Skin transcriptome profiling of Changthangi goats highlights the relevance of genes involved in Pashmina production

Sonika Ahlawat,Upasna Sharma,Ashish Kumar,Karan Veer Singh,Reena Arora,Rekha Sharma,Ramesh Kumar Vijh,Mandeep Kaur,Manoj Kumar Singh

doi:10.1038/s41598-020-63023-6

Abstract

Pashmina, the world’s finest natural fiber is derived from secondary hair follicles of Changthangi goats which are domesticated in Ladakh region of Jammu and Kashmir by nomadic pastoralists. Complex epithelial-mesenchymal interactions involving numerous signal molecules and signaling pathways govern hair follicle morphogenesis and mitosis across different species. The present study involved transcriptome profiling of skin from fiber type Changthangi goats and meat type Barbari goats to unravel gene networks and metabolic pathways that might contribute to Pashmina development. In Changthangi goats, 525 genes were expressed at significantly higher levels and 54 at significantly lower levels with fold change >2 (padj < 0.05). Functional annotation and enrichment analysis identified significantly enriched pathways to be formation of the cornified envelope, keratinization and developmental biology. Expression of genes for keratins (KRTs) and keratin-associated proteins (KRTAPs) was observed to be much higher in Changthangi goats. A host of transcriptional regulator genes for hair follicle keratin synthesis such as GPRC5D, PADI3, HOXC13, FOXN1, LEF1 and ELF5 showed higher transcript abundance in Pashmina producing goats. Positive regulation of Wnt signaling pathway and negative regulation of Oncostatin M signaling pathway may be speculated to be important contributors to hair follicle development and hair shaft differentiation in Changthangi goats.

Highlights

Apart from genes for various keratin proteins, expression of genes for some keratin-associated proteins (KRTAPs) was observed to be much higher in Changthangi goats
We focused on the keratinization pathway since a substantial proportion of differentially expressed genes (DEGs) (43 genes) showed higher transcript abundance in Changthangi goats for this process (Table 2)
The top nodes are ranked by Maximal Clique Centrality (MCC) scores and the decrease in score is indicated by change in the color of the node from red to orange

Summary

Results

In order to quantify the gene expression patterns of goat skin samples, cDNA libraries were constructed from 4 animals each of Changthangi and Barbari breeds and these libraries were subjected to deep sequencing using Illumina HiSeq platform. Significant Gene Ontology terms for the genes with higher expression in Changthangi goats included cell differentiation, multicellular organism development, keratinocyte differentiation, hair follicle morphogenesis and establishment of skin barrier. Most of these genes were components of nucleus, cytoplasm, extracellular exosome, intermediate filament, keratin filament and cytoskeleton. The top nodes are ranked by Maximal Clique Centrality (MCC) scores and the decrease in score is indicated by change in the color of the node from red to orange Another noteworthy observation was that genes such as KRT25, KRT27, KRT17, SOSTDC1 and KRT71 that are involved in hair follicle morphogenesis and DSG4, HOXC13, FOXN1 and DNASE1L2 associated with hair follicle development showed higher transcript abundance in Changthangi goats. The expression profile of these genes obtained by qRT-PCR showed similar trend with the RNAseq results, thereby substantiating our transcriptome data (Fig. S1)

Discussion

40 KRT80 41 EVPL

Conclusion

Materials and methods