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Related Concept Videos

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization
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Genome-wide association analysis for feed efficiency in Angus cattle.

M M Rolf1, J F Taylor, R D Schnabel

  • 1Division of Animal Sciences, University of Missouri, Columbia, 65211, USA. mmr5x7@mail.missouri.edu

Animal Genetics
|April 14, 2012
PubMed
Summary

Genomic analysis identified significant single nucleotide polymorphisms (SNPs) associated with feed efficiency traits in Angus steers. These SNPs explain substantial genetic variation and highlight metabolic gene functions, aiding in breeding value prediction.

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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
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Area of Science:

  • Animal Genetics and Genomics
  • Quantitative Genetics
  • Livestock Production

Background:

  • Accurate estimation of breeding values for feed efficiency traits is crucial for sustainable cattle production.
  • Genomic selection offers a powerful tool to improve traits like average daily feed intake (AFI), residual feed intake (RFI), and average daily gain (ADG).
  • Understanding the genetic architecture underlying feed efficiency can accelerate genetic gain in beef cattle.

Purpose of the Study:

  • To identify single nucleotide polymorphisms (SNPs) associated with estimated breeding values (EBVs) for AFI, RFI, and ADG in Angus steers.
  • To determine the proportion of additive genetic variation explained by significant SNPs for feed efficiency traits.
  • To explore the potential biological functions of genes located in genomic regions associated with these traits.

Main Methods:

  • A mixed linear model incorporating genomic relationships was used for 698 Angus steers genotyped with the Illumina BovineSNP50 assay.
  • Genome-wide association analyses were performed for EBVs of AFI, RFI, and ADG, with significance thresholds established by permutation analysis.
  • A forward selection algorithm identified significant SNPs and their associated genomic regions, followed by pathway analysis.

Main Results:

  • A total of 53, 66, and 68 SNPs explained significant portions of the additive genetic variation for AFI (54.12%), RFI (62.69%), and ADG (55.13%), respectively.
  • Pathway analysis indicated that many associated SNPs are located in genomic regions containing genes with metabolic functions.
  • Genetic correlations between traits were observed, with some SNPs selected for AFI and RFI also being significant for ADG.

Conclusions:

  • This study successfully identified panels of SNPs significantly associated with feed efficiency traits in the studied Angus steer population.
  • The identified SNPs and associated genes provide valuable targets for improving feed efficiency through genomic selection.
  • Further validation of these SNPs in independent populations is recommended for potential commercial application in breeding programs.