Rumen Bacteria and Serum Metabolites Predictive of Feed Efficiency Phenotypes in Beef Cattle.
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ABSTRACT:
SUBMITTER: Clemmons BA
PROVIDER: S-EPMC6917770 | biostudies-literature | 2019 Dec
REPOSITORIES: biostudies-literature
Publications
Rumen Bacteria and Serum Metabolites Predictive of Feed Efficiency Phenotypes in Beef Cattle.
Clemmons Brooke A BA Martino Cameron C Powers Joshua B JB Campagna Shawn R SR Voy Brynn H BH Donohoe Dallas R DR Gaffney James J Embree Mallory M MM Myer Phillip R PR
Scientific reports 20191217 1
The rumen microbiome is critical to nutrient utilization and feed efficiency in cattle. Consequently, the objective of this study was to identify microbial and biochemical factors in Angus steers affecting divergences in feed efficiency using 16S amplicon sequencing and untargeted metabolomics. Based on calculated average residual feed intake (RFI), steers were divided into high- and low-RFI groups. Features were ranked in relation to RFI through supervised machine learning on microbial and meta ...[more]
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Project description:BackgroundThis study was conducted to: (1) identify new SNPs for residual feed intake (RFI) and performance traits within candidate genes identified in a genome wide association study (GWAS); (2) estimate the proportion of variation in RFI explained by the detected SNPs; (3) estimate the effects of detected SNPs on carcass traits to avoid undesirable correlated effects on these economically important traits when selecting for feed efficiency; and (4) map the genes to biological mechanisms and pathways. A total number of 339 SNPs corresponding to 180 genes were tested for association with phenotypes using a single locus regression (SLRM) and genotypic model on 726 and 990 crossbred animals for feed efficiency and carcass traits, respectively.ResultsStrong evidence of associations for RFI were located on chromosomes 8, 15, 16, 18, 19, 21, and 28. The strongest association with RFI (P = 0.0017) was found with a newly discovered SNP located on BTA 8 within the ELP3 gene. SNPs rs41820824 and rs41821600 on BTA 16 within the gene HMCN1 were strongly associated with RFI (P = 0.0064 and P = 0.0033, respectively). A SNP located on BTA 18 within the ZNF423 gene provided strong evidence for association with RFI (P = 0.0028). Genomic estimated breeding values (GEBV) from 98 significant SNPs were moderately correlated (0.47) to the estimated breeding values (EBVs) from a mixed animal model. The significant (P < 0.05) SNPs (98) explained 26% of the genetic variance for RFI. In silico functional analysis for the genes suggested 35 and 39 biological processes and pathways, respectively for feed efficiency traits.ConclusionsThis study identified several positional and functional candidate genes involved in important biological mechanisms associated with feed efficiency and performance. Significant SNPs should be validated in other populations to establish their potential utilization in genetic improvement programs.
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