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Identification and characterization of microRNAs in white and brown alpaca skin

Xue Tian1, Junbing Jiang1, Ruiwen Fan1, Haidong Wang1, Xiaolin Meng1, Xiaoyan He1, Junping He1, Hongquan Li1, Jianjun Geng1, Xiuju Yu1, Yunfei Song1, Danli Zhang1, Jianbo Yao12, George W Smith13 and Changsheng Dong1*

Author Affiliations

1 College of Animal Science and Technology, Shanxi Agricultural University, Taigu, 030801, People's Republic of China

2 Division of Animal and Nutritional Sciences, Laboratory of Animal Biotechnology and Genomics, West Virginia University, Morgantown, WV, 26506, USA

3 Laboratory of Mammalian Reproductive Biology and Genomics, Departments of Animal Science and Physiology, Michigan State University, East Lansing, MI, 48824, USA

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BMC Genomics 2012, 13:555  doi:10.1186/1471-2164-13-555

Published: 16 October 2012



MicroRNAs (miRNAs) are small, non-coding 21–25 nt RNA molecules that play an important role in regulating gene expression. Little is known about the expression profiles and functions of miRNAs in skin and their role in pigmentation. Alpacas have more than 22 natural coat colors, more than any other fiber producing species. To better understand the role of miRNAs in control of coat color we performed a comprehensive analysis of miRNA expression profiles in skin of white versus brown alpacas.


Two small RNA libraries from white alpaca (WA) and brown alpaca (BA) skin were sequenced with the aid of Illumina sequencing technology. 272 and 267 conserved miRNAs were obtained from the WA and BA skin libraries, respectively. Of these conserved miRNAs, 35 and 13 were more abundant in WA and BA skin, respectively. The targets of these miRNAs were predicted and grouped based on Gene Ontology and KEGG pathway analysis. Many predicted target genes for these miRNAs are involved in the melanogenesis pathway controlling pigmentation. In addition to the conserved miRNAs, we also obtained 22 potentially novel miRNAs from the WA and BA skin libraries.


This study represents the first comprehensive survey of miRNAs expressed in skin of animals of different coat colors by deep sequencing analysis. We discovered a collection of miRNAs that are differentially expressed in WA and BA skin. The results suggest important potential functions of miRNAs in coat color regulation.

Alpaca; MicroRNAs; Deep sequencing; Coat color; Skin