This is a draft schedule. Presentation dates, times and locations may be subject to change.
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The Role of Diet Composition Fed during Residual Feed Intake Determinations and the Impact of the Diet on the Gene Sets Associated with Efficiency As Determined By a Gene Set Enrichment Analysis
The Role of Diet Composition Fed during Residual Feed Intake Determinations and the Impact of the Diet on the Gene Sets Associated with Efficiency As Determined By a Gene Set Enrichment Analysis
Tuesday, July 11, 2017
Exhibit Hall (Baltimore Convention Center)
To examine the potential role of diet fed during the residual feed intake (RFI) measurement period on the leading edge genes (LEG) associated with feed efficiency, a gene set enrichment analysis using SNP (GSEA-SNP) was completed using data from 887 Simmental-cross steers. The steers were fed a range of diets during their RFI measurement period with NDF content ranging from 14.40 to 44.73%. To determine if this NDF range had an impact on the enrichment of gene sets, steers were separated into two groups, one with a diet >40% NDF (n=611) and one with NDF content <40% (n=276). Significant SNPs (p<0.05) within the average haplotype block length for the population (8.5 kb) that were associated with RFI by genome-wide association analysis for RFI were used as a proxy for each of 19,723 annotated genes from the UMD3.1 genome assembly. Gene sets from five databases were used for the GSEA-SNP: Panther (n=165), Kyoto Encyclopedia of Genes and Genomes (KEGG; n=186), Biocarta (n=217), Reactome (n=674), and Gene Ontology (GO; n=3,147). The null distribution for testing the normalized enrichment score was estimated with GenABEL (R package) and 10,000 permutations. Enriched gene sets (NES>3.0) and their LEG associated with RFI were identified. Mean DMI and RFI for the steers fed a diet with >40% NDF was 10.67 kg±1.36 and -0.39 ± 0.05 and 10.08 kg ±1.30 and 0.44 ±0.07 for the <40% NDF. Enriched gene sets for steers fed <40% NDF were GO Behavior (GO:0007610) with 128 LEG and GO Ras Protein Signal Transduction (GO:0007265) with 136 LEG. Four LEG genes were common across the Behavior (GO:0007610) and Ras Protein Signal Transduction (GO:0007265) pathways indicating their importance to the RFI trait. Four gene sets were enriched for steers fed >40% NDF: KEGG Glycerophospholipid Metabolism (map00564) with 65 LEG, GO Ubiquitin Ligase Complex (GO:00001051) with 54 LEG, Reactome Synthesis of Phosphatidic Acid (R-HSA-1483166) with 25 LEG and the Panther Opioid Proopiomelanocortin pathway (P05917) with 18 LEG. The GSEA-SNP analysis based on dietary NDF level resulted in no common gene sets. Steers fed diets containing higher NDF levels had enriched gene sets for lipid metabolism and feed intake while those steers fed diets containing lower NDF levels were enriched for protein transduction and general behavior genes. The diet fed during the determination of RFI had an impact on the gene sets and LEG genes, suggesting differences in metabolic pathways associated with the trait.