Department of Molecular Biology and Genetics, Aarhus University, Tjele DK-8830, Denmark.
Genet Sel Evol. 2013 Mar 21;45(1):7. doi: 10.1186/1297-9686-45-7.
In China, the reference population of genotyped Holstein cattle is relatively small with to date, 80 bulls and 2091 cows genotyped with the Illumina 54 K chip. Including genotyped Holstein cattle from other countries in the reference population could improve the accuracy of genomic prediction of the Chinese Holstein population. This study investigated the consistency of linkage disequilibrium between adjacent markers between the Chinese and Nordic Holstein populations, and compared the reliability of genomic predictions based on the Chinese reference population only or the combined Chinese and Nordic reference populations.
Genomic estimated breeding values of Chinese Holstein cattle were predicted using a single-trait GBLUP model based on the Chinese reference dataset, and using a two-trait GBLUP model based on a joint reference dataset that included both the Chinese and Nordic Holstein data.
The extent of linkage disequilibrium was similar in the Chinese and Nordic Holstein populations and the consistency of linkage disequilibrium between the two populations was very high, with a correlation of 0.97. Genomic prediction using the joint versus the Chinese reference dataset increased reliabilities of genomic predictions of Chinese Holstein bulls in the test data from 0.22, 0.15 and 0.11 to 0.51, 0.47 and 0.36 for milk yield, fat yield and protein yield, respectively. Using five-fold cross-validation, reliabilities of genomic predictions of Chinese cows increased from 0.15, 0.12 and 0.15 to 0.26, 0.17 and 0.20 for milk yield, fat yield and protein yield, respectively.
The linkage disequilibrium between the two populations was very consistent and using the combined Nordic and Chinese reference dataset substantially increased reliabilities of genomic predictions for Chinese Holstein cattle.
在中国，已分型荷斯坦牛的参考群体相对较小，目前已有 80 头公牛和 2091 头母牛使用 Illumina 54K 芯片进行了分型。将其他国家的已分型荷斯坦牛纳入参考群体可以提高中国荷斯坦牛群体基因组预测的准确性。本研究调查了中荷和北欧荷斯坦牛群体间相邻标记间连锁不平衡的一致性，并比较了仅基于中国参考群体或中荷北欧联合参考群体进行基因组预测的可靠性。
使用基于中国参考数据集的单性状 GBLUP 模型预测中国荷斯坦牛的基因组估计育种值，并使用包含中荷北欧数据的联合参考数据集的两性状 GBLUP 模型进行预测。
中国荷斯坦牛和北欧荷斯坦牛群体间的连锁不平衡程度相似，且两群体间连锁不平衡的一致性非常高，相关系数为 0.97。与仅使用中国参考数据集相比，使用联合参考数据集进行基因组预测可分别将中国荷斯坦公牛在测试数据中的基因组预测可靠性提高 0.22、0.15 和 0.11 个百分点，达到 0.51、0.47 和 0.36 个百分点，用于牛奶产量、脂肪产量和蛋白质产量。使用五重交叉验证，中国荷斯坦母牛的基因组预测可靠性从 0.15、0.12 和 0.15 个百分点分别提高到 0.26、0.17 和 0.20 个百分点，用于牛奶产量、脂肪产量和蛋白质产量。
两个群体间的连锁不平衡非常一致，使用中荷北欧联合参考数据集可显著提高中国荷斯坦牛基因组预测的可靠性。
