Histological and Strand-Specific Transcriptomic Analyses Reveal Developmental Dynamics and Pigmentation-Associated Candidate Genes in Black and White Skin Regions of Bama Miniature Pigs

Guangxi Bama miniature pigs are a highly inbred population developed from Bama Xiang pigs and exhibit a stable “two-end black” skin phenotype, making them a useful model for studying regional skin pigmentation. However, the developmental timing and molecular basis of this color difference remain unclear. In this study, black and white skin samples were collected from the posterior head/neck region at six developmental stages: embryonic days 65, 90, and 105, birth, and postnatal days 30 and 180. Histological examination and strand-specific RNA sequencing showed that developmental stage was the major factor shaping skin gene expression, whereas black–white skin differences varied across stages. Transcriptomic differences were already detectable at embryonic day 65, although visible regional differences were not obvious. Pigmentation-associated genes, including DCT, SLC24A5, TRPM1, and TYRP1, showed black-skin-biased expression during embryonic development, especially at embryonic day 105. Histological analysis also revealed progressive skin maturation and qualitative differences in darkly stained structures between black and white skin. These findings suggest that molecular differences between black and white skin emerge during embryonic development and persist after birth, providing resources and candidate genes for studying regional pigmentation in Bama miniature pigs.