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

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...

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Autores principales:	Basharat Bhat, Mifftha Yaseen, Ashutosh Singh, Syed Mudasir Ahmad, Nazir A. Ganai
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c45d5461951c4b97b820967dc6da0f05
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spelling	oai:doaj.org-article:c45d5461951c4b97b820967dc6da0f052021-12-02T15:23:47ZIdentification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis10.1038/s41598-021-81471-62045-2322https://doaj.org/article/c45d5461951c4b97b820967dc6da0f052021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-81471-6https://doaj.org/toc/2045-2322Abstract 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.Basharat BhatMifftha YaseenAshutosh SinghSyed Mudasir AhmadNazir A. GanaiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Basharat Bhat Mifftha Yaseen Ashutosh Singh Syed Mudasir Ahmad Nazir A. Ganai Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis
description	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.
format	article
author	Basharat Bhat Mifftha Yaseen Ashutosh Singh Syed Mudasir Ahmad Nazir A. Ganai
author_facet	Basharat Bhat Mifftha Yaseen Ashutosh Singh Syed Mudasir Ahmad Nazir A. Ganai
author_sort	Basharat Bhat
title	Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis
title_short	Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis
title_full	Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis
title_fullStr	Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis
title_full_unstemmed	Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis
title_sort	identification of potential key genes and pathways associated with the pashmina fiber initiation using rna-seq and integrated bioinformatics analysis
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/c45d5461951c4b97b820967dc6da0f05
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Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis

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