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Open Access Highly Accessed Research article

Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle

Mohammed K Abo-Ismail12, Gordon Vander Voort1, James J Squires1, Kendall C Swanson13, Ira B Mandell1, Xiaoping Liao4, Paul Stothard4, Stephen Moore5, Graham Plastow4 and Stephen P Miller1456*

Author Affiliations

1 Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario N1G 2W0, Canada

2 Department of Animal and Poultry Science, Damanhour University, Damanhour, Egypt

3 Animal Sciences Department, North Dakota State University, Fargo, ND, USA

4 Livestock Gentec, University of Alberta, Edmonton, AB, Canada

5 Queensland Alliance Agr & Food Innovation, University of Queensland, St Lucia, Qld 4072, Australia

6 Animal and Poultry Science Department, Ontario Agriculture College, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada

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BMC Genetics 2014, 15:14  doi:10.1186/1471-2156-15-14

Published: 30 January 2014

Abstract

Background

This 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.

Results

Strong 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.

Conclusions

This 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.

Keywords:
Candidate genes; Single nucleotide polymorphism; Feed efficiency; Carcass traits