Comparative transcriptomic analysis reveals breed-specific developmental characters of skin and feather follicles between Anser Cygnoides and Anser Anser

Feather follicle development is essential for the phenotypic characteristics and economic value of domesticated geese. In this study, we conducted a comparative transcriptomic analysis to explore the breed-specific molecular mechanisms involved in feather follicle development in Zhedong white goose (Anser cygnoides) and Hungarian white goose (Anser anser) at five critical embryonic stages (E10, E13, E18, E23, and E28). A total of 19,622 differentially expressed genes (DEGs) were identified in geese feather follicles across the comparison groups, with significant enrichment in pathways associated with neuroactive ligand-receptor interaction, melanogenesis, tyrosine metabolism, metabolic pathways, PPAR, p53, VEGF, and Hedgehog signaling pathways. Thirty-six DEGs, such as SOX10, NEK3, PMEL, KRT1, TRPM1, CYP27B1, and EDNRB, were commonly discovered among the five comparison groups. These DEGs were mainly involved in metabolic pathways, neuroactive ligand-receptor interaction, calcium signaling pathway, melanogenesis, and lysosome. Moreover, the weighted gene co-expression network analysis (WGCNA) classified all co-expressed genes in feather follicles between the two goose breeds into 15 modules. Two critical modules were identified: the green module, associated with early-stage feather follicle development, and the yellow module, linked to later-stage feather follicle maturation. Genes in these modules were enriched in cell cycle, melanogenesis, ECM-receptor interaction, PPAR, MAPK, Wnt, FOXO, mTOR, Hedgehog, and calcium signaling pathways. Hub genes such as PCNA, SMAD3, LEF1, WNT2, WNT3, MAP4K1, FOXO3, FZD1, FZD4, CTNNB1, and FOXM1 were found to be key regulators in feather follicle formation. Our findings offer new perspectives on the genetic mechanisms driving breed-specific feather follicle development, which could inform breeding strategies to enhance feather quality in geese.