Abstract
Sheep production is vital to the global agricultural economy, particularly for meat and wool. However, fertility varies significantly among breeds, influenced by genetics, nutrition, and environment. MicroRNAs (miRNAs) are crucial post-transcriptional regulators of gene expression, binding to target messenger RNAs (mRNAs) to inhibit translation or trigger degradation. Despite their importance, little is known about ovary-specific miRNAs and their target genes in high and low fecundity sheep breeds. Here, we investigated miRNA expression profiles in ovarian tissues from Small Tail Han (high fecundity) and Dolang sheep (low fecundity) using miRNA sequencing. The analysis identified 51 significantly differentially expressed miRNAs (DEmiRNAs), with only nine mapping to the reference genome (including oar-miR-103, oar-miR-16b). We predicted 88,699, 176,629, and 240,753 target mRNAs for these DEmiRNAs from sheep, goat, and cow, respectively. Functional enrichment analysis revealed significant biological processes and signaling pathways potentially associated with fecundity. Subsequently, we constructed a DEmiRNA-mRNA regulatory network, highlighting candidate miRNA-mRNA pairs like chi-miR-130a-3p-WNT2B, oar-miR-103-FSHR, and oar-miR-16b-AMH. These findings provide insights into the potential regulators of sheep fecundity. We further validated these candidate miRNA-mRNA interactions using qRT-PCR to explore their roles in regulating sheep fecundity. Overall, this study utilized miRNA sequencing to analyze ovarian miRNA expression in sheep and identified potential miRNA-mRNA targets associated with fecundity. This lays the foundation for future research on the molecular mechanisms underlying sheep ovarian physiology and improving reproductive traits.