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Impact of Pedigree Information and Genome Assembly Errors on Inference of SNP Haplotypes in Cattle

Authors
  • Ziqing Weng (Iowa State University)
  • Dorian J. Garrick (Iowa State University)
  • Mahdi Saatchi (Iowa State University)
  • Robert Schnabel (University of Missouri–Columbia)
  • Jeremy Taylor (University of Missouri–Columbia)

Abstract

The impact of pedigree information and SNP location determined from either the UMD3.1 genome sequence assembly or the USDA-AIPL map on phasing accuracy were evaluated for 2 chromosomes in 2,778 parent verified Angus sire/offspring pairs. DAGPHASE (Druet and Georges, 2010), using a single generation pedigree was superior to BEAGLE software (Browning and Browning, 2007) for phasing. Results based on USDA-AIPL map are closer to expectation than those based on UMD3.1, but the difference is not significant. Recombination hotspots weredetected near 4 and 82Mb on BTA14, and near 25Mb on BTA15.

Keywords: ASL R2770

How to Cite:

Weng, Z., Garrick, D. J., Saatchi, M., Schnabel, R. & Taylor, J., (2013) “Impact of Pedigree Information and Genome Assembly Errors on Inference of SNP Haplotypes in Cattle”, Iowa State University Animal Industry Report 10(1). doi: https://doi.org/10.31274/ans_air-180814-632

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Published on
01 Jan 2013
Peer Reviewed
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