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

Abstract

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.

Keywords: Coat Color; Goat; Hair Follicle; Whole Transcriptome; ceRNA.

Figure 1

Skin phenotype indicators of two types of goats. (A) The phenotypic differences in animal individual, skin surface, skin histolgical section between DBG and IMCG. (B) The hair follicle and fiber perimeter of DBG and IMCG. The data are expressed as mean values±standard deviations, and ** significant differences (p<0.01) as determined by t-test. DBG, Dazu black goat; IMCG, Inner Mongolia cashmere goat.

Figure 2

Distribution of total RNA and differential RNA. (A) Correlation analysis matrix diagram. (B) Boxplot of all RNA expression levels. (C) Proportion distribution of total RNA. (D) Differential RNA distribution. (E) Circos diagram of chromosome distribution of DERNAs.

Figure 3

Functional analysis of DEmRNA in skin tissue of DBG and IMCG. (A) Dynamic circular heat map of DEmRNAs in skin tissue of DBG and IMCG. (B) PPI network analysis of the DEmRNAs. (C) Top20 terms of GO enrichment analysis. The number of differentially expressed genes at the end of the bar representation. (D) Top20 pathways of KEGG enrichment analysis. DBG, Dazu black goat; IMCG, Inner Mongolia cashmere goat; PPI, protein-protein interaction; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 4

Expression profles of lncRNAs in the skin of DBG and IMCG. (A) Heat map of DElncRNAs. (B) Top20 pathways of KEGG enrichment analysis. (C) GO enrichment analysis of lncRNAs. (D) The KOG analysis of target genes of lncRNA. (E) The COG analysis of target genes of lncRNA. DBG, Dazu black goat; IMCG, Inner Mongolia cashmere goat; KEGG, Kyoto Encyclopedia of Genes and Genomes; GO, Gene Ontology; KOG, eukaryotic orthologous group; COGs, clusters of orthologous groups.

Figure 5

Functional analysis of DEmiRNAs between skin tissues of Dazu black goat and Inner Mongolia cashmere goat. (A) Heat map of 72 DEmiRNAs; red represents up-regulated and blue represents down-regulated. (B) KEGG_Pathway network diagram of target gene of DEmiRNAs. (C) GO terms of target genes of DEmiRNAs. (D) Sankey diagram of DEmiRNAs and target gene. KEGG, Kyoto Encyclopedia of Genes and Genomes; GO, Gene Ontology.

Figure 6

Functional analysis of DEcircRNAs in skin tissue of Dazu black goat and Inner Mongolia cashmere goat. (A) Heat map of 177 DEcircRNAs; red represents up-regulated and green represents down-regulated. (B) Volcano plot of DEcircRNA. (C)The most enriched GO terms of host genes of circRNAs in DBG and MCG. (D) KEGG pathways of the host genes. GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 7

The co-expression network of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA. (A) LncRNA miRNA mRNA co expression network. Brown, light purple, pink represent lncRNA, miRNA, and mRNA, respectively. (B) circRNA-miRNA-mRNA co-expression network. Green, pink and brown represent circRNA, miRNA, and mRNA, respectively.

Figure 8

DEmRNAs, DElncRNAs, DEmiRNAs, and DEcircRNAs verified by RT-qPCR in skin of DBG and IMCG RNA-seq results. (A) Expression levels of mRNA by RNA-seq and RT-qPCR, (B) expression levels of lncRNA by RNA-seq and RT-qPCR, (C) expression levels of miRNA by RNA-seq and RT-qPCR, (D) expression levels of circRNA by RNA-seq and RT-qPCR. * p<0.05, ** p<0.01. qPCR, quantitative polymerase chain reaction; DBG, Dazu black goat; IMCG, Inner Mongolia cashmere goat; RT-qPCR, reverse transcription quantitative polymerase chain reaction.