Integrative Whole-Transcriptome Sequencing Analysis of Skin Tissues with Different Coat Types in Cashmere Goats Across Stages of Hair Follicle Development

Background Cashmere goat coat types determine cashmere quality and economic value, making elucidating their underlying molecular regulatory mechanisms crucial for targeted breeding and developing high-quality cashmere products. Results We collected skin tissues from Jinlan Cashmere Goats of two coat types (CHSC and CHLC) at three hair follicle developmental stages—anagen (AN), catagen (CA), and telogen (TE)—for whole-transcriptome sequencing analysis. Results showed that 178 differentially expressed (DE) lncRNAs and 267 DE mRNAs were identified in the AN phase, 62 DE lncRNAs and 93 DE mRNAs in the CA phase, and 65 DE lncRNAs and 158 DE mRNAs in the TE phase. GO and KEGG functional enrichment analyses revealed that during the AN stage, DE target genes were enriched in processes related to material and energy metabolism—including purine nucleoside triphosphate metabolism, oxidative phosphorylation, and purine metabolism—as well as glycosylation modifications such as protein N-linked glycosylation and protein glycosylation. These activities likely furnish the energy and biosynthetic precursors required for rapid cellular proliferation. In the CA stage, DE target genes were predominantly associated with immune-related functions. Enriched GO terms included immune response, immune system process, and cytokine activity, while KEGG pathways comprised Cytokine-Cytokine Receptor Interaction, IL-17 Signaling Pathway, and NF-kappa B Signaling Pathway. These changes are thought to facilitate adaptation to the microenvironmental alterations of hair follicles during the CA phase. In the TE phase, Wnt-related GO terms and KEGG pathways (Wnt signaling pathway and cell-cell signaling by wnt) were enriched, which serve crucial roles in maintaining the quiescent state of hair follicles and initiating the transition to the AN phase. Finally, ceRNA mechanism analysis revealed that the lncRNAs-chi-miR-671-5p-ADIPOQ regulatory axis in the AN phase, two regulatory axes ( XR_001918825.1-chi-miR-128-5p-RFX2 and XR_001296715.2-chi-miR-324-3p-RFX2 ) in the CA phase, and TCONS_00062482-chi-miR-874-3p-PGLYRP1 in the TE phase may play crucial roles in regulating the development of different coat types in cashmere goats. Conclusions These insights not only enhance our knowledge of hair follicle biology but also offer potential strategies for improving cashmere production through genetic selection and environmental management.