Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis

Basharat Bhat,Ashutosh Singh,Nazir A Ganai,Mifftha Yaseen,Syed Mudasir Ahmad

doi:10.1038/s41598-021-81471-6

Abstract

Pashmina goat (Capra hircus) is an economically important livestock species, which habitats the cold arid desert of the Ladakh region (India), and produces a princely animal fiber called Pashmina. The Pashmina goat has a double coat fleece as an adaptation to the very harsh cold winters the outer long coarse hair (guard hair) produced from primary hair follicles and the inner fine Pashmina fiber produced from secondary hair follicles. Pashmina fiber undergoes a circannual and synchronized growth cycle. In the present study, we analyzed transcriptome profiles from 10 different Pashmina goats during anagen and telogen to delineate genes and signaling pathways regulating active (anagen) and regressive (telogen) phases of the follicle growth. During anagen, 150 genes were expressed at significantly higher levels with log (FC) > 2 and padj < 0.05. The RNA seq results were subjected to qRT-PCR validation. Among the nine genes selected, the expression of HAS1, TRIB2, P2RX1. PRG4, CNR2, and MMP25 were significantly higher (p < 0.05) in the anagen phase, whereas MC4R, GIPC2, and CDO1 were significantly expressed (p < 0.05) in the telogen phase which supports and validates the gene expression pattern from the RNA-sequencing. Differentially expressed genes revealed that Pashmina fiber initiation is largely controlled by signaling pathways like Wnt, NF-Kappa, JAK-STAT, Hippo, MAPK, Calcium, and PI3K-Akt. Expression of genes from the Integrin family, Cell adhesion molecules, and ECM-receptors were observed to be at much higher levels during anagen. We identified key genes (IL36RN, IGF2, ITGAV, ITGA5, ITCCR7, CXCL5, C3, CCL19, and CXCR3) and a collagen cluster which might be tightly correlated with anagen-induction. The regulatory network suggests the potential role of RUNX3, NR2F1/2, and GATA family transcription factors in anagen-initiation and maintaining fiber quality in Pashmina goats.

Highlights

Pashmina goat (Capra hircus) is an economically important livestock species, which habitats the cold arid desert of the Ladakh region (India), and produces a princely animal fiber called Pashmina
Understanding the genetic basis of fibre production phenotypes could contribute to the improvement of the fibre production efficiency in Pashmina goats and help in identifying molecular determinants involved in anagen initiation
Skin samples containing secondary hair follicles (SHF) were collected during anagen and telogen to identify key regulators and pathways associated with the telogen–anagen (TA) transition

Summary

Introduction

Pashmina goat (Capra hircus) is an economically important livestock species, which habitats the cold arid desert of the Ladakh region (India), and produces a princely animal fiber called Pashmina. Pashmina goat (Capra hircus) is an economically important animal genetic resource adapted to very harsh cold arid agro-climatic conditions of Ladakh region (Jammu and Kashmir—India). The mercury level of this landlocked high-altitude habitat (5500–6000 m above mean sea level) of Pashmina goat fluctuates between + 35 °C (short summers) and – 40 °C (long winters) Under these stressful conditions (cold, arid, hypoxic and scanty vegetation), Pashmina goats remain active with different adaptation strategies. This goat produces the world’s finest (11–14 μ) natural fibre (Pashmina fiber) which is used in the making of world-famous Pashmina/Cashmere shawls. Asynchronous hair growth, the difference in skin anatomy and physiology restricts the identification of key molecular determinants mediating fiber transition

Methods

Results

Conclusion