Objective This study aims to mine functional genes related to the Yili horse competition route, in the hope of providing data references for early selection materials and breeding of different Yili horse competition routes.

Methods The study selected horses that ranked among the top six Yili horse regular competition for both the 2 and 80 km events as research subjects. Blood samples were collected from the horses in their resting state prior to the competitions, with transcriptome sequencing performed using the Illumina platform. Meanwhile, differential expressed genes between the two groups were identified, followed by functional enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).

Results The results showed that out of 839 differentially expressed genes in the 2000-meter group compared to the 80-kilometer group, 305 were up-regulated while 534 were down-regulated, with |log2(FoldChange)| > 1 and P-value < 0.05 serving as the filtering criteria for differential genes. GO functional enrichment analysis annotated 20 significantly enriched terms, including four biological processes, six cellular components, and ten molecular functions (Padj < 0.05). These terms mainly focused on metabolism, immunity and inflammation, as well as cell membrane function. KEGG pathway enrichment analysis were significantly enriched in pathways such as cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and hematopoietic cell lineage (Padj < 0.05).

Conclusion By further analysis of related pathways, it is found that the genes IL20RA, IL1B, IL18, FAS, P2RY6, and CD36 may be related with the Yili horse race route, which could potentially serve as reference points for selecting different race routes for the Yili horse.