Technical note: Efficient parentage assignment and pedigree reconstruction with dense single nucleotide polymorphism data
Technical note: Efficient parentage assignment and pedigree reconstruction with dense single nucleotide polymorphism data
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DOI：
10.3168/jds.2010-3896
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发表时间：
2011-04-01
影响因子：
3.5
通讯作者：
Hayes, B. J.
中科院分区：
文献类型：
--
作者：
Hayes, B. J.
现在对大量奶牛进行常规的致密单核苷酸多态(SNP)基因分型，以预测基因组估计的育种值。这样的SNP数组包含非常好的亲子关系分配和谱系重建信息。利用这些信息进行亲子关系分配和谱系重建的主要挑战是开发出计算效率高的策略，使候选动物能够被分配给它的父亲和与大量的数据打交道。在这里，我们描述了一种利用SNP数据进行亲子关系分配的高效算法，并通过50,000-SNP和3,000-SNP面板演示了非常准确的分配。实现该算法的计算机代码在附录中给出。
Large numbers of dairy cattle are now routinely genotyped for dense single nucleotide polymorphism (SNP) arrays for the purpose of predicting genomic estimated breeding values. Such SNP arrays contain very good information for parentage assignment and pedigree reconstruction. The main challenge in using this information for parentage assignment and pedigree reconstruction is development of computationally efficient strategies that enable a candidate animal to be assigned its sire and darn with the large volume of data. Here we describe an efficient algorithm for parentage assignment with SNP data and demonstrate very accurate assignment with 50,000-SNP and 3,000-SNP panels. The computer code implementing the algorithm is given in the Appendix.