Differing genetic trend estimates from traditional and genomic evaluations of genotyped animals as evidence of preselection bias in US Holsteins

in BLUP) with the QP transformation. For ssGBLUP, 18,359 genotyped animals were randomly chosen as core animals to calculate the inverse of the genomic relationship matrix with the APY algorithm. Computations took 6.5 h and 1.4 GB of memory for BLUP, and 13 h and 115 GB of memory for ssGBLUP. For genotyped sires with at least 10 daughters, the average genetic levels for predicted transmitting ability (PTA) and genomic PTA were similar up to 2008, with a higher level for ssGBLUP later (approximately by 36 kg for milk, 2.1 kg for fat, and 1.1 kg for protein for bulls born in 2010). For genotyped cows, the average genetic levels were similar up to 2006, with a higher level for ssGBLUP (approximately by 91 kg for milk, 3.6 kg for fat, and 2.7 kg for protein for cows born in 2012). For all cows, the average levels were slightly higher for ssGBLUP, with much smaller differences than for genotyped cows. Trends for BLUP indicate bias due to genomic preselection for genotyped sires and cows. For official evaluations released in December 2016, traditional PTA had the same trend as multiple-step genomic PTA for both genotyped bulls and cows except for the youngest bulls, who had traditional PTA slightly lower than genomic PTA. For genotyped bulls born in recent years, genetic gain for official traditional and genomic evaluations was similar in contrast to ssGBLUP and BLUP differences. Official PTA for cows were adjusted so that the Mendelian sampling variance was comparable with that for bulls, and those adjustments likely removed bias due to genomic preselection from traditional PTA, especially for genotyped cows. The ssGBLUP method seems to account partially for that bias and is computationally suitable for national evaluations.