Single-Cell Omics in Animal Reproductive Biology: A Cellular and Molecular Atlas Across Developmental Stages

Abstract

The cutting-edge technologies of single-cell omics have revolutionized the study of animal reproduction, enabling the visualization of cellular and molecular domains in organisms during various growth stages. This review presents a conceptual framework grounded in the latest developments from single-cell RNA sequencing (scRNA-seq), ATAC sequencing (scATAC-seq), spatial transcriptomics, and multi-omics approaches applied to the reproductive organs of livestock and model species. Technologies survey molecular types of the cell, the course of transcription, chromatin accessibility, and regulatory networks for specific tissues in the development of gonads, gametogenesis, and embryo formation. In comparative analysis, both common and species-specific characteristics have been identified in models of cattle, pigs, goats, sheep, and avian species. This has made them a valuable resource for the development of trait-based breeding protocols. We discuss how single-cell data are being integrated with genomic selection frameworks to enhance fertility prediction and assisted reproduction strategies, leading to improvements in artificial insemination and reproductive disease modelling. The rapid evolution of protocols and tools has enabled the livestock science field to expand the use of these technologies, despite technical and computational challenges such as tissue dissociation bias, genome annotation gaps, and data complexity. The livestock science sector, therefore, is experiencing the broad adoption of single-cell differentials not just in the transformation of reproductive science but also in practical decision-making guidance for the new generation of animal breeding and fertility management.