Aarhus University, Faculty of Science and Technology, Department of Genetics and Biotechnology, Tjele, Denmark.
J Dairy Sci. 2011 Sep;94(9):4700-7. doi: 10.3168/jds.2010-3765.
This study investigated the possibility of increasing the reliability of direct genomic values (DGV) by combining reference populations. The data were from 3,735 bulls from Danish, Swedish, and Finnish Red dairy cattle populations. Single nucleotide polymorphism markers were fitted as random variables in a Bayesian model, using published estimated breeding values as response variables. In total, 17 index traits were analyzed. Reliabilities were estimated using a 5-fold cross validation, and calculated as the within-year squared correlation between estimated breeding values and DGV. Marker effects were estimated using reference populations from individual countries, as well as using a combined reference population from all 3 countries. Single-country reference populations gave mean reliabilities across 17 traits of 0.19 to 0.23, whereas the combined reference gave mean reliabilities of 0.26 for all populations. Using marker effects from 1 population to predict the other 2 gave a loss in mean reliability of 0.14 to 0.21 when predicting Swedish or Finnish animals with Danish marker effects, or vice versa. Using Swedish or Finnish marker effects to predict each other only showed a loss in mean reliability of 0.03 to 0.05. A combined Swedish-Finnish reference population led to an average reliability as high as that from the 3-country reference population, but somewhat different for individual traits. The results from this study show that it is possible to increase the reliability of DGV by combining reference populations from related populations.
本研究探讨了通过组合参考群体来提高直接基因组值（DGV）可靠性的可能性。数据来自丹麦、瑞典和芬兰红牛奶牛群体的 3735 头公牛。单核苷酸多态性标记被拟合为贝叶斯模型中的随机变量，使用已发表的估计育种值作为响应变量。总共分析了 17 个指数性状。可靠性使用 5 倍交叉验证进行估计，并计算为估计育种值和 DGV 之间的年内平方相关。使用来自各个国家的参考群体以及来自所有 3 个国家的组合参考群体来估计标记效应。单一国家的参考群体在 17 个特征上的平均可靠性为 0.19 到 0.23，而组合参考群体在所有群体上的平均可靠性为 0.26。使用 1 个群体的标记效应来预测其他 2 个群体，当使用丹麦标记效应预测瑞典或芬兰动物时，平均可靠性损失为 0.14 到 0.21，反之亦然。使用瑞典或芬兰的标记效应来预测彼此，平均可靠性仅损失 0.03 到 0.05。一个组合的瑞典-芬兰参考群体导致的平均可靠性与来自 3 个国家的参考群体一样高，但对于个别特征略有不同。本研究的结果表明，通过组合来自相关群体的参考群体，可以提高 DGV 的可靠性。
