Whole-transcriptome RNA sequencing reveals global expression dynamics and ceRNA regulatory networks related to hair follicle development and melanogenesis in goats.

Objective: Domestic animals, fur is a product of long-term selection by humans and the natural environment. It is generally used to distinguish between different breeds. This study aims to dissect the molecular mechanisms underlying the distinct fur characteristics of goats, particularly focusing on the molecular and regulatory differences between the Dazu Black Goat (DBG) and the Inner Mongolia Cashmere Goat (IMCG). Through whole-transcriptome analysis, we aim to identify differentially expressed RNAs and construct a ceRNA network to reveal the genetic regulation of goat hair follicle development and melanin production.

Methods: Skin, hair, and cashmere samples were collected from DBG (n = 15) and IMCG (n = 17) to assess hair follicle density, length, diameter, and melanin content. Whole-transcriptome sequencing of skin tissues from DBG (n = 3) and IMCG (n = 3) identified 50,652 RNAs. Differential expression analysis was performed on mRNAs, lncRNAs, miRNAs, and circRNAs.

Results: IMCG exhibited significantly higher hair follicle density, hair length, and cashmere diameter than DBG (p < 0.01), whereas DBG had significantly thicker hair and higher melanin content (p < 0.01). A total of 640 differentially expressed RNAs were identified, including 157 mRNAs, 234 lncRNAs, 72 miRNAs, and 177 circRNAs. These were enriched in pathways related to melanogenesis, hair follicle development, and GO terms such as collagen fiber organization and pigmentation. ceRNA networks constructed from differentially expressed RNAs revealed key regulatory mechanisms of coat color and hair traits.

Conclusion: Whole-transcriptome sequencing revealed expression profiles and ceRNA networks involved in hair follicle development and melanogenesis in goats. These findings provide insights into the roles of coding and non-coding RNAs in fur traits, supporting future breeding strategies and textile applications.