Exploring the Cyclic Patterns of Secondary Hair Follicles in Cashmere Goats Based on Skin Transcriptome Data

The cashmere fibers produced by the secondary hair follicles of cashmere goats are precious textile raw materials. The secondary hair follicles exhibit a distinct annual cyclical pattern, comprising anagen, catagen, and telogen phases. Although a large amount of skin transcriptome data is currently available for cashmere goats, this study aims to systematically investigate the regulatory factors controlling the cyclical dynamics of secondary hair follicles through re-analysis of these data. Skin transcriptome data of Inner Mongolian cashmere goats were downloaded from the Sequence Read Archive (SRA) database. Bioinformatics analyses, including quality control, read mapping, quantification, differential expression analysis, Gene Ontology (GO) enrichment analysis, and KEGG pathway analysis, were performed to identify key regulatory genes governing the secondary hair follicle cycle. The results revealed a total of 1232 differentially expressed genes (DEGs) from comparisons across different phases. KEGG pathway analysis identified three signaling pathways associated with cashmere development: the cAMP signaling pathway (chx04024), the relaxin signaling pathway (chx04926), and the estrogen signaling pathway (chx04915). GO analysis yielded 335 terms, of which 236 were statistically significant (P-adj < 0.05). The DEGs were predominantly involved in biological processes such as regulation of transcription by RNA polymerase II, proteolysis, and positive regulation of transcription by RNA polymerase II. Significantly enriched cellular components included the plasma membrane, membrane, and extracellular space, and molecular functions were mainly related to protein binding, identical protein binding, and DNA-binding transcription factor activity, RNA polymerase II-specific. Based on their expression patterns, five key genes were selected: KRT25, KRT39, MAPK12, SPP1, and TCHHL1. These genes displayed significantly distinct expression profiles across the hair follicle cycle. TCHHL1 exhibited the highest expression in anagen, intermediate expression in catagen, and the lowest expression in telogen, with significant differences among all three phases. MAPK12 was specifically upregulated in telogen and was significantly more highly expressed than in both anagen and catagen. SPP1 showed high expression in anagen and catagen but extremely low expression in telogen. KRT39 displayed significantly higher expression in both anagen and catagen compared to telogen. KRT25 reached its highest expression in catagen, which was significantly different from that in telogen, while its expression in anagen showed no significant difference from either telogen or catagen. This study characterized the regulatory genes of the secondary hair follicle cycle in cashmere goats at the transcriptional level and analyzed the association between their expression patterns and cycle regulation.