Understanding the biological processes and gene network pathways and their relationship with the host microbiota that directly affect complex fertility traits and embryo survival in beef cattle.

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Embryo survival is one of the major factors affecting fertility and economic efficiency in cattle production systems. In cattle, most embryonic loss occurs before day 16 after breeding with some evidence of greater losses before day 8. Late embryonic loss, while numerically smaller than early embryonic mortality, nevertheless causes serious economic losses to producers because it is often too late to rebreed females when they repeat estrous.*** Despite decades of research on embryo survival, little is known about the genes determining the traits and their precise function. Therefore, a more complete understanding of the genes, regulatory pathways and networks involved in economically important traits in cattle will provide the knowledge to improve fertility by genetic selection and reproductive management. Recent studies on cattle fertility have examined the expression of several genes in the uterus related to conception rate. Also, genomic tools such as genotyping using the Bovine High-Density Chip (Illumina) have been incorporated into the genetic evaluations identifying several associations between specific genotypes and traits related to fertility and pregnancy in cattle. However, minimum genetic progress to reduce cattle embryo loss has been made. Previously, researchers studied the uterus microbiota using cell culture techniques reporting that the uterus is a sterile environment, overlooking the limitation of the technique which only is capable of culturing some specific bacteria. Interestingly, metagenomics or the study of the bacteria profile using high-throughput level has not been yet been used to examine effects of the microbiota on early embryonic loss. *** This program of research is designed to provide further insight into the underlying fundamentals of cattle embryo survival and the establishment of pregnancy by comparing “Pregnant” and “Non Pregnant” cows. This research is expected to lead to the identification of key regulator genes (and functional SNP) as well as causal networks and metabolic pathways affecting embryo survival. The state-of-the-art approach will be to integrate structural and functional genomic data from new high-throughput OMICS technologies (i.e., transcriptomics (RNA-Seq), metabolomics (GC-MS, NMR) and metagenomics (16S (bacterial, archaeal) and 18S (protozoa, fungal) sequencing of microbe populations), keeping in mind that these methods will no doubt evolve over time as we attempt to integrate the various biological processes associated with embryo survival. This knowledge could be incorporated into breeding programs to increase the rate of genetic progress to improve embryo survival. This work will also contribute to training of highly qualified students and personnel, and has implications for other livestock species and humans.