Summary and Implications
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.
Iowa State University
Weng, Ziqing; Garrick, Dorian J.; Saatchi, Mahdi; Schnabel, Robert; and Taylor, Jeremy
"Impact of Pedigree Information and Genome Assembly Errors on Inference of SNP Haplotypes in Cattle,"
Animal Industry Report:
AS 659, ASL R2770.
Available at: https://lib.dr.iastate.edu/ans_air/vol659/iss1/21