Comparative Analyses of Metabolic Gene Expression in Emaciated and Moderately Conditioned Horses: Insights from RNA-Seq and RT-qPCR

Starvation in horses poses critical challenges for welfare, management, and rehabilitation, yet the underlying molecular mechanisms that drive adaptation and recovery are not fully understood. Caloric deprivation forces systemic shifts in energy balance, with transitions from carbohydrate to lipid utilization, suppression of anabolic pathways, and activation of catabolic processes. These metabolic changes are reflected in tissue-specific gene expression patterns, making transcriptomic analysis a valuable tool for understanding equine responses to emaciation and subsequent refeeding. This work combines review and experimental approaches to investigate how metabolic gene expression differs between emaciated and moderately conditioned horses. Horses were evaluated using body condition scores and tissues were collected post-mortem from multiple systems, including muscle, adipose, gastrointestinal tract, and vital organs. Gene expression was first assessed using real-time quantitative PCR (RT-qPCR) to examine key genes involved in glucose transport, fatty acid oxidation, and protein synthesis. While no significant differences were detected between body condition groups, tissue-specific variation highlighted the importance of organ- and system-level contributions to metabolism. To extend beyond targeted gene analysis, RNA sequencing (RNA-seq) was employed to provide a broader view of transcriptional activity. This revealed distinct molecular profiles between E and M horses, identifying hundreds of differentially expressed genes associated with mitochondrial function, oxidative phosphorylation, and glucose metabolism. These findings suggest that metabolic adaptation in emaciated horses is more complex than single-gene assays can capture, emphasizing the value of high-throughput approaches. Together, these results underscore that starvation and recovery in horses involve coordinated, tissue-specific transcriptional responses that are best understood through combined molecular methods. The work highlights both the challenges of interpreting post-mortem data and the opportunities for RNA-seq to uncover biologically meaningful pathways. A more comprehensive understanding of these molecular mechanisms will guide the development of evidence-based rehabilitation strategies, reduce the risk of refeeding syndrome, and improve long-term survival and welfare outcomes for affected horses.