Transcriptomic profiles reveal differences in gene expression between the testes and epididymis in stallions

Spermatogenesis and sperm maturation take place in the testes and epididymis, respectively. These complex physiological processes are regulated by multiple genes, which have not been studied in the stallion. In this study, Illumina sequencing was used to analyze the transcriptomes of the testes, head, body and tail of the epididymis from three reproductively normal stallions. The mRNA was extracted and the libraries were generated using Next Generation Sequencing (NGS). The expression patterns of differentially expressed genes (DEGs) in the testes and epididymis were determined by bioinformatics analysis. Gene Ontology (GO) enrichment analysis of DEGs was implemented and gene length bias was corrected. Differentially expressed genes were compared between the different segments of the epididymis and the testis (control tissue). GO-terms with adjusted p < 0.05 were considered significantly enriched. Among the four libraries, 18,732 genes were identified. Of those, 6,574 genes (39.1%) were tissue-specific. The distribution of tissue-specific genes was 14.2 % in the testes, 2.2 % in the epididymal head, 1.1 % in the epididymal body, and 1.4 % in the epididymal tail. Compared with testicular tissue, there were 13,349 DEGs (5,595 up-regulated and 7,754 down-regulated) in the epidydimal head, 14,207 DEGs (5,884 up-regulated and 8,323 down-regulated) in the epididymal body, and 14,822 DEGs (5,842 up-regulated and 8,980 down regulated) in the epididymal tail. In the epididymal head,the main downregulated terms were male gamete generation (224 DEGs), spermatogenesis (224 DEGs), organelle fission (264 DEGs), sexual reproduction (343 DEGs) and nuclear division (233 DEGs). The main upregulated terms were associated with the ribosome (322 DEGs), lymphocyte activation (226 DEGs), and cytosolic part (104 DEGs). In the epididymal body, the most significantly downregulated terms were male gamete generation (232 DEGs), spermatogenesis (232 DEGs), sexual reproduction (358 DEGs), cilium morphogenesis (151 DEGs) and cilium (235 DEGs). The most significantly upregulated terms were lysosome (150 DEGs), lytic vacuole (150 DEGs), positive regulation of locomotion (197 DEGs), cytosolic ribosome (71 DEGs), vacuole (182 DEGs). In the epididymal tail, the most significantly downregulated terms were male gamete generation (239 DEGs), spermatogenesis (193 DEGs), cilium (253 DEGs), ciliary part (186 DEGs), cilium morphogenesis (158 DEGs). The most significantly upregulated terms were associated with the ribosome (438 DEGs) and cytosolic part (109 DEGs). In summary, we found decreased expression of genes involved in gamete production, and increased expression of genes involved in protein synthesis, immunity and sperm transport in different segments of the epididymis. These findings provide genome-wide mRNA expression profiles for the horse epididymis and testes, providing a biological basis for future research on stallion fertility.