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

Abo-Ismail, Mohammed K., Vander Voort, Gordon, Squires, James J., Swanson, Kendall C., Mandell, Ira B., Liao, Xiaoping, Stothard, Paul, Moore, Stephen, Plastow, Graham and Miller, Stephen P. (2014) Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle. BMC Genetics, 15 14.1-14.14. doi:10.1186/1471-2156-15-14

Author Abo-Ismail, Mohammed K.
Vander Voort, Gordon
Squires, James J.
Swanson, Kendall C.
Mandell, Ira B.
Liao, Xiaoping
Stothard, Paul
Moore, Stephen
Plastow, Graham
Miller, Stephen P.
Title Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle
Journal name BMC Genetics   Check publisher's open access policy
ISSN 1471-2156
Publication date 2014-01-30
Year available 2014
Sub-type Article (original research)
DOI 10.1186/1471-2156-15-14
Open Access Status DOI
Volume 15
Start page 14.1
End page 14.14
Total pages 14
Place of publication London, United Kingdom
Publisher BioMed Central Ltd.
Language eng
Subject 1311 Genetics
2716 Genetics (clinical)
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.
Keyword Candidate genes
Carcass traits
Feed efficiency
Single nucleotide polymorphism
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2015 Collection
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Citation counts: TR Web of Science Citation Count  Cited 9 times in Thomson Reuters Web of Science Article | Citations
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