Comparative transcriptomic analysis of the hypothalamus between tumbler and white king pigeons

Tumbler pigeons (Columba livia) were shaped by long-term artificial selection, and their superior flight performance is closely linked to neural regulatory mechanisms. However, the molecular bases of neural regulation-particularly at the hypothalamic transcriptomic level-remain insufficiently characterized. Here, we conducted neurochemical and whole-transcriptome comparisons of the hypothalamus (HYP) in tumbler pigeons (FF) and meat-type White King pigeons (BY), analyzing neurotransmitters and the transcriptome, including mRNA, long non-coding RNA (lncRNA), microRNA (miRNA), and circular RNA (circRNA). Neurotransmitter quantitation revealed that γ-aminobutyric acid (GABA) levels in FF HYP were significantly higher than those in BY. Transcriptome analysis identified 514 differentially expressed mRNAs, 317 differentially expressed lncRNAs, 49 differentially expressed miRNAs and 304 differentially expressed circRNAs. Functional enrichment showed that differentially expressed genes (DEGs) were significantly overrepresented in metabolic pathways, cytokine-cytokine receptor interactions and TGF-β signaling. Differential expression changes in PDK4, PCK1, and POMC reveal complex molecular mechanisms during flight in tumbler pigeons, characterized by increased energy dependence on fatty acids, inhibition of gluconeogenesis, and enhanced stress response. In this study, we systematically elucidated the molecular regulatory mechanisms of the pigeon hypothalamus (HYP) controlling energy metabolism, neural excitability, and stress response through neurochemical and transcriptomic analyses. It provides a theoretical basis for the neurogenetic basis of behavioral adaptation in birds and for the conservation and selective breeding of local pigeon genetic resources.