Weller J I, Stoop W M, Eding H, Schrooten C, Ezra E
Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel.
CRV BV, 6800 AL Arnhem, the Netherlands.
J Dairy Sci. 2015 Jul;98(7):4945-55. doi: 10.3168/jds.2014-9086. Epub 2015 Apr 29.
The objectives were to investigate the accuracy of genomic evaluations obtained for a small dairy cattle population (Israeli Holsteins) via joint evaluation with a larger population (Dutch Holsteins), and to evaluate the use of pedigree data from foreign bulls computed by Interbull without daughter records in Israel. The training population included 4,010 Dutch bulls and 713 Israeli bulls. The validation population included 185 Israeli bulls with daughter records for milk production traits and slightly fewer bulls for the nonproduction traits. Milk, fat, and protein yields, somatic cell score, longevity, female fertility, direct and maternal calving ease, direct and maternal stillbirth, and the Israeli breeding index were analyzed. The genomic prediction model was based on the Bayesian multi-QTL model of Meuwissen and Goddard, where the effects of dense single nucleotide polymorphisms across the whole genome are fitted directly, without the use of haplotypes or identical-by-descent probabilities. Correlations of May 2014 estimated breeding values (EBV14) with genomic EBV (GEBV) were higher than the correlations of EBV14 with parent averages (PA) computed from the June 2009 evaluation for all traits. For the Israel selection index, the difference between EBV14 and GEBV correlation on the one hand and EBV14 and PA computed using Interbull data on the other hand was 15 percentage points. For protein, the difference between the corresponding correlations was 14 percentage points. Generally, correlations of EBV14 with PA based on Israeli EBV only were similar to correlations of EBV14 with PA including Interbull evaluations. Relative to EBV14, milk production traits were biased upwards for both GEBV and PA, but the bias was greater for PA. The Y-intercepts of regressions of EBV14 were significantly different from zero for regression on GEBV for all 3 milk production traits and the Israeli selection index. This was not the case for regression of EBV14 on PA. The regression line intersected with the line of unbiased estimation near the EBV of the bulls with highest values. Because only bulls with high evaluations are of interest for selection, GEBV for these bulls were less biased compared with that of bulls with lower evaluations. The difference in mean EBV14 between bulls born during 2007-2008 selected by GEBV and PA was 65 units. If half of all inseminations are by young bulls, then the annual genetic gain obtained by implementation of genomic evaluation will be 8 units per year (65/8). Because annual gain is currently 107 units, this is a gain of 7%.
目标是通过与更大的群体（荷兰荷斯坦奶牛）联合评估，研究针对小型奶牛群体（以色列荷斯坦奶牛）获得的基因组评估的准确性，并评估国际公牛组织（Interbull）计算的、在以色列没有女儿记录的国外公牛系谱数据的使用情况。训练群体包括4010头荷兰公牛和713头以色列公牛。验证群体包括185头有牛奶生产性状女儿记录的以色列公牛，以及非生产性状的公牛数量略少。分析了牛奶、脂肪和蛋白质产量、体细胞评分、长寿、雌性生育力、直接和母系产犊难易度、直接和母系死产以及以色列育种指数。基因组预测模型基于Meuwissen和Goddard的贝叶斯多QTL模型，其中直接拟合整个基因组中密集单核苷酸多态性的效应，不使用单倍型或同源概率。2014年5月估计育种值（EBV14）与基因组估计育种值（GEBV）的相关性高于EBV14与2009年6月评估计算的亲本平均值（PA）的相关性。对于以色列选择指数，一方面EBV14与GEBV的相关性和另一方面EBV14与使用国际公牛组织数据计算的PA的相关性之间的差异为15个百分点。对于蛋白质，相应相关性之间的差异为14个百分点。一般来说，仅基于以色列EBV的EBV14与PA的相关性与包括国际公牛组织评估的EBV14与PA的相关性相似。相对于EBV14，牛奶生产性状的GEBV和PA都向上偏倚，但PA的偏倚更大。对于所有3个牛奶生产性状和以色列选择指数，EBV14对GEBV回归的Y轴截距显著不同于零。EBV14对PA回归则不是这种情况。回归线在最高值公牛的EBV附近与无偏估计线相交。因为只有高评估值的公牛才对选择有意义，所以这些公牛的GEBV与较低评估值公牛的GEBV相比偏倚较小。GEBV和PA选择的2007 - 2008年出生的公牛之间的平均EBV14差异为65个单位。如果所有授精中有一半是由年轻公牛进行的，那么实施基因组评估每年获得的遗传进展将是每年8个单位（65/8）。因为目前每年的进展是107个单位，这是7%的增益。
