Whole transcriptome analysis for identification of exercise-related markers in thoroughbred racing horse

Thoroughbred is the main horse breed in the horse racing industry. The horses which record excellent performance are valuable in the aspects of economics and industry. Because of the limitation of the conventional breeding methods, it is needed to develop a reliable system for the selection of stallion stud based on molecular breeding. Therefore we conducted high throughput analysis to discover exercise-related single nucleotide variations (SNVs) and differentially expressed genes (DEGs). We sequenced the whole mRNA from the blood and muscle tissues of six thoroughbred horses before and after exercise. By comparing current horse genome annotation, we identified 32,361 unigene clusters and 189,973 SNVs from the sequence aligned against the horse reference genome. We also identified genes regulated by exercise: 62 up-regulated and 80 down-regulated genes in the blood, and 878 up-regulated and 285 down-regulated genes in the muscle, respectively. In addition to DEGs, we also found differentially expressed alternative splicing forms of AXL, DYNC1, PLEKHG1, and COBLL1 before and after exercise. Overall, our results indicated that exercise stress induces massive gene expression change. Further studies should be focused on the mechanism of exercise-induced change and their relation in excellent performance in racing horses. Our data would be valuable information to develop exercise-related markers in horses and ultimately applied to establish a reliable selection system for producing a better stallion.