Whole-Transcriptome Sequencing and ceRNA Network Analysis of the Hypothalamus During the Follicular Phase in High-...

Fecundity affects herd expansion and economic efficiency in goats and is under the control of the hypothalamic-pituitary-gonadal (HPG) axis and intricate RNA regulatory networks. Herein, hypothalamic tissues from high- and low-fecundity Xinjiang goats during the follicular phase were analyzed using integrated mRNA/lncRNA transcriptome sequencing and small RNA sequencing, followed by differential expression, functional enrichment, and competing endogenous RNA (ceRNA) network analyses. Sixty-nine differentially expressed mRNAs, 202 differentially expressed lncRNAs, and 1 differentially expressed miRNA were identified between the two groups. Functional enrichment revealed that differentially expressed RNA-associated genes were mainly involved in hormone regulation and secretion; neuroactive ligand-receptor interactions; cAMP signaling; oxidative phosphorylation; the electron transport chain; and MAPK, TGF-β, and PI3K-Akt pathways. These findings link fecundity differences in Xinjiang goats to hypothalamic neuroendocrine signaling, mitochondrial energy metabolism, and post-transcriptional regulation during the follicular phase. ceRNA analysis suggested that 16 lncRNAs may be involved in the putative regulation of PCDHB13 through chi-miR-141, highlighting five key candidate lncRNA-chi-miR-141-PCDHB13 axes. PCDHB13, a protocadherin involved in neuronal adhesion and neural circuit formation, suggests that the lncRNA-chi-miR-141-PCDHB13 module may influence hypothalamic signaling and reproductive regulation during the follicular phase. Overall, this study identifies candidate RNAs and ceRNA axes that underlie fecundity differences in Xinjiang goats.