A Nutrigenomic Perspective to Search for Gene Variants That Influence Carcass Traits of Feedlot Cattle

Abstract

Vitamin A (VA) has a nutrigenomic effect on intramuscular fat. Discovering variants in genes involved in fat deposition that are also affected by vitamin A could allow feedlots to precision feed to optimize carcass traits. A single nucleotide polymorphism (SNP) in alcohol dehydrogenase 1C (ADH1C) has previously shown promise for this approach but has yet to be effective at a commercial level; therefore we hypothesized a variant in another gene or its interaction with ADH1Cc.-64T>C might be the solution. Genes previously shown to be affected by retinoic acid, a metabolite of vitamin A: aminopeptidase (ANPEP), clusterin (CLU), adipose differentiation-related protein (ADFP), glutathione peroxidase (GPX3), secreted protein, acidic, cysteine-rich (SPARC), and insulin growth factor binding protein 6 (IGFBP6) were sequenced and screened for variants. The ANPEPc.410G>A SNP was selected for genotyping in a population of mixed breed steers (n=988). This population was fed vitamin A at 100% (100VA) or 50% (50VA the NRC recommended level (2200 IU/kg dry matter). No interaction was found with ADH1Cc.-64T>C however, ANPEPc.410G>A affected carcass yield (P<0.01; AA=2.47±0.03, GA=2.36±0.03, GG=2.14±0.08), marbling score (P<0.01; AA=397.2±2.7, GA=388.6±3.3, GG=370.4±7.2), and fat (P<0.01; AA=8.52±0.17 GA=7.58±0.21, GG=7.04±0.44; mm). Vitamin A also had an effect on backfat (P<0.05; 100VA= 8.13±0.24, 50VA = 7.35±0.25), and an interaction with ANPEPc.410c.G>A affected rib-eye area (P<0.05). The ANPEP SNP was genotyped in a second population of mixed breed steers (N=708) fed a standard feedlot ration with the NRC recommended level of vitamin A. There was an association with yield, marbling, fat, and rib-eye area (P<0.01). The AA genotype was more marbled, while GG animals were leaner with higher yields. Interestingly, ANPEPc.410G>A is the fourth variant in a haplotype containing twelve SNPs that are in linkage disequilibrium in exon 1 and intron 1. This was confirmed by sequencing cattle of various breeds from different populations. The three haplotypes could affect gene expression by altering transcription or translation efficiency. Investigation of the functional effects of these variants needs to be completed in order to understand how it alters traits related to feedlot cattle performance.