Systems Genomics Approaches to Identify Regulatory Genes and Potential Biomarkers in Donor Cows for In Vitro Embryo Production

The combination of Genomic Selection (GS) with Ovum Pick Up–In vitro Production (OPU-IVP) of embryos is foreseen to have a huge impact in cattle production. IVP procedures still need refinements. Our objectives were to identify candidate genes in donor cows for favorable IVP-related traits as well as to provide a better understanding of the gene regulatory mechanisms involved in the IVP process.

We sequenced the RNA content of granulosa cells collected from 24 Holstein cows at oocyte aspiration. Oocytes were in vitro matured, inseminated and cultured until the blastocyst (BL) stage. Throughout the process, cumulus-oocyte complexes (COCs) and their descendants were kept as separate pools from each individual donor cow. COCs from each cow were inseminated with semen from one bull, either having extremely high or low Nordic Total Merit (NTM) index.

We identified 56 genes associated with IVP scores (BL rate, kinetic and morphology). Among these, seven (two positively and five negatively associated) were common for all the traits. Weighted co-expression network analysis identified four modules of co-expressed genes associated with IVP scores. Nodes with high module membership were selected as additional candidate genes. Functional analysis highlighted mechanisms controlling apoptosis and cell development. Our study suggests that pools of subordinate follicles in early atresia are associated with improved IVP outcomes. Furthermore, we showed that high NTM index bulls can be used in GS-IVP without reducing the IVP performances. These findings can contribute to biomarker development and improve GS methods that utilize functional information in cattle breeding.