GWAS & Selection signatures

Leveraging Embryos to Uncover the Molecular Basis of Heterosis in Beef Cattle

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Abstract

The additional performance of crossbred individuals resulting from heterosis is widely exploited across plant and animal breeding programs. Despite its clear impacts, it remains underutilized in the beef industry, where less than 50% of commercial operations implement structured crossbreeding programs. Further, our understanding of how heterosis functions at the molecular level remains limited. Understanding the molecular intermediaries that drive organism-level heterosis could help breeding programs optimize crosses that maximize heterosis. We used a model system of in vitro-derived blastocysts from a diallel-like cross between Angus (Bos taurus) and Brahman (Bos indicus) animals to study heterosis of gene expression phenotypes. We performed total RNA-Sequencing on 412 total embryos (purebred Angus, purebred Brahman, and reciprocal F1s). While there were no significant differences between stage or quality of purebred and F1 embryos, we observed extensive patterns of non-additive differential gene expression. We identified 137 differentially expressed genes (FDR-adjusted p-value 1.5) between purebred and F1 groups. Despite the relatively low number of differentially expressed genes, the first eigenvector explaining the breed spectrum accounted for 31% of the total variation after the batch effect for embryo sex was removed. A model that tested the best-fitting inheritance pattern for each gene identified non-additive patterns as the best fit for over 18% of the genes. Of these non-additively expressed genes, 42% appeared over- or underdominant (exceeding both parents). We found that underdominance in gene expression was more common than other patterns. In the 9,102 genes differentially expressed between purebred Brahman and Angus embryos, average normalized expression in F1 individuals tended to be lower in the crossbred offspring. Genes with greater fold changes between breeds tended to exhibit greater underdominance in F1 embryos. Biological processes and pathways related to cell cycle control and developmental checkpoints were significantly overrepresented in non-additively expressed gene sets, suggesting that widespread differences may exist between crossbred and purebred embryos at very early stages of development. Further, we observed widespread parent-of-origin biased expression in embryos, which sheds light on the directionality that may be important for maximizing heterosis in crosses. Ongoing work is imputing intergenic variation into transcriptomes for use in additive and non-additive expression QTL mapping. Taken together, this work demonstrates that widespread differences exist between purebred and crossbred individuals early in development, which may have notable effects on the long-term expression of heterosis.

Keywords: 2026

How to Cite:

Rowan, T., Franklin, G., Henniger, M., Mohamed, R., Seay, T., Edwards, J., Payton, R. & Beever, J., (2026) “Leveraging Embryos to Uncover the Molecular Basis of Heterosis in Beef Cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286461. doi: https://doi.org/10.31274/wcgalp.24017

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