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Infinium Assay for Large-scale SNP Genotyping Applications
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Published on: November 19, 2013

Genomic imputation and evaluation using high-density Holstein genotypes.

P M VanRaden1, D J Null, M Sargolzaei

  • 1Animal Improvement Programs Laboratory, Agricultural Research Service, US Department of Agriculture (USDA), Beltsville, MD 20705-2350, USA. paul.vanraden@ars.usda.gov

Journal of Dairy Science
|October 16, 2012
PubMed
Summary
This summary is machine-generated.

Genomic evaluations using high-density (HD) markers in Holstein cattle showed a slight increase in reliability compared to 50K markers. Imputation accuracy improved with denser marker sets, but gains were modest, highlighting the importance of imputation strategies.

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Area of Science:

  • Animal Genetics
  • Bioinformatics
  • Quantitative Genetics

Background:

  • Genomic evaluations are crucial for dairy cattle breeding.
  • High-density (HD) genotyping offers potential for improved accuracy.
  • Imputation methods are essential for utilizing diverse marker densities.

Purpose of the Study:

  • To evaluate the accuracy of genomic evaluations using different marker densities in Holstein cattle.
  • To assess the impact of imputation methods on genotype accuracy.
  • To compare genomic evaluations with traditional parent averages.

Main Methods:

  • Genomic evaluations computed for 161,341 Holsteins using up to 311,725 markers from the Illumina BovineHD Genotyping BeadChip.
  • Genotypes from various densities (HD, 50K, 8K, 6K, 3K, 0K) were utilized and imputed using findhap and FImpute programs.
  • Imputation accuracy was tested on simulated data, and genomic reliability was compared against traditional parent averages using deregressed evaluations.

Main Results:

  • Imputation accuracy was high, with findhap and FImpute achieving >90% correct genotypes across marker densities.
  • Genomic reliability averaged 61.1% with 311,725 markers and 60.7% with 45,187 markers, compared to 29.6% from parent average.
  • A modest 0.4 percentage point average increase in reliability was observed with HD markers compared to 50K markers.

Conclusions:

  • High-density genotyping provides a slight but consistent improvement in genomic evaluation reliability for Holsteins.
  • Imputation strategies significantly impact genotype accuracy, with multi-step imputation showing benefits for lower-density chips.
  • Further increases in HD genotypes beyond 1,074 did not substantially enhance Holstein genomic evaluation reliability in this study.