Exploring Differentially Expressed Genes by RNA-Seq in Cashmere Goat (Capra hircus) Skin during Hair Follicle Development and Cycling

Abstract

Cashmere goat (Capra hircus) hair follicle development and cycling can be divided into three stages: anagen, catagen and telogen. To elucidate the genes involved in hair follicle development and cycling in cashmere goats, transcriptome profiling of skin was carried out by analysing samples from three hair follicle developmental stages using RNA-Seq. The RNA-Seq analysis generated 8487344, 8142514 and 7345335 clean reads in anagen, catagen and telogen stages, respectively, which provided abundant data for further analysis. A total of 1332 differentially expressed genes (DEGs) were identified, providing evidence that the development of hair follicles among the three distinct stages changed considerably. A total of 683 genes with significant differential expression were detected between anagen and catagen, 530 DEGs were identified between anagen and telogen, and 119 DEGs were identified between catagen and telogen. A large number of DEGs were predominantly related to cellular process, cell & cell part, binding, biological regulation and metabolic process among the different stages of hair follicle development. In addition, the Wnt, Shh, TGF-β and Notch signaling pathways may be involved in hair follicle development and the identified DEGs may play important roles in these signaling pathways. These results will expand our understanding of the complex molecular mechanisms of hair follicle development and cycling in cashmere goats and provide a foundation for future studies.

Expression profiles of differentially expressed genes affecting fecundity in goat ovarian tissues

“…Although other studies have provided reference genomes of cattle and other close relatives of the domestic goat (Geng et al, 2013), these are of limited value to goat breeders due to species differences. However, the recently available goat genome sequence (published online 23 December 2012) has enabled the current analysis to be performed directly in the goat (Dong et al, 2013).…”

De novo assembly and characterization of skin transcriptome using RNAseq in sheep (Ovis aries)

“…Most of our current and rapidly growing knowledge on the genes controlling skin and fiber development is provided by studies on the hair follicles of mice and humans (Botchkarev and Paus, 2003;Schmidt-Ullrich and Paus, 2005;Bostjancic and Glavac, 2008;Wang et al, 2012). Currently, the development of new-generation sequencing and RNA sequencing (RNASeq) provides new approaches that may elucidate the molecular regulation mechanism of hair follicle development (Jager et al, 2011;Okano et al, 2012;Geng et al, 2013). New-generation sequence technologies have opened the door to genome-scale experiments in organisms that lack comprehensive genome or transcriptome information, thus making it possible to assemble novel transcripts and identify differential regulation in a single experiment (Birzele et al, 2010;Sun et al, 2010;Abyzov et al, 2012).…”

The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats

“…Next generation sequencing has also been applied to characterize the transcriptome of goats [103,130] as well as to generate large collections of SNPs mapping to transcripts [131]. Cashmere fine hair fiber, mainly produced in India and Mongolia, is derived from the hair secondary follicles that form part of the undercoat of Cashmere goats.…”

“…Amongst the differentially expressed genes, there were two keratin genes, 10 keratin-associated protein genes, fibroblast growth factor 21, asparagine synthetase, phosphoserine aminotransferase, and desmoglein 1. In another study, Geng et al [130] compared skin mRNA expression at different hair follicle developmental stages (i.e., anagen, catagen, and telogen), thus identifying hundreds of differentially expressed genes. There has also been a sudden burst of studies analysing the expression profiles of miRNAs in the mammary gland [132][133][134][135], testis [136], and skin and hair follicles [137].…”