Integrated analysis of lncRNAs and mRNAs by RNA-Seq in secondary hair follicle development and cycling (anagen, catagen and telogen) of Jiangnan cashmere goat (Capra hircus)

Abstract

Background Among the world’s finest natural fiber composites is derived from the secondary hair follicles (SHFs) of cashmere goats yield one of the world's best natural fibres. Their development and cycling are characterized by photoperiodism with diverse, well-orchestrated stimulatory and inhibitory signals. Long non-coding RNA (lncRNAs) and mRNAs play important roles in hair follicle (HF) development. However, not many studies have explored their specific functions in cashmere development and cycling. This study detected mRNAs and lncRNAs with their candidate genes and related pathways in SHF development and cycling of cashmere goat. We utilized RNA sequencing (RNA-Seq) and bioinformatics analysis on lncRNA and mRNA expressions in goat hair follicles to discover candidate genes and metabolic pathways that could affect development and cycling (anagen, catagen, and telogen). Results We identified 228 differentially expressed (DE) mRNAs and 256 DE lncRNA. For mRNAs, catagen and anagen had 16 upregulated and 35 downregulated DEGs, catagen and telogen had 18 upregulated and 9 downregulated DEGs and telogen and anagen had 52 upregulated and 98 downregulated DEGs. LncRNA witnessed 22 upregulated and 39 downregulated DEGs for catagen and anagen, 36 upregulated and 29 downregulated DEGs for catagen and telogen as well as 66 upregulated and 97 downregulated DEGs for telogen and anagen. Several key genes, including MSTRG.5451.2, MSTRG.45465.3, MSTRG.11609.2, CHST1, SH3BP4, CDKN1A, GAREM1, GSK-3β, DEFB103A KRTAP9–2, YAP1, S100A7A, FA2H, LOC102190037, LOC102179090, LOC102173866, KRT2, KRT39, FAM167A, FAT4 and EGFL6 were shown to be potentially important in hair follicle development and cycling. They were related to, WNT/β-catenin, mTORC1, ERK/MAPK, Hedgehog, TGFβ, NFkB/p38MAPK, caspase-1, and interleukin (IL)-1a signaling pathways. Conclusion This work adds to existing understanding of the regulation of HF development and cycling in cashmere goats via lncRNAs and mRNAs. It also serves as theoretical foundation for future SHF research in cashmere goats.

Convergent Genomic Signatures of Cashmere Traits: Evidence for Natural and Artificial Selection

“…Most of these goats live in cold northern regions of China, and their cashmere has undergone intense artificial selection for protection from the cold and as a textile material. Cashmere is produced from the secondary hair follicle of cashmere goat [ 45 ], which is finer, softer and lighter, and it is considered a luxury textile fiber [ 46 ]. The morphological structure and development of secondary hair follicles directly affect the output and quality of cashmere.…”

Effect of Fasted Live-Weight Gain during the Cashmere Non-Growing Period on Cashmere Production Performance and Secondary Hair Follicle Activity of Cashmere Goats

“…Cashmere fiber is characterized by cyclical and seasonal growth, and does not grow during the period from the fall of the cashmere (late April and early May) to the regrowth of the body surface (late July and early August). Therefore, the growth cycle of cashmere fiber is divided into a non-growing period (from late spring to late summer) and a growing period (from early autumn to late winter) [2,3]. At present, it has been confirmed that nutrient levels during the cashmere growing period had a significant effect on cashmere production performance; however, the effect of nutrient levels during the cashmere nongrowing period on cashmere production performance remains unknown.…”

“…Cashmere fiber is characterized by cyclical and seasonal growth, which begins to appear and grow on the body surface in summer, continues to grow in autumn to early winter, stops growing in winter, and naturally sheds from the body surface in spring [1]. Therefore, the growth cycle of cashmere fiber is divided into a non-growing period (from late spring to late summer) and a growing period (from late summer to winter) [2,3]. Cashmere yield is determined by length, diameter, and number of cashmere fibers [4,5].…”

LncRNAs regulate the cyclic growth and development of hair follicles in Dorper sheep

“…To study hair follicle cyclic growth and development, the majority of the researchers have used different developmental stages of the same population. For example, Wu et al selected three 2-year-old female Jiangnan Cashmere goats as experimental animals to screen the candidate lncRNAs, mRNAs, and related pathways affecting the three developmental stages of secondary hair follicles by RNA-seq ( 45 ). Similarly, Wang et al selected five 1-year-old female Capra hircus in their comprehensive analysis of genes encoding and non-coding RNAs of the hair follicle cycle, of which three were used to construct and analyze the lncRNA library and two for constructing miRNA library ( 46 ).…”