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.

胚胎存活率是影响牛生产系统繁殖力和经济效益的主要因素之一。在牛身上，大多数胚胎损失发生在繁殖后第16天之前，一些证据表明在第8天之前损失更大。晚期胚胎损失虽然在数量上小于早期胚胎死亡，但会给生产者造成严重的经济损失，因为当雌性牛重复发情时，往往太晚了。*尽管对胚胎存活进行了数十年的研究，但人们对决定特征及其确切功能的基因知之甚少。因此，更全面地了解牛的重要经济性状所涉及的基因、调控途径和网络，将为通过遗传选择和繁殖管理提高繁殖力提供知识。最近关于牛生育能力的研究已经检测了几个与受孕率有关的基因在子宫中的表达。此外，使用牛高密度芯片(Illumina)进行基因分型等基因组工具已被纳入遗传评估，以确定特定基因类型与牛的生育和怀孕相关性状之间的几个关联。然而，在减少牛胚胎损失方面取得了最小的遗传进展。此前，研究人员使用细胞培养技术研究子宫微生物区系，报告称子宫是一个无菌环境，忽略了只能培养某些特定细菌的技术的局限性。有趣的是，元基因组学或使用高通量水平对细菌图谱的研究尚未被用于检查微生物区系对早期胚胎丧失的影响。*这项研究旨在通过比较“怀孕”和“非怀孕”奶牛，进一步深入了解牛胚胎存活和怀孕的基本原理。这项研究有望导致识别关键调节基因(和功能SNP)以及影响胚胎存活的因果网络和代谢途径。最先进的方法将是整合来自新的高通量OMICS技术(即转录组学(RNA-Seq)、代谢组学(GC-MS、核磁共振)和元基因组学(微生物种群的16S(细菌、古生菌)和18S(原生动物、真菌)测序)的结构和功能基因组数据，记住，随着我们试图整合与胚胎存活相关的各种生物过程，这些方法无疑将随着时间的推移而演变。这些知识可以被纳入育种计划，以提高遗传进步的速度，以提高胚胎存活率。这项工作还将有助于培训高素质的学生和人员，并对其他牲畜物种和人类产生影响。

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.