Transcriptome meta-analysis reveals the hair genetic rules in six animal breeds and genes associated with wool fineness

Abstract

Wool plays an irreplaceable role in the lives of livestock and the textile industry. The variety of hair quality and shape leads to the diversity of its functions and applications, and the finer wool has a higher economic value. In this study, 10 coarse and 10 fine ordos fine wool sheep skin samples were collected for RNA-seq, and coarse and fine skin/hair follicle RNA-seq datasets of other five animal breeds were obtained from NCBI. Weighted gene co-expression network analysis showed that the common genes were clustered into eight modules. Similar gene expression patterns in sheep and rabbits with the same wool types, different gene expression patterns in animal species with different hair types, and brown modules were significantly correlated with species and breeds. GO and KEGG enrichment analyses showed that, most genes in the brown module associated with hair follicle development. Hence, gene expression patterns in skin tissues may determine hair morphology in animal. The analysis of differentially expressed genes revealed that 32 highly expressed candidate genes associated with the wool fineness of Ordos fine wool sheep. Among them, KAZALD1 (grey module), MYOC (brown module), C1QTNF6 (brown module), FOS (tan module), ITGAM, MX2, MX1, and IFI6 genes have been reported to be involved in the regulation of the hair follicle cycle or hair loss. Additionally, 12 genes, including KAZALD1, MYOC, C1QTNF6, and FOS, are differentially expressed across various animal breeds and species. The above results suggest that different sheep breeds share a similar molecular regulatory basis of wool fineness. Finally, the study provides a theoretical reference for molecular breeding of sheep breeds as well as for the investigation of the origin and evolution of animal hair.

Keywords: Ordos fine wool sheep; WGCNA; meta-analysis; six livestock breeds; wool fineness.

FIGURE 1

Analysis of gene expression patterns in 54 RNA-seq data of six breeds of livestocks. (A) PCA analysis of gene expression in 54 RNA-seq data of six breeds of livestocks; (B) Clustering dendrogram of samples based on their Euclidean distance; (C) Clustering dendrogram of genes, with dissimilarity based on topological overlap, together with assignedmerged module colors and the original module colors; (D) Module-trait associations. Each row corresponds to a module eigengene, column to a trait. Each cellcontains the corresponding correlation and p-value. The table is color-coded by correlation according to the colorlegend; (E) Visualization of the eigengene network representing the relationships among the modules and the clinical trait weight. Panel shows a hierarchical clustering dendrogram of the eigengenes in which the dissimilarity of eigengenes EI, EJ is given by 1-cor (EI, EJ). The heatmap in panel shows the eigengene adjacency AIJ = [1 + cor (EI, EJ)]/2.

FIGURE 2

Results of the analysis of DEGs in the six varieties. (A) Volcano plot of DEGs in Ordos fine wool sheep (C) vs. Ordos fine wool sheep (F); (B) Venn diagram of Ordos fine wool sheep (C) vs. Ordos fine wool sheep (F), Hetian sheep (C) vs. Hetian sheep (F), and Merino sheep (C) vs. Merino sheep (F); (C) Bubble chart of functional enrichment analysis of downregulated expressed genes in the Ordos fine wool sheep (C) vs. Ordos fine wool sheep (F) group; (D) Venn diagram of Ordos fine wool sheep, Tibetan northwest white cashmere goat, Angora rabbit, and mallard; (E) Bubble chart of functional enrichment analysis of upregulated genes expressed in the Ordos fine wool sheep (C) vs. Ordos fine wool sheep (F) group.

FIGURE 3

Expression patterns of DEGs, KRTs and KRTAPs and protein interaction network analysis of differential genes. (A) Protein interaction network analysis of differential genes in the Ordos fine wool sheep (C) vs. Ordos fine wool sheep (F) group; (B) |log₂ fold change| values of 32 candidate DEGs in different comparison groups; (C) Expression patterns of 32 DEGs in different breeds; (D) Expression patterns of KRTs and KRTAPs in six breeds.

FIGURE 4

The expression level of candidate genes was detected by RT-qPCR.