Marker imputation with low-density marker panels in Dutch Holstein cattle
Marker imputation with low-density marker panels in Dutch Holstein cattle
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DOI：
10.3168/jds.2010-3501
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发表时间：
2010-11-01
影响因子：
3.5
通讯作者：
Druet, T.
中科院分区：
文献类型：
--
作者：
Zhang, Z.;Druet, T.
高密度牛基因分型阵列的出现使奶牛基因组选择的实现成为可能。低密度单核苷酸多态(SNP)板的开发将允许将基因组选择扩展到更大比例的人群。非基因分型标记的预测，称为归因；是一种允许对所有性状(以及不同品种)使用相同的低密度芯片的策略。在本研究中，我们评估了低密度基因分型阵列在荷兰荷斯坦人群中应用的准确性。测试了五种不同大小的基因分型阵列，从384到6,000个SNP。根据标记密度，依赖于连锁不平衡和连锁的DAG阶段程序获得的等位基因归属错误率在11.7%~2.0%之间，而依赖于连锁和所有基因祖先集合的程序CHROMIBD得到的等位基因归属错误率在10.7%~3.3%之间。然而，低密度和高密度的基因分型动物之间的关系影响了归因效率。双亲都有基因分型的动物的归罪错误率特别低：
The availability of high-density bovine genotyping arrays made implementation of genomic selection possible in dairy cattle. Development of low-density single nucleotide polymorphism (SNP) panels will allow the extension of genomic selection to a larger portion of the population. Prediction of ungenotyped markers, called imputation; is a strategy that allows using the same low-density chips for all traits (and for different breeds). In the present study, we evaluated the accuracy of imputation with low-density genotyping arrays in the Dutch Holstein population. Five different sizes of genotyping arrays were tested, from 384 to 6,000 SNP. According to marker density, the overall allelic imputation error rate obtained with the program DAG-PHASE, which relies on linkage disequilibrium and linkage, ranged from 11 7 to 2.0%, and that obtained with the program CHROMIBD, which relies on linkage and the set of all genotyped ancestors, ranged from 10.7 to 3.3%. However, imputation efficiency was influenced by the relationship between low-density and high-density genotyped animals. Animals with both parents genotyped had particularly low imputation error rates: