Omics & gene networks

Gene co-expression network analysis of liver transcriptomic data of cattle fed contrasting diets and interaction with production traits

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Abstract

Provision of feed accounts for a large proportion of the variable cost in beef production and consequently is a major determinant of overall profitability. Thus, understanding the molecular basis of feed efficiency in beef cattle is essential for improving productivity and sustainability of beef production systems. The liver plays a central role in energy metabolism and nutrient processing, making it a key target for molecular evaluations related to feed efficiency and energy intake. The objective of this study was to investigate the interaction of genes, through gene co-expression network analysis, of liver transcriptomic data derived from Charolais steers fed three contrasting diets offered during different stages of development: (i) high-concentrate during the growing phase; (ii) zero-grazed grass during the growing phase and; (iii) high-concentrate during the finishing phase. From approximately 10 months of age, 90 steers were individually offered each of the diets for 70 days, following a dietary adaptation period before each dietary phase. Upon completion of each dietary phase, residual feed intake (RFI) phenotype was determined for all steers and liver tissue biopsies collected from animals most divergent for RFI phenotype (high-RFI (feed-inefficient, n=12); low-RFI (feed-efficient, n=12)). RNA-sequencing was undertaken on liver samples and a network-based systems biology analysis performed using PCIT incorporating the gene expression data well as the phenotypes of RFI, dry matter intake (DMI) and average daily gain (ADG) as network nodes. A total of 257 hepatic genes were connected (P0.8) to the phenotypes examined across the three dietary phases; however, no single gene was commonly connected to all contrasts. For the two high-concentrate diets, the majority of genes were connected to the DMI phenotype. For the grass diet, the RFI phenotype displayed the largest number of gene connections. The ADG phenotype had the fewest number of gene connections across all three diets. Despite the lack of commonality for gene-phenotype interactions across the three diets, genes connected to the various phenotypes examined showed commonality in function. For example, genes with functions related to transcriptional processes, including EBF1 and RASL11A were significantly connected to DMI, ADG and RFI phenotypes across the three diets. Moreover, genes with functions in lipid and cholesterol metabolism (CERS5, CYP26B1, OSBPL6) as well as adipose differentiation (CREBL2) were associated with the RFI and DMI phenotypes across the dietary phases. Results from this study highlight the importance of transcriptional regulation and lipid metabolism not only to the RFI phenotype but also for DMI and ADG across contrasting diets at various stages of development. Acknowledgement: this work was funded by the Irish Department of Agriculture, Food and the Marine (RSF13/S/519) and the European Union's Horizon 2020, Marie Skłodowska-Curie and Teagasc co-fund (Research Leaders 2025; 754380).

Keywords: 2026

How to Cite:

Keogh, K., Kenny, D., McGee, M. & Reverter, A., (2026) “Gene co-expression network analysis of liver transcriptomic data of cattle fed contrasting diets and interaction with production traits”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2283831. doi: https://doi.org/10.31274/wcgalp.23518

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