Integration of single-cell transcriptome of female early gonadal development in bovine, goats, and pigs

The molecular programs governing early female gonadal development in livestock remain incompletely characterized. Here, we generated a single-cell transcriptomic atlas of bovine fetal ovaries spanning sex determination to early folliculogenesis and performed an integrated cross-species comparison with goats and pigs. We identified major germline and somatic cell populations and reconstructed germ cell differentiation trajectories, revealing conserved stages of pluripotency, retinoic acid (RA) response, and meiotic initiation, alongside species-specific developmental dynamics. Notably, goats exhibited delayed meiotic progression compared with bovine and pigs. Transcription factor analysis uncovered both conserved and bovine-specific regulators in granulosa cells. Cell-cell communication analysis further highlighted prominent RA-responsive MDK/PTN-NCL signaling and increased network interactions during meiotic entry in bovine and porcine but absent in pre-meiotic goat gonads. These findings provide a cross-species framework for early ovarian development in livestock and offer novel insights into mammalian gametogenesis and reproduction.