptome and metabolome. (B) Correlation heatmap of differentially expressed genes and metabolites for the integrated pathway. *, **: significant positive or negative correlation. (C) Correlation network of differentially expressed genes and metabolites for the integrated pathway.
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