The effect of using genealogy-based haplotypes for genomic prediction.
The effect of using genealogy-based haplotypes for genomic prediction.
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DOI：
10.1186/1297-9686-45-5
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发表时间：
2013-03-06
期刊：
影响因子：
--
通讯作者：
Guldbrandtsen B
中科院分区：
文献类型：
--
作者：
Edriss V;Fernando RL;Su G;Lund MS;Guldbrandtsen B
基因组预测使用两个信息源：标记和数量性状基因座之间的连锁不平衡，以及个体之间的加性遗传关系。提高基因组预测准确性的一种方法是通过单倍型回归而不是单个标记回归来捕获更多连锁不平衡。本研究的目的是调查使用基于当地谱系信息的单倍型进行基因组预测的准确性。使用 50K SNP 芯片对总共 4429 头丹麦荷斯坦公牛进行了基因分型。单倍型是使用当地的家谱树构建的。使用两种类型的预测模型来估计单倍型协变量的影响：（1）假设所有单倍型协变量的影响具有相同的分布，即GBLUP方法；（2）假设大部分（π）单倍型协变量的影响为零，即贝叶斯混合方法。与拟合个体标记相比，基于本地谱系树拟合单倍型时估计的协变量效应大约高 7.5 倍。基于谱系的单倍型聚类略微提高了基因组预测的准确性，并且在某些情况下降低了预测的偏差。与拟合标记相比，使用贝叶斯方法拟合单倍型时，预测的准确性对参数 π 不太敏感。使用基于谱系的单倍型可以稍微提高基因组预测的准确性。对根据当地谱系构建的单倍型进行聚类的改进方法可能会带来额外的准确性提升。
Genomic prediction uses two sources of information: linkage disequilibrium between markers and quantitative trait loci, and additive genetic relationships between individuals. One way to increase the accuracy of genomic prediction is to capture more linkage disequilibrium by regression on haplotypes instead of regression on individual markers. The aim of this study was to investigate the accuracy of genomic prediction using haplotypes based on local genealogy information. A total of 4429 Danish Holstein bulls were genotyped with the 50K SNP chip. Haplotypes were constructed using local genealogical trees. Effects of haplotype covariates were estimated with two types of prediction models: (1) assuming that effects had the same distribution for all haplotype covariates, i.e. the GBLUP method and (2) assuming that a large proportion (π) of the haplotype covariates had zero effect, i.e. a Bayesian mixture method. About 7.5 times more covariate effects were estimated when fitting haplotypes based on local genealogical trees compared to fitting individuals markers. Genealogy-based haplotype clustering slightly increased the accuracy of genomic prediction and, in some cases, decreased the bias of prediction. With the Bayesian method, accuracy of prediction was less sensitive to parameter π when fitting haplotypes compared to fitting markers. Use of haplotypes based on genealogy can slightly increase the accuracy of genomic prediction. Improved methods to cluster the haplotypes constructed from local genealogy could lead to additional gains in accuracy.
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影响因子：
3.3
作者：
Habier, D.;Fernando, R. L.;Dekkers, J. C. M.
通讯作者：
Dekkers, J. C. M.
DOI：
10.1186/1297-9686-42-5
发表时间：
2010-02-19
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Habier D;Tetens J;Seefried FR;Lichtner P;Thaller G
通讯作者：
Thaller G
DOI：
10.1016/0301-6226(85)90024-7
发表时间：
1985-12-01
期刊：
LIVESTOCK PRODUCTION SCIENCE
影响因子：
--
作者：
GODDARD, M
通讯作者：
GODDARD, M
影响因子：
3.3
作者：
Daetwyler, H. D.;Kemper, K. E.;Hayes, B. J.
通讯作者：
Hayes, B. J.
影响因子：
3.3
作者：
Calus, M P L;Meuwissen, T H E;Veerkamp, R F
通讯作者：
Veerkamp, R F