Beef

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