Hair Follicle Transcriptome Analysis Reveals Differentially Expressed Genes That Regulate Wool Fiber Diameter in Angora Rabbits

Abstract

Wool fiber diameter (WFD) is an important index of wool traits and the main determinant of wool quality and value. However, the genetic determinants of fiber diameter have not yet been fully elucidated. Here, coarse and fine wool of Wan strain Angora rabbits and their hair follicle traits were characterized. The results indicated significant differences in the diameters of wool fibers and their hair follicles. The RNA sequencing (RNA-Seq) technique was used to identify differences in gene expression in hair follicles between coarse and fine wool. In total, 2574 differentially expressed genes (DEGs) were found between the two hair follicle groups. Transcription factors, keratin-associated protein (KAP) and keratin (KRT) families, and ECM-related genes may control the structure of fine fibers in rabbits. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that skin development, epidermal cell and keratinocyte differentiation, epithelium development, and Notch and ribosome signaling pathways were significantly enriched, respectively. GSEA further filtered six important pathways and related core genes. PPI analysis also mined functional DEGs associated with hair structure, including LEF1, FZD3, SMAD3, ITGB6, and BMP4. Our findings provide valuable information for researching the molecular mechanisms regulating wool fiber and could facilitate enhanced selection of super-fine wool rabbits through gene-assisted selection in the future.

Integration Analysis of Hair Follicle Transcriptome and Proteome Reveals the Mechanisms Regulating Wool Fiber Diameter in Angora Rabbits

“…The transcriptome data of the hair follicles of coarse and fine wool from our previous study were used for integrated analyses [ 13 ]. A total of 1228 genes were quantified at both the transcriptomic and proteomic levels ( Figure 5 A).…”

“…Correlation analysis of genes and proteins was performed using the R function core test. The transcriptome data from the hair follicles of coarse and fine wool were from our previous study [ 13 ].…”

“…( C ) Venn plot of up-regulated and down-regulated DEPs and differentially expressed genes (DEGs) detected at both the protein and transcript levels in comparison groups. The transcriptome data used in this analysis was taken from our previous study [ 13 ].…”

“…Down hairs are fine fibers with a diameter of 15 μm and arise from secondary hair follicles [ 4 , 9 , 11 , 12 ]. The diameters of coarse fibers and primary hair follicles significantly exceed those of fine fibers and secondary hair follicles [ 13 ]. Fiber diameter is not determined by embryonic hair follicle precursors, but rather by specific genes expressed during the formation of the follicle [ 14 ].…”

“…Fiber diameter is not determined by embryonic hair follicle precursors, but rather by specific genes expressed during the formation of the follicle [ 14 ]. In our previous study, we analyzed the fiber diameter of coarse and fine wool as well as the morphology and transcriptome of hair follicles from coarse and fine fibers in Angora rabbits [ 13 ]. The morphology of the secondary hair follicle plays a crucial role in determining wool quality [ 15 ].…”