Integrated analysis of mRNA and miRNA in testis and cauda epididymidis reveals candidate molecular markers associated with reproduction in Dezhou donkey

Abstract In China, donkeys are raised for fur, meat, and milk. Reproduction and breeding are crucial to maintain the donkey industry, and conventional breeding is currently applied. This study explored functional factors related to spermatogenesis, maturation, and storage and to identify molecular markers associated with donkey reproduction by analyzing the regulatory elements and target genes in testis and epididymidis. This research is essential to extending donkey genetic information resources and will lay a foundation for molecular breeding. High-throughput sequencing techniques can analyze genetic variations and candidate genes related to different traits. In this study, we identified 6,097 significant differentially expressed genes (DEGs) between testis and cauda epididymidis, including 1,245 transcription factors (TFs). We also found putative SNPs located in coding regions. Alternative splicing events of expressed genes were identified, among which skipping exon and alternative 3′ splice site events were the most ubiquitous. We obtained 169 miRNAs that were differentially expressed. 5,285 DE-targets were involved in 286 pathways according to KEGG functional annotations, including focal adhesion, ECM-receptor interaction, actin cytoskeleton regulation, rap1 signaling pathway, and PI3K-Akt signaling pathway possibly related to spermatogenesis. We have distinguished pivotal DEGs (Col6a2, ITGA4, ITGA6, ITGB1, PRKCA, and AKT1), three TFs (COL6A3, AKT1, and KIT), and some miRNAs (miR-141, let-7, miR-148, and miR-221). These high-quality transcriptome and microRNA data of donkey testis and epididymis will facilitate functional studies on the donkey genome. The identified DE-targets and DE-microRNAs are candidate factors for donkey reproduction traits and can be applied to molecular breeding programs.