Skin transcriptome profiles associated with coat color in sheep

Ruiwen Fan,George W Smith,Jianbo Yao,Wenjun Gao,Xue Tian,Lei Yang,Yunfei Song,Haidong Wang,Xiaoyun Jia,Jianshan Xie,Changsheng Dong,Rui Bai,Muren Herrid,Xiaoyan He,Junming Bai

doi:10.1186/1471-2164-14-389

Abstract

BackgroundPrevious molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins. To identify additional genes that may play important roles in coat color regulation, Illumina sequencing technology was used to catalog global gene expression profiles in skin of sheep with white versus black coat color.ResultsThere were 90,006 and 74,533 unigenes assembled from the reads obtained from white and black sheep skin, respectively. Genes encoding for the ribosomal proteins and keratin associated proteins were most highly expressed. A total of 2,235 known genes were differentially expressed in black versus white sheep skin, with 479 genes up-regulated and 1,756 genes down-regulated. A total of 845 novel genes were differentially expressed in black versus white sheep skin, consisting of 107 genes which were up-regulated (including 2 highly expressed genes exclusively expressed in black sheep skin) and 738 genes that were down-regulated. There was also a total of 49 known coat color genes expressed in sheep skin, from which 13 genes showed higher expression in black sheep skin. Many of these up-regulated genes, such as DCT, MATP, TYR and TYRP1, are members of the components of melanosomes and their precursor ontology category.ConclusionThe white and black sheep skin transcriptome profiles obtained provide a valuable resource for future research to understand the network of gene expression controlling skin physiology and melanogenesis in sheep.

Highlights

Previous molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins
To investigate genes that may play important roles in coat color regulation in sheep skin and gain insight into molecular mechanisms responsible for biochemistry of skin and fibers in animals producing hair such as sheep and alpaca, we investigated the transcriptome profiles in skin of sheep with black versus white coat color using high throughput RNA deep sequencing
Of unigenes After the raw reads were filtered, 51,297,002 clean reads with 52.2% GC percentage and 51,655,390 clean reads with 53.7% GC percentage were obtained from white and black sheep skin, respectively. These clean reads were assembled into unigenes, yielding 90,006 and 74,533 unigenes from white and black sheep skin, respectively

Summary

Introduction

Previous molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins. Sheep are the most important fiber producing animals worldwide. Length and color are key traits contributing to the economic value of sheep and are determined by both genetics [1,2] and environment [3]. Factors that determine coat color in sheep are becoming of increasing interest. Coat color is determined associated with differences in coat color phenotype are not well understood. This information is critical to enhanced basic understanding of regulation of melanogenesis, and to the identification of novel pharmacological and molecular genetics approaches to regulate or select for coat color in fiber producing species

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