Imputation accuracy from low to medium-density SNP chips for US crossbred dairy cattle

This study aimed at evaluating the quality of imputation accuracy (IA) by marker (IAm) and individual (IAi) in US crossbred dairy cattle. Holstein × Jersey crossbreds were used to evaluate from a low (7K) medium density (50K) SNP chip. Crossbred animals, as well their sires (53), dams (77), maternal grandsires (63), all genotyped with 78K Seven different scenarios reference populations tested which some family relationships other added random unrelated purebred individuals those relationship scenarios. The same on animals compare these outcomes attained animals. genotype was performed findhap (version 4) software. There no significant differences IA results depending whether sire imputed dam Jersey, or vice versa. increased significantly addition related population, 86.70 ± 0.06% when only included population 90.09 sires, dams, genomic information combined population. In including IAm IAi superior than crossbreds, ranging 90.75 0.06 94.02 0.06%, 90.88 0.11 94.04 0.10%, respectively. Additionally, scenario called SPB+DLD that is similar evaluations tested. this scenario, 5 evaluated breeds (Ayrshire, Brown Swiss, Guernsey, Holstein, Jersey) 50K chip 7K 80.87 80.85 0.08%, Adding randomly nonrelated reduced for both cows, except SPB+DLD, where adding values. Our findings demonstrate ranged 85 90%, emphasize significance designing defining improved IA.