Whole-Transcriptome Sequencing and ceRNA Network Analysis of the Hypothalamus During the Follicular Phase in High- and Low-Fecundity Xinjiang Goats

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.