Sex-related changes in liver and muscle transcriptome of calves derived from artificial insemination or the transfer of an in vitro–produced embryo

The conditions imposed during in vitro embryo culture may cause modifications of the embryo epigenome and transcriptome, potentially affecting post-natal organ function. This study compared the liver and muscle transcriptome in 4-month-old male and female dairy calves conceived by artificial insemination (AI) or by the transfer of an in vitro-produced (IVP) embryo (n = 4 per sex per treatment). Biopsy tissue samples were collected and processed for RNA sequencing. Analysis of the RNAseq data revealed a distinct separation between the liver transcriptomes of female and male calves, regardless of method of production. Moreover, within the cohort of female calves, a strong separation between those derived from IVP vs AI was observed. Analysis of differentially expressed genes indicated downregulation of oxidative phosphorylation pathways and upregulation of immune system-related enriched terms, including Th17 cell differentiation and antigen processing and presentation. For the muscle transcriptome, the separation between male and female calves was less apparent compared with the liver transcriptome, but there was still a clear separation between female calves derived from IVP vs AI, with downregulated genes enriching for p53 signaling and upregulated genes enriching terms related to muscle structure development. These results suggest that female embryos derived from IVP vs AI exhibit developmental differences that manifest as differential transcriptomic profiles post-natally. In conclusion, these findings demonstrate that the IVP process induces significant alterations in the liver and muscle transcriptome of female post-natal calves. Further longitudinal studies are required to understand the potential implications for lifetime growth, health, and production characteristics.