Integration Analysis of Transcriptome Sequencing and Whole-Genome Resequencing Reveal Wool Quality-Associated Key Genes in Zhexi Angora Rabbits

Abstract

Wool quality is a crucial economic trait in Angora rabbits, closely linked to hair follicle (HF) growth and development. Therefore, understanding the molecular mechanisms of key genes regulating HF growth and wool fiber formation is essential. In the study, fine- and coarse-wool groups were identified based on HF morphological characteristics of Zhexi Angora rabbits. According to the results, the diameters of fine and coarse fibers, and the percentage of coarse fibers, were significantly lower in the fine-wool group than in the coarse-wool group. Additionally, the HF density was higher in the fine-wool group than in the coarse-wool group, and the diameters of both primary hair follicles and second hair follicles were finer in this fine-wool group. Moreover, RNA sequencing (RNA-seq) and whole-genome resequencing (WGRS) were performed to identify key candidate genes and potential genetic variations between fine- and coarse-wool groups. RNA-seq analysis revealed 182 differentially expressed genes (DEGs), with 138 upregulated and 44 downregulated genes in the fine-wool group. The WGRS analysis identified numerous genetic variants including 15,705 InDels and 83,055 SNPs between the two groups. Additionally, the joint analysis of RNA-seq and WGRS showed enrichment of the Wnt, JAK-STAT, and TGF-β signaling pathways. The key overlapping candidate genes such as DKK4, FRZB, CSNK1A1, TLR2, STAT4, and BMP6 were identified as potential crucial regulators of wool growth. In summary, this study provides valuable theoretical insights into wool quality and offers the potential for improving the molecular breeding of Angora rabbits.

Keywords: Angora rabbit; RNA sequencing; whole-genome resequencing; wool quality.

Figure 1

Morphological analysis between fine- and coarse-wool groups on the dorsal skin in Zhexi Angora rabbits. (A) The fine fiber diameter, coarse fiber diameter, and percentage of coarse fibers were measured between the fine- and coarse-wool groups in Zhexi Angora rabbits. (B) Histology of transverse sections of dorsal skin between the fine- and coarse-wool groups. (C) HF-related parameter analysis between the fine- and coarse-wool groups. PHF: primary hair follicle, SHF: second hair follicle. ** p < 0.01.

Figure 2

Screening of DEGs between fine- and coarse-wool groups in Zhexi Angora rabbits through RNA-seq. (A) Upregulated and downregulated mRNAs between the fine- and coarse-wool groups are shown in the volcano plot. (B) Validation of mRNA relative expression of DEGs between the fine- and coarse-wool groups through RT-qPCR. (C) GO enrichment analysis of DEGs between the fine- and coarse-wool groups. (D) KEGG enrichment analysis of DEGs between the fine- and coarse-wool groups. (E) The gene network of the DEGs was constructed using the STRING database. ** p < 0.01.

Figure 3

GO enrichment and KEGG pathway analyses of InDels and SNP sites located within genes. (A) GO enrichment analysis of InDel sites located within genes in CC, MF, and BP. (B) KEGG pathway enrichment analysis of InDel sites located within genes. (C) GO enrichment analysis of SNP sites located within genes in CC, MF, and BP. (D) KEGG pathway enrichment analysis of SNP sites located within genes.