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

• Published in: Scientific reports 2019-04, Vol.9 (1), p.6361-6361, Article 6361
• Main Authors: Bhat, Basharat, Singh, Ashutosh, Iqbal, Zaffar, Kaushik, Jai K., Rao, A. R., Ahmad, Syed Mudasir, Bhat, Hina, Ayaz, Aadil, Sheikh, F. D., Kalra, Shalini, Shanaz, Syed, Mir, Masood Salim, Agarwal, Pawan Kumar, Mohapatra, Trilochan, Ganai, Nazir A.
• Format: Article
• Language: English
• Subjects: 38/91; 631/114/129/2043; 631/1647/48; 631/61/514/1949; Animals; Biopsy; Biosynthesis; Biotechnology; Color; Coloration; Gene expression; Gene Expression Profiling; Gene Expression Regulation; Gene Ontology; Genetic analysis; Genetic diversity; Genetics; Genome; Genomes; Goats - genetics; Humanities and Social Sciences; Melanin; multidisciplinary; Next-generation sequencing; Pigmentation; Reproducibility of Results; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; Science; Science (multidisciplinary); Skin; Skin Pigmentation - genetics; Transcriptome - genetics; User-Computer Interface
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-019-42676-y

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/ .