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/.
Highlights
The genetics of coat color variation remains a classic area
We investigated the differentially expressed transcripts, the relationship between lncRNAs with their target mRNA and explored pathways and biological processes that might have caused the variation in the Pashmina coat color
We obtained a total of 60.20 Gb RNA-seq data, all sequence data were at 2 × 100 bp length (43,868,700 to 59,356,541 PE reads per sample)
Summary
The genetics of coat color variation remains a classic area. Earlier studies have focused on a limited number of genes involved in color determination; the complete set of trait determinants are still not well known. 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. Understanding the gene networks and metabolic pathways controlling the coat color should help in devising effective breeding strategies for high quality and quantity of precious animal fiber like Pashmina. We investigated the differentially expressed transcripts (mRNA and lncRNA), the relationship between lncRNAs with their target mRNA (in cis and trans configuration) and explored pathways and biological processes that might have caused the variation in the Pashmina coat color. The results provided several candidate genes and lncRNAs that might play an important role in the Pashmina coat color and pigmentation. Some of the highly differentially expressed genes (DEGs) were validated by qPCR
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