Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat

Abstract The genetics of coat color variation remains a classic area. Earlier studies have focused on a limited number of genes involved in color determination; however, the complete set of trait determinants are still not well known. In this study, we used high-throughput sequencing technology to i...

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Autores principales:	Basharat Bhat, Ashutosh Singh, Zaffar Iqbal, Jai K. Kaushik, A. R. Rao, Syed Mudasir Ahmad, Hina Bhat, Aadil Ayaz, F. D. Sheikh, Shalini Kalra, Syed Shanaz, Masood Salim Mir, Pawan Kumar Agarwal, Trilochan Mohapatra, Nazir A. Ganai
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fe616a12c1cc4bb59628c38f51deddff
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spelling	oai:doaj.org-article:fe616a12c1cc4bb59628c38f51deddff2021-12-02T15:08:59ZComparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat10.1038/s41598-019-42676-y2045-2322https://doaj.org/article/fe616a12c1cc4bb59628c38f51deddff2019-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-42676-yhttps://doaj.org/toc/2045-2322Abstract The genetics of coat color variation remains a classic area. Earlier studies have focused on a limited number of genes involved in color determination; however, the complete set of trait determinants are still not well known. In this study, we used high-throughput sequencing technology to identify and characterize intricate interactions between genes that cause complex coat color variation in Changthangi Pashmina goats, producer of finest and costly commercial animal fiber. We systematically identified differentially expressed mRNAs and lncRNAs from black, brown and white Pashmina goat skin samples by using RNA-sequencing technique. A pairwise comparison of black, white and brown skin samples yielded 2479 significantly dysregulated genes (2422 mRNA and 57 lncRNAs). Differentially expressed genes were enriched in melanin biosynthesis, melanocyte differentiation, developmental pigmentation, melanosome transport activities GO terms. Our analysis suggested the potential role of lncRNAs on color coding mRNAs in cis and trans configuration. We have also developed online data repository as a component of the study to provide a central location for data access, visualization and interpretation accessible through http://pcd.skuastk.org/.Basharat BhatAshutosh SinghZaffar IqbalJai K. KaushikA. R. RaoSyed Mudasir AhmadHina BhatAadil AyazF. D. SheikhShalini KalraSyed ShanazMasood Salim MirPawan Kumar AgarwalTrilochan MohapatraNazir A. GanaiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-9 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Basharat Bhat Ashutosh Singh Zaffar Iqbal Jai K. Kaushik A. R. Rao Syed Mudasir Ahmad Hina Bhat Aadil Ayaz F. D. Sheikh Shalini Kalra Syed Shanaz Masood Salim Mir Pawan Kumar Agarwal Trilochan Mohapatra Nazir A. Ganai Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat
description	Abstract The genetics of coat color variation remains a classic area. Earlier studies have focused on a limited number of genes involved in color determination; however, the complete set of trait determinants are still not well known. In this study, we used high-throughput sequencing technology to identify and characterize intricate interactions between genes that cause complex coat color variation in Changthangi Pashmina goats, producer of finest and costly commercial animal fiber. We systematically identified differentially expressed mRNAs and lncRNAs from black, brown and white Pashmina goat skin samples by using RNA-sequencing technique. A pairwise comparison of black, white and brown skin samples yielded 2479 significantly dysregulated genes (2422 mRNA and 57 lncRNAs). Differentially expressed genes were enriched in melanin biosynthesis, melanocyte differentiation, developmental pigmentation, melanosome transport activities GO terms. Our analysis suggested the potential role of lncRNAs on color coding mRNAs in cis and trans configuration. We have also developed online data repository as a component of the study to provide a central location for data access, visualization and interpretation accessible through http://pcd.skuastk.org/.
format	article
author	Basharat Bhat Ashutosh Singh Zaffar Iqbal Jai K. Kaushik A. R. Rao Syed Mudasir Ahmad Hina Bhat Aadil Ayaz F. D. Sheikh Shalini Kalra Syed Shanaz Masood Salim Mir Pawan Kumar Agarwal Trilochan Mohapatra Nazir A. Ganai
author_facet	Basharat Bhat Ashutosh Singh Zaffar Iqbal Jai K. Kaushik A. R. Rao Syed Mudasir Ahmad Hina Bhat Aadil Ayaz F. D. Sheikh Shalini Kalra Syed Shanaz Masood Salim Mir Pawan Kumar Agarwal Trilochan Mohapatra Nazir A. Ganai
author_sort	Basharat Bhat
title	Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat
title_short	Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat
title_full	Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat
title_fullStr	Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat
title_full_unstemmed	Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat
title_sort	comparative transcriptome analysis reveals the genetic basis of coat color variation in pashmina goat
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/fe616a12c1cc4bb59628c38f51deddff
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Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat

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