Objective
The expression patterns of development-related genes during bovine embryo development are highly regulated processes influenced by genetic and environmental factors. This study provides novel insights into these patterns, offering an enhanced insight into embryonic development and identifying promising candidates to improve reproductive technologies in bovine breeding.
Materials and methods
We examined gene expression profiles from bovine embryos (GEO accession: GSE18290) using GEO2R to detect genes showing differential expression across critical phases of development: oocyte to 2-cell, 4-cell to 16-cell, and morula to blastocyst. Following this, gene ontology (GO) and KEGG pathway enrichment analyses were conducted to reveal key biological processes linked to the discovered DEGs. Moreover, a protein-protein interaction (PPI) network was built to explore connections among central genes, together with identifying relevant microRNAs (miRNAs) and transcription factors.
Results
The analysis identified differential expression of 2,244 genes (1,026 upregulated, 1,218 downregulated) during the transition from oocyte to 2-cell, 2,379 genes (1,146 upregulated, 1,233 downregulated) across the progression from 4-cell to 16-cell, and 1,544 genes (821 upregulated, 723 downregulated) through the shift from morula to blastocyst periods. GO and KEGG analyses highlighted enriched biological processes such as mRNA catabolism, nonsense-mediated decay, mast cell activation, protein phosphorylation, nerve growth factor signaling, regulation of angiogenesis, MAPK and Rap1 signaling pathways, and protein processing in the endoplasmic reticulum. Key hub genes (HSPA1A, PPARGC1A, AKT2, EGR1, HSDL2) were pinpointed, along with related miRNAs (bta-miR-103a-3p, bta-miR-769-5p) and transcription factors (HSF1, FOXA2, FOXO1, CREB).
Conclusions
Our analysis revealed stage-specific gene expression changes and highlighted key biological pathways and regulatory networks involved in bovine embryonic development. Central hub genes, miRNAs, and transcription factors were identified as potential biomarkers and targets. These findings offer valuable molecular insights that can be applied to improve reproductive technologies and fertility in cattle breeding.
