Comparative Transcriptomic Profiling Identifies Region- and Phenotypic-Background-Associated Transcriptional Programs Linked to Coat-Color Variation in Junken Meat Sheep

Junken meat sheep display distinct coat-color phenotypes, including a white body with a black head and an entirely black coat at birth, but the transcriptional basis of variation across skin regions and phenotypic backgrounds remains unclear. We performed bulk RNA sequencing (RNA-seq) on nine skin samples from six 1-month-old lambs: black-haired head skin (BT), white-haired dorsal trunk skin (WT), and black-haired dorsal trunk skin from lambs born entirely black (B), with three biological replicates per group. The paired BT–WT comparison characterized within-individual regional differences, whereas B–WT represented a composite phenotypic-background comparison. Cross-comparison integration identified 2056 region-associated genes, 8027 phenotypic-background-associated genes, and 5615 shared genes. Region-associated genes were enriched in mitochondrial and lipid-metabolic processes, phenotypic-background-associated genes in cell communication and adhesion, and shared genes in epidermal keratinization, cytoskeletal organization, and extracellular matrix–integrin-related processes. Network analysis identified a pigmentation-effector subnetwork containing TYR, TYRP1, PMEL, OCA2, SLC45A2 and MYO5A. Signature scoring suggested that some contractile signals may reflect tissue-composition differences. Reverse transcription quantitative PCR broadly supported the RNA-seq expression trends. These findings provide a multilayered transcriptional framework for subsequent functional validation of coat-color variation in Junken meat sheep.