The maternal blood transcriptome reflects bovine fetal traits and can be harnessed to predict fetal sex during the first trimester

Abstract Despite cattle having superficial placentation, the maternal blood transcriptome may reflect fetal characteristics. The aims were to investigate the effects of fetal breed and sex on the maternal blood transcriptome at day 63 of gestation and to identify maternal blood biomarkers predictive of fetal sex across gestation. Blood samples from 20 recipients carrying beef or dairy breed fetuses derived from in vitro-produced embryos were subjected to RNA sequencing. Differential expression analysis revealed 1,095 and 741 differentially expressed genes (DEG; FDR <0.1) associated with fetal breed and sex, respectively. Additionally, maternal blood datasets comprising beef fetuses from gestational days 55 and 105 were integrated to investigate temporal changes in maternal blood gene expression across gestation in response to fetal sex. Co-expression analysis of genes associated with fetal sex identified three temporal expression clusters enriched for metabolic pathways and platelet activation. Candidate biomarkers (n = 43) were identified from the overlap between day 63 sex-associated DEG and two of the three temporal expression clusters. Biomarkers were trained using the day 63 beef dataset and tested for fetal sex prediction using the data from different gestational ages. The resulting biomarkers achieved accuracies of 0.90, 0.75, and 0.90 in the day-55, day-63 dairy, and day-105 datasets, respectively, and an accuracy of 1.00 in an additional dataset comprising beef fetuses at gestational day 42. In conclusion, both fetal sex and breed influence the recipient blood transcriptome, and the identified biomarkers can predict fetal sex during the first trimester. A maternal blood-based tool for early assessment of fetal characteristics could enhance reproductive management.