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Across-breeds systems biology analysis reveals key genes contributing to feed efficiency in beef cattle
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Abstract
Provision of feed in beef production systems is a major determinant of overall profitability as it
typically accounts for over 75% of the variable cost. Thus, improving cattle feed efficiency by way
of determining the underlying molecular control and subsequently selecting for feed efficient cattle
through genomic selection provides a method through which feed costs may be reduced. The
objective of this study was to undertake gene co-expression network analysis on RNAseq data
generated from Longissimus dorsi tissue samples collected from steers divergent for residual feed
intake (RFI) within two contrasting breed types (Charolais and Holstein-Friesian). Several gene
categories, including differentially expressed genes (DEG) based on the contrasts of both breed and
RFI phenotype as well as key transcription factors and proteins secreted in plasma were utilised as
nodes of the gene co-expression networks. Significant network connections were identified using an
algorithm that exploits the dual concepts of partial correlation and information theory (PCIT).
Results revealed 530 and 531 DEG for the RFI and breed contrasts, respectively. PCIT network
analysis resulted in the formation of one RFI specific cluster which included genes related to
metabolic processes and cell cycle. A second cluster which included genes related to both RFI and
breed was enriched for immune-related pathways such as coagulation system and the complement
cascade. This latter network was of particular interest due to the potential identification of genes
contributing to RFI that are sufficiently robust across breed type. Moreover, genes included within
this network also encode proteins secreted in plasma, highlighting the potential use of these genes
as blood-based biomarkers for RFI in beef cattle.