Transcriptomic insights into the heart and cerebellar vermis of pigeons: Breed-specific differences driven by selective breeding

To reveal the molecular regulatory differences in physiological adaptations of pigeons with different breeding objectives, this study compared the transcriptomic differences in the hearts and cerebellar vermis of homing pigeons (HP) and meat pigeons (MP). Phenotypic analysis showed that the heart index of HP was significantly higher than that of MP, which helps enhance functions such as blood circulation, supporting the metabolic demands for long-duration activity. However, no significant differences were observed in the cerebellar vermis indices. Transcriptomic analysis identified 162 differentially expressed genes (DEGs) in the heart and 192 in the cerebellar vermis. Differential genes in the heart were primarily enriched in pathways related to circulatory system processes, ventricle development, fatty acid metabolism, and hypoxia response, including key genes related to angiogenesis and metabolism, such as HSP90AA1, ACACB, and LPIN1, suggesting that HP have stronger cardiovascular function and energy metabolism capacity. Differential genes in the cerebellar vermis were enriched in extracellular matrix organization, synaptic organization, axon guidance, and NRF2 pathway, indicating enhanced cerebellar neural adaptability and oxidative stress resistance in HP. Notably, circadian rhythm-related genes (PER2, PER3) were downregulated in both the hearts and cerebellar vermis of HP, which may affect the adaptive growth and remodeling of the heart. Alternative splicing analysis revealed 149 and 151 significant splicing events in the heart and cerebellar vermis, respectively, with exon skipping being the predominant splicing type. These results systematically reveal the tissue-specific molecular characteristics of the heart and cerebellar vermis in MP and HP, providing new insights into the molecular basis of their cardiac and metabolic adaptation.