Dissecting The Transcriptional Atlas And Molecular Characteristics Of Embryonic Hair Follicles Of Shanbei White Cashmere Goat At Single-cell Resolution

Shanbei White Cashmere goat is one of the most important Cashmere goat varieties in China.Its wool and cashmere have important economic value.The hair characteristics of adult cashmere goats are determined by the embryonic hair follicle development process,but the development process of hair follicle involves a variety of cell specialization and intercellular communication,which leads to little understanding of the embryonic hair follicle development process.Therefore,to reveal the cell heterogeneity and molecular regulation mechanism during the embryonic hair follicle development of cashmere goats can provide a clearer understanding the process of hair follicle morphogenesis,and it has important guiding significance for the breeding of cashmere goats.In order to analyze the growth and development process of embryonic hair follicles at the cellular level,this study uses single cell RNA sequencing(sc RNA-seq)technology to delineated single cell transcriptional atlas of hair follicles of Shanbei White Cashmere goat E120,and 10 main cell types were identified.We constructed pseudotime differentiation trajectory of the inner layer subpopulations and described the molecular characteristics underlying cell fate decisions.The main results were as follows:1.The single cell transcriptional atlas of hair follicles of Shanbei White Cashmere goat E120 was successfully constructed at single-cell resolution.Based on UMAP clustering analysis,cortex/cuticle(CX),transient amplifying cells(TAC),inner root sheath(IRS),medulla(ME),endothelial cells,outer root sheath(ORS),dermal papilla(DP),dermal sheath(DS),pericyte and immune cells were successfully identified.We also counted the number of cell types,showed the cell cycle phase of cell types,and analyzed the correlation between cell types.2.We clustered 7 subpopulations of the inner layer cells of cashmere goat hair follicles,described their gene expression profiles,and analyzed the correlation between cell subpopulations.Based on monocle analysis,we successfully constructed pseudotime differentiation trajectory of the inner layer subpopulations,and found three branches with different differentiation directions in the trajectory.The origin of all branches was TAC,and each branch had its unique intermediate state and terminal differentiation.We recapitulated the pseudotime gene expression dynamics during the origin,intermediate state,and endpoint of differentiation trajectory.We identified the core downregulated genes and uniquely upregulated genes in all three branches and analyzed their functional enrichment.We also identified keratin genes and transcription factors that were uniquely expressed in branches.We found that all branches not only had unique transcription factors(KCNIP3,GATA3,SMAD1),but also shared unique transcription factors(LEF1,NOTCH3)with CX branches,and three branches shared two transcription factors(HSPB1,HTATIP2).In conclusion,the main cell types of embryonic hair follicles were identified at the single-cell level,and we detailed gene changes during inner layer cell differentiation.Our results here also enriched people’s understanding on hair follicle morphogenesis in Cashmere goats and provide a strong theoretical support for the breeding researh of Shanbei White Cashmere goats.