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Traditional Chinese herbal medicine Cistanche deserticola Y.C. Ma has been recorded and treatment for infertility and impotence since ancient times, which is widely distributed in northwest China, and is mainly composed of phenylethanol glycosides, iridoids, lignans, polysaccharides, alkaloids, etc. C. deserticola polysaccharides (CDPs) is one of its main active ingredients, studies of its effect on germline stem cells are limited so far. Aim of the study: The aim of this study was to clarify that CDPs promoted the differentiation of FGSCs in vitro , and to initially clarify its possible cell signaling pathways. The cells were randomly divided into two groups. Normal FGSCs culture medium and the optimal concentration of CDPs (0.5 μg/mL) were added for culture, which was the selected treatment concentration that could promote cell differentiation on the basis of maintaining cell viability. After treatment for different time periods (12 h, 24 h, 36 h, 48 h), the cell proliferation and differentiation were evaluated by CCK-8, real-time PCR (qPCR), cell immunofluorescence and Western blot. Subsequently, RNA-Seq and data analysis were used to preliminarily analyze and verify the different genes and possible signal pathways. Under the treatment of CDPs, cell viability was relatively better, and the expression of meiotic markers stimulated by retinoic acid gene 8 protein (Stra8) and synaptonemal complex protein 3 (Sycp3) significantly increased. In addition, their cell morphology was more similar to oocytes. Comparison of gene expression in FGSCs identified key differential expression genes (DEGs) by RNA-Seq that consisted of 549 upregulated and 465 downregulated genes. The DEGs enriched in the functional categories of germline cell development and relevant signaling pathways, which jointly regulate self-renewal and differentiation of FGSCs. The transforming growth factor β (TGF-β) signaling pathway and bone morphogenetic protein (BMP) signaling pathway might be activated to synergistically influence cell differentiation during the CDPs treatment of FGSCs. These findings indicated that CDPs could promote the differentiation of FGSCs in vitro and could be regulated by different DEGs and signal transduction. Preliminary mechanism studies have shown that CDPs can exert their biological activities by regulating the TGF-β and BMP signaling pathways. [ABSTRACT FROM AUTHOR]