Junken meat sheep exhibit a characteristic postnatal coat-color transition, in which the initially black fleece gradually fades and develops into a white-trunk phenotype; however, the transcriptional basis of this developmental change in follicular pigment output remains unclear. In this study, three Junken meat sheep lambs showing a natural postnatal black-to-white coat-color transition were sampled longitudinally at the newborn black-fleece stage and the 179-day white-trunk stage, generating three matched biological pairs for RNA-seq analysis. Representative candidate genes were further validated by RT-qPCR. Differential expression analysis identified 1657, 400, and 1086 differentially expressed genes in the C11 vs. C1, C22 vs. C2, and C33 vs. C3 comparisons, respectively. Functional enrichment analysis indicated that these genes were mainly associated with tyrosine metabolism, ECM–receptor interaction, focal adhesion, Phosphoinositide 3-kinase-Akt signaling pathway (PI3K-Akt), arachidonic acid metabolism, estrogen signaling, and immune-related pathways. Integrated analysis of shared downregulated genes and expression patterns highlighted candidate genes related to pigmentation, the ECM/follicular microenvironment, and regulatory or metabolic processes. Pigmentation-related genes, including SOX10, TYR, TYRP1, PMEL, OCA2 and SLC45A2, were generally downregulated in 179-day white-trunk-stage skin, while changes in ECM- and metabolism-related genes suggested altered follicular microenvironmental regulation. These findings identify candidate transcriptional features associated with developmental coat-color fading in Junken meat sheep and support a follicular microenvironment–melanogenesis expression axis as a transcriptome-based framework for further investigation.

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.