The objective of this study was to compare genetic trends from single-step genomic BLUP (ssGBLUP) and traditional BLUP models for milk production traits of US Holsteins. Phenotypes were 305-d milk, fat, and protein yields from 21,527,040 cows recorded between January 1990 and August 2015. The pedigree file included 29,651,623 animals and was limited to 3 generations back from recorded or genotyped animals. Genotypes for 764,029 animals were used, and analyses were by a 3-trait repeatability model as used in the US official genetic evaluation. Unknown-parent groups were incorporated into the inverse of a relationship matrix (H⁻¹ in ssGBLUP and A⁻¹ 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.

这项研究的目的是比较单步基因组BLUP（ssGBLUP）和传统BLUP模型对美国荷斯坦奶类生产性状的遗传趋势。表型是1990年1月至2015年8月记录的21,527,040头母牛的305天牛奶，脂肪和蛋白质的产量。谱系文件包括29,651,623只动物，并且仅限于从记录或基因分型的动物回来的3代。使用了764,029只动物的基因型，并通过美国官方遗传评估中使用的3性状可重复性模型进行了分析。将未知父母组合并到关系矩阵的逆矩阵中（ssGBLUP中的H ^-1和A ^-1在BLUP中）进行QP转换。对于ssGBLUP，随机选择18359个基因型动物作为核心动物，用APY算法计算基因组关系矩阵的逆。BLUP的计算需要6.5小时和1.4 GB的内存，而ssGBLUP则需要13小时和115 GB的内存。对于拥有至少10个子代的基因型父亲，预测的传播能力（PTA）和基因组PTA的平均遗传水平在2008年之前是相似的，随后ssGBLUP的平均遗传水平更高（牛奶约36千克，脂肪约2.1千克， 1.1公斤蛋白质用于2010年出生的公牛）。对于基因型奶牛，直到2006年的平均遗传水平相似，ssGBLUP的水平更高（2012年出生的奶牛的ssGBLUP水平更高，牛奶约为91公斤，脂肪约为3.6公斤，蛋白质约为2.7公斤）。对于所有奶牛，ssGBLUP的平均水平略高，与基因型奶牛相比，差异要小得多。BLUP的趋势表明由于基因型公牛和母牛的基因组预选而造成的偏倚。在2016年12月发布的官方评估中，除了基因组PTA略低于基因组PTA的最年轻的公牛外，基因型公牛和母牛的传统PTA都具有与多步基因组PTA相同的趋势。对于近年来出生的基因型公牛，官方传统和基因组评估的遗传增益与ssGBLUP和BLUP差异相似。对母牛的官方PTA进行了调整，以使孟德尔抽样方差与公牛相似，并且这些调整可能消除了传统PTA中基因组预选所致的偏见，尤其是对于基因型母牛。