Investigating RNA-Seq-based Differential Gene Expression during Hair Follicle Development in Angora Goat Skin

Mohair, an important source of fiber, is only obtained from Angora goats. The important characteristics that determine the economic value of mohair are fiber diameter and quantity. In countries where mohair is produced, efforts are made to improve these characteristics. It is stated that hair follicle characteristics and/or genetic regulation mechanisms that form animal fibers directly affect fiber production and quality. In this study, it was aimed to determine the genes affecting mohair development in two varieties of Angora goat and the molecular mechanisms affecting these genes. The biopsy samples were collected during three distinct phases of the hair growth cycle: anagen (active growth, September), catagen (transition, January), and telogen (resting, March). The specific timing and location of the biopsies suggest a potential influence of seasonality or a controlled experimental design. RNA was isolated from these biopsy samples, and differentially expressed genes and the pathways affected by these genes were evaluated using the RNA sequencing method. It has been observed that the expression of <italic>KRTAP8-1, KRTAP16.4,</italic> and <italic>KRTAP21-1</italic> genes was quite high in the group in which catagen and telogen phases were compared in Eskisehir variety females. Interestingly, the <italic>KRTAP21-1</italic> gene was found to be expressed in four different protein isoforms. Interestingly, the analysis revealed a cluster of keratin-associated protein genes (<italic>KRT40, KRT72, KRTAP10</italic>) solely differentially expressed in the male Eskisehir versus Lalahan comparison. This suggests potential sex-specific regulatory mechanisms involving keratinocyte differentiation during the catagen phase, which might be unique to the Eskisehir variety. In the Eskisehir variety, unlike the Lalahan variety, DEGs identified in the anagen-catagen comparison in males were significantly enriched in the Reactome mediated keratinization pathway, and these genes were down regulated. The results showed that <italic>KRT</italic> and <italic>KRTAP</italic> genes are highly functional and have different expression patterns between males and females, in addition to being different between the Eskisehir and Lalahan varieties. This study provides valuable insights into the genetic regulation of mohair development, potentially paving the way for targeted breeding strategies to improve mohair quality and production.