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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle
BMC Genetics, Volume 15, Article 14, Year 2014
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Description
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. © 2014 Abo-Ismail et al.; licensee BioMed Central Ltd.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3927660/bin/1471-2156-15-14-S1.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC3927660/bin/1471-2156-15-14-S2.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC3927660/bin/1471-2156-15-14-S3.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC3927660/bin/1471-2156-15-14-S4.xlsx
Authors & Co-Authors
Abo-Ismail, Mohammed K.
Canada, Guelph
Centre for the Genetic Improvement of Livestock
Egypt, Damanhour
Damanhour University
Vander Voort, Gordon
Canada, Guelph
Centre for the Genetic Improvement of Livestock
Squires, E. J.
Canada, Guelph
Centre for the Genetic Improvement of Livestock
Swanson, Kendall Carl
Canada, Guelph
Centre for the Genetic Improvement of Livestock
United States, Fargo
North Dakota State University
Mandell, I. B.
Canada, Guelph
Centre for the Genetic Improvement of Livestock
Liao, Xiaoping
Canada, Edmonton
University of Alberta
Stothard, Paul M.
Canada, Edmonton
University of Alberta
Moore, Stephen Stewart
Australia, Brisbane
The University of Queensland
Plastow, G. S.
Canada, Edmonton
University of Alberta
Miller, Stephen P.
Canada, Guelph
Centre for the Genetic Improvement of Livestock
Canada, Edmonton
University of Alberta
Australia, Brisbane
The University of Queensland
Canada, Guelph
Ontario Agricultural College
Statistics
Citations: 10
Authors: 10
Affiliations: 6
Identifiers
Doi:
10.1186/1471-2156-15-14
e-ISSN:
14712156
Research Areas
Genetics And Genomics