Improving Cattle Feed Efficiency Through '-OMIC's technologies and Functional Genomics

Improved genetic selection for feed efficiency in beef and dairy cattle may improve the Canadian cattle production industry profitability and environmental sustainability. However, the application of RNA-Sequencing (RNA-Seq) analysis in livestock research is novel and the underlying biology and genetic architecture of feed efficiency in cattle is not well studied. The aim of this thesis was to characterize the functional genetic architecture underlying feed efficiency using transcriptomic and metagenomic tools, including RNA-Sequencing (RNA-Seq), and Amplicon-Sequencing (Amplicon-Seq) technologies, to identify functional genetic markers (SNPs and INDELs), novel transcripts, metabolic processes, and potential host-microbiome genetic interactions that are playing a role in the regulation of feed efficiency in cattle. First, an optimized RNA-Seq pipeline for genetic variant detection was developed, and applied to a Nellore beef cattle population to determine functional genetic variants (SNPs and INDELs) associated with feed efficiency. The optimized RNA-Seq pipeline was then applied to a Holstein and Jersey population to identify functional variants and associated functional information (candidate genes, biological pathways, overlapping QTLs) related with feed efficiency. Then de novo assembly was performed to identify novel mRNA isoforms associated with feed efficiency, using rumen epithelium tissue transcriptome data from two pure (Angus and Charolais) and one composite (Kinsella) beef breed. Using the transcriptomic data from the latter study, and Amplicon-sequencing (Amplicon-Seq) data of rumen contents from the same animals, correlations were determined between the host transcriptome and rumen microbiome (archaea and bacteria profiles) which were different between extreme RFI groups. These studies lead to accurate detection of functional genetic variants and associated functional information which may influence the regulation of feed efficiency. Additionally, potential host-microbiome genetic interactions that may be influencing the regulation of feed efficiency were identified. In conclusion, this thesis provides valuable information on the underlying genetic architecture of feed efficiency in both beef and dairy cattle, which may serve to help select genetic markers to improve the selection for superior feed efficient beef and dairy cattle, leading to improved of the efficiency and profitability of the beef and dairy industry, and may serve as important information for future genomic research on feed efficiency.