Transcriptomic insights into skin pigmentation differences between black and white skinned chickens

The present study investigated the transcriptional differences between black skinned Kadaknath and white skinned Broiler chickens using RNA sequencing analysis of skin tissue. A total of 339 high confidence, differentially expressed genes with a log₂ fold change ≥ 4 were identified, of which 294 were upregulated in Kadaknath while 45 were upregulated in Broiler skin samples. Comparative gene expression analysis revealed strong activation of melanogenesis related pathways in black skin, indicating enhanced pigment synthesis and melanocyte activity. Pathway enrichment also underscored the role of biological processes related to melanin biosynthesis, ion homeostasis and mitochondrial regulation in Kadaknath. In contrast, Broiler skin showed enrichment of pathways associated with developmental regulation and tissue patterning, suggesting a greater role of transcriptional programs involved in skin development and structural organization. Gene co-expression network analysis also revealed distinct regulatory architectures between the two groups. Key genes identified in black skin were associated with structural and cytoskeletal functions, while developmental transcription factors and regulatory genes were enriched in white skin. These findings suggest that transcriptomic differences between the two chicken types are regulated by pigment synthesis pathways and developmental regulatory networks in in black and white skin, respectively. This study provides valuable insights into the transcriptional profiles associated with diverse skin types in chicken.