Integrative mRNA and lncRNA Transcriptome 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. Elucidating the molecular regulatory mechanisms is crucial for targeted breeding and the development of high-quality cashmere products. Methods: Skin tissues from Jinlan cashmere goats with two distinct coat types (CHSC and CHLC) were collected at three hair follicle developmental stages—anagen (AN), catagen (CA), and telogen (TE)—for RNA-seq. Results: A total of 178 differentially expressed (DE) lncRNAs and 267 DE mRNAs were screened 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 showed that DE target mRNAs at the AN stage were mainly enriched in processes of material and energy metabolism and in protein glycosylation modification pathways. In the CA stage, DE target mRNAs were primarily enriched in immune-related GO terms and signaling pathways, including immune response, cytokine activity, cytokine–cytokine receptor interaction, IL-17 signaling pathway, and NF-kappa B signaling pathway. The Wnt signaling-related GO terms and pathways were enriched in the TE phase, which is closely associated with the maintenance of hair follicle quiescence and follicle cycle transition. Furthermore, ceRNA network analysis identified several key regulatory axes corresponding to different developmental stages, including the lncRNAs-chi-miR-671-5p-ADIPOQ, XR_001918825.1-chi-miR-128-5p-RFX2, and TCONS_00062482-chi-miR-874-3p-PGLYRP1. Conclusions: These findings advance our understanding of hair follicle biology and provide potential molecular targets for improving cashmere production through genetic selection.