Using Embryos to Dissect Molecular Gene Expression Heterosis in Beef Cattle

The impacts of heterosis through the utilization of crossbreeding are easily observed across traits in beef cattle. However, our understanding of how heterosis functions at a molecular level remains limited, especially in livestock. Crossbreeding is one of the most underutilized tools in U.S. beef cattle production, with only 50% of operations taking advantage of the added performance provided by heterosis (USDA APHIS, 2009). Understanding the functional biology that underlies heterosis at the molecular level could enable the industry to better predict and harness the benefits of hybrid vigor in breeding programs. We use gene expression phenotypes to understand how heterosis is modulated between genetic variation and animal-level phenotypes. To quantify gene expression heterosis (i.e., differential expression of genes in F1 animals compared with purebreds of the same origin), we measure gene expression heterosis in in vitro-derived embryos. This allowed us to largely regulate environmental conditions and observe the effects of heterosis at a critical point in early development. We produced over 400 embryos via in vitro fertilization using abattoir-derived oocytes from Angus and Brahman cull cows and Angus and Brahman sires in a diallel-like cross. We generated transcriptomes via RNA-Sequencing on each individual embryo. We identified 526 genes that were differentially expressed between F1 and purebred individuals. We identify multiple types of non-additive gene expression (e.g., overdominance, underdominance, global underdominance, parent-biased expression, etc.) that are likely responsible for these heterosis-related differences. Gene set enrichment analyses suggest that many of these genes that are non-additively expressed in F1s are involved in mitotic cell division. Knowledge of misexpressed genes and the networks in which they operate can aid in dissecting the molecular basis of heterosis in cattle while allowing us to understand transcriptional dynamics at an early point in mammalian development.