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Background  Arabian horses are believed to be one of the oldest and most influential horse breeds in the world. Blood is the main tissue involved in maintaining body homeostasis, and it is considered a marker of the processes taking place in the other tissues. Thus, the aim of our study was to identify the genetic basis of changes occurring in the blood of Arabian horses subjected to a training regimen and to compare the global gene expression profiles between different training periods (T 1 : after a slow canter phase that is considered a conditioning phase, T 2 : after an intense gallop phase, and T 3 : at the end of the racing season) and between trained and untrained horses (T 0 ). RNA sequencing was performed on 37 samples with a 75-bp single-end run on a HiScanSQ platform (Illumina), and differentially expressed genes (DEGs) were identified based on DESeq2 (v1.11.25) software.    Results  An increase in the number of DEGs between subsequent training periods was observed, and the highest amount of DEGs (440) was detected between untrained horses (T 0 ) and horses at the end of the racing season (T 3 ). The comparisons of the T 2  vs. T 3  transcriptomes and the T 0  vs. T 3  transcriptomes showed a significant gain of up-regulated genes during long-term exercise (up-regulation of 266 and 389 DEGs in the T 3  period compared to T 2  and T 0 , respectively). Forty differentially expressed genes were detected between the T 1  and T 2  periods, and 296 between T 2  and T 3 . Functional annotation showed that the most abundant genes up-regulated in exercise were involved in pathways regulating cell cycle (PI3K-Akt signalling pathway), cell communication (cAMP-dependent pathway), proliferation, differentiation and apoptosis, as well as immunity processes (Jak-STAT signalling pathway).    Conclusions  We investigated whether training causes permanent transcriptome changes in horse blood as a reflection of adaptation to conditioning and the maintenance of fitness to compete in flat races. The present study identified the overrepresented molecular pathways and genes that are essential for maintaining body homeostasis during long-term exercise in Arabian horses. Selected DEGs should be further investigated as markers that are potentially associated with racing performance in Arabian horses.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-017-0499-1) contains supplementary material, which is available to authorized users.

Transcriptome profiling of Arabian horse blood during training regimens