BACKGROUND: Thoroughbred horses are the most expensive domestic animals, and 
their running ability and knowledge about their muscle-related diseases are 
important in animal genetics. While the horse reference genome is available, 
there has been no large-scale functional annotation of the genome using 
expressed genes derived from transcriptomes.
RESULTS: We present a large-scale analysis of whole transcriptome data. We 
sequenced the whole mRNA from the blood and muscle tissues of six thoroughbred 
horses before and after exercise. By comparing current genome annotations, we 
identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 
(36.87%) annotated genes. More than 60% (20,428) of the unigene clusters did not 
match any current equine gene model. We also identified 189,973 single 
nucleotide variations (SNVs) from the sequences aligned against the horse 
reference genome. Most SNVs (171,558 SNVs; 90.31%) were novel when compared with 
over 1.1 million equine SNPs from two SNP databases. Using differential 
expression analysis, we further identified a number of exercise-regulated genes: 
62 up-regulated and 80 down-regulated genes in the blood, and 878 up-regulated 
and 285 down-regulated genes in the muscle. Six of 28 previously-known 
exercise-related genes were over-expressed in the muscle after exercise. Among 
the differentially expressed genes, there were 91 transcription factor-encoding 
genes, which included 56 functionally unknown transcription factor candidates 
that are probably associated with an early regulatory exercise mechanism. In 
addition, we found interesting RNA expression patterns where different 
alternative splicing forms of the same gene showed reversed expressions before 
and after exercising.
CONCLUSION: The first sequencing-based horse transcriptome data, extensive 
analyses results, deferentially expressed genes before and after exercise, and 
candidate genes that are related to the exercise are provided in this study.