Gene set enrichment analysis for feed efficiency in beef cattle

Selection for improved feed efficiency in cattle would decrease the amount of feed consumed for the same or greater levels of production resulting in enhanced profitability and sustainability. Selection for feed efficient cattle has been hampered by a lack of phenotypic data on feed intake and weights from cattle in production due to the cost and difficulty in collecting these data. The aim of this study was to better understand the molecular functions and biological processes associated with residual feed intake (RFI) by identifying gene sets (biological pathways) associated with RFI in Hereford cattle and to use this information to facilitate genomic selection for RFI. Feed intake and body weight were measured on 847 Herefords at Olsen Ranches in Harrisburg, NE. Animals were genotyped with the Illumina BovineSNP50 or BovineHD Bead Chips. Genome-wide association analysis was conducted with GRAMMAR mixed model software as part of the gene set enrichment analysis (GSEA). Single nucleotide polymorphisms were mapped to 19,723 genes based on the UMD 3.1 reference genome assembly based on coordinates within 8.5 kb either side of each gene. Gene sets (4,389) were compiled from Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, Biocarta and Panther for the GSEA. Gene sets associated (Normalized Enrichment Score > 3.0) with RFI after 10,000 permutations in GenABEL were centrosome (5) (GO:0005813), cytoskeleton organization (4) and peroxisome (KEGG:04146). Most (191) of the identified genes enriched within the gene set for RFI (leading edge genes) were unique to a single gene set although 15 leading edge genes were shared between centrosome (5) and cytoskeleton organization (4) and one gene was shared between cytoskeleton organization and peroxisome gene sets. Further GSEA are being conducted with Angus, Angus x Simmental and crossbred beef cattle to validate these results.