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A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle.

Troy N Rowan1, Jesse L Hoff1, Tamar E Crum1

  • 1Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.

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|December 28, 2019
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Summary
This summary is machine-generated.

A large, multi-breed reference panel significantly improves cattle genotype imputation accuracy, especially for rare variants. Using 50K SNP assays offers a cost-effective balance for imputing to 850K SNP sets.

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Area of Science:

  • Genomics
  • Animal Breeding
  • Bioinformatics

Background:

  • Medium- to low-density SNP genotyping in cattle yields valuable data but has limitations in detecting rare and causal variants.
  • High-density assays (Illumina BovineHD and GGP-F250) provide comprehensive genomic information, including rare variants.

Purpose of the Study:

  • To maximize genotype imputation accuracy from medium- and low-density assays to an 850K SNP marker set.
  • To evaluate the utility of combining two high-density assays for imputation and downstream analysis.

Main Methods:

  • Constructed a large, multi-breed imputation reference panel with 36,131 samples genotyped on BovineHD and/or GGP-F250 assays.
  • Assessed imputation accuracy using varying reference panel compositions and SNP densities.
  • Investigated the impact of rare variants from the GGP-F250 assay on imputation accuracy.

Main Results:

  • A large multi-breed reference panel significantly increased imputation accuracy compared to within-breed panels, particularly for low-frequency variants.
  • Imputation accuracy was highest with genetically similar animals and complete 850K genotypes in the reference panel.
  • Incorporating rare variants from the GGP-F250 assay improved imputation accuracy for rare variants present on the BovineHD assay.
  • A 50K SNP assay density demonstrated a balance between cost and accuracy for imputation to 850K.

Conclusions:

  • High-density genotypes within a multi-breed reference panel maximize imputation accuracy across cattle populations.
  • High imputation accuracy was achieved even for admixed animals or breeds with limited representation.
  • The inclusion of rare variants from the GGP-F250 assay is expected to enhance sequence-level imputation accuracy.