# Comparative Skin Transcriptomics Reveals Key Regulators of Cashmere Fiber Production in Inner Mongolian Goats

## TL;DR

Researchers compared gene activity in the skin of cashmere and normal goats to identify genes and pathways involved in producing high-quality cashmere fibers.

## Contribution

The study identifies key genes and pathways, including Wnt, MAPK, and PI3K–Akt, and highlights alternative splicing as a major regulatory mechanism in cashmere fiber formation.

## Key findings

- 1543 differentially expressed genes were found, linked to hair follicle development and extracellular matrix organization.
- Wnt, MAPK, and PI3K–Akt signaling pathways were significantly enriched in cashmere goats.
- Alternative splicing, especially exon skipping, was a common regulatory mechanism in goat skin.

## Abstract

Cashmere fiber is a valuable natural textile produced by specialized secondary hair follicles in cashmere goats. Improving fiber yield and quality requires a better understanding of the biological mechanisms that distinguish cashmere producing goats from normal goats. In this study, we compared the skin transcriptomes of Inner Mongolian cashmere goats and normal goats using RNA sequencing to identify genes and pathways associated with fleece type. We detected 1543 differentially expressed genes enriched in processes related to hair follicle development, epidermal differentiation, and extracellular matrix organization. Key signaling pathways, including Wnt, MAPK, and PI3K–Akt, were significantly involved, highlighting their importance in regulating secondary hair follicle activity. We also found that alternative splicing, particularly exon skipping, is a common regulatory mechanism in goat skin. These findings improve our understanding of the molecular basis of cashmere fiber formation and provide candidate genes for future functional research and breeding programs aimed at enhancing economically important fleece traits in cashmere goats.

Cashmere goats produce high-value fine fibers derived from secondary hair follicles; however, the molecular mechanisms underlying this trait remain incompletely understood. In this study, comparative transcriptome sequencing was performed on skin tissues from Inner Mongolian cashmere goats and normal goats to characterize gene expression differences associated with cashmere fiber production. High-quality RNA-seq data with strong mapping efficiency and reproducibility were obtained across all samples. Differential expression analysis identified 1543 significantly differentially expressed genes (DEGs) between cashmere and normal goats, including genes involved in hair follicle morphogenesis, epidermal differentiation, cell proliferation, and extracellular matrix organization. Multivariate analyses showed a clear transcriptomic separation between fleece types, indicating that fleece phenotype is the primary driver of variation in global gene expression. Functional enrichment revealed significant involvement of the Wnt, MAPK, and PI3K–Akt signaling pathways, and several biologically relevant regulators of hair follicle development and hair cycle control, including FGF5, SOX9, LHX2, and VDR, were differentially expressed. Gene fusion events were rare and showed no group specific patterns, whereas alternative splicing was widespread, with exon skipping as the predominant splicing event in goat skin. Overall, these results provide quantitative transcriptomic evidence linking signaling regulation, follicle development, and structural differentiation to secondary hair follicle activity and cashmere fiber formation, offering candidate genes and molecular pathways for functional validation and molecular breeding in cashmere goats.