Transcriptome Analysis of Individual Ovine Oocytes and Preimplantation Embryos From In Vitro Fertilization Source

In this study, we examine the transcriptional profiles of eight stages of preimplantation embryo development, from germinal vesicle (GV) oocytes to blastocysts, in in vitro fertilized sheep embryos using RNA sequencing. Between 12,744 and 15,539 genes were detected from the GV moving forward to blastocyst, with cluster analysis revealing two distinct clusters related to developmental stage. The largest change for differentially expressed genes (DEGs) numbers took place between 2- to 4-cell comparison and 4- to 8-cell comparison, with a c. 35-fold increase from 19 to 670 DEGs. This suggests that zygotic genome activation occurred at 8-cell stage in sheep. All the DEGs had gene ontology annotations in three classes, and these comprised 53 subclasses. Most of the pathways (89 of 93) were enriched through KEGG analysis of the DEGs, and the most enriched pathway was oxidative phosphorylation. The 2- and 16-cell stage embryos possessed the highest and lowest numbers, respectively, of single nucleotide polymorphisms and insertion-deletion markers. Five major types of alternative splicing were found. A total of 2361 transcription factor genes were mutually expressed among the eight developmental stages. The top five differential transcription factor protein families were Zf-C2H2, bHLH, Homeobox, Others, and HMG. This is the first study to investigate the transcriptional profiling of sheep preimplantation embryos at different developmental stages, and it displays a comprehensive transcriptome landscape in sheep oocytes and embryos.