Short communication: Genomic evaluations of final score for US Holsteins benefit from the inclusion of genotypes on cows

Currently, the US Department of Agriculture Animal Improvement Programs Laboratory utilizes a multi-step procedure in genomic evaluations for US Holstein bulls and cows, with adjustments for cows. We used a single-step procedure to investigate whether adding cows' genotypes could increase reliability in genomic breeding values for bulls while minimizing bias. The first data set to 2007 was used to calculate genomic estimated breeding values (GEBV) for animals, including young genotyped bulls with no daughters and young cows (heifers) with no records in 2007. The second data set to 2011 was used to calculate GEBV for the same animals, including those young bulls with daughters and young cows with records in 2011. Genotypes (42,503 single nucleotide polymorphism markers) for 34,506 bulls and 5,235 cows from 356,413 bulls and 9,245,619 cows in pedigree were used to calculate single-step GEBV (ssGEBV) and multi-step GEBV (msGEBV). Regression coefficients of 2007 GEBV on 2011 progeny deviations and coefficients of determination were used as indicators of bias and reliability in 2007 GEBV for bulls with no daughters and for cows with no records in 2007, using bull genotypes only and using bull and cow genotypes. Parent averages were also calculated from estimated breeding values of parents to compare with GEBV. For genotyped bulls, inflation was larger for ssGEBV than for msGEBV, whereas reliability was higher for ssGEBV. Using all genotyped bulls and cows, reliabilities were increased by 2 to 3%. Use of genotypes of high-profile cows improves reliability in ssGEBV and msGEBV for bulls.