The importance of information on relatives for the prediction of genomic breeding values and the implications for the makeup of reference data sets in livestock breeding schemes.
The importance of information on relatives for the prediction of genomic breeding values and the implications for the makeup of reference data sets in livestock breeding schemes.
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DOI：
10.1186/1297-9686-44-4
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发表时间：
2012-02-09
期刊：
影响因子：
--
通讯作者：
van der Werf JH
中科院分区：
文献类型：
--
作者：
Clark SA;Hickey JM;Daetwyler HD;van der Werf JH
基因组选择理论的基础是预测遗传标记在数量性状位点连锁不平衡中的作用。然而，基因组选择也依赖于个体之间的关系来准确预测遗传价值。本研究旨在检验亲属信息与非亲属或远亲个体信息在基因组育种价值估计中的重要性。模拟和真实数据被用来检验不同程度的关系对基因组选择准确性的影响。将基因组最佳线性无偏预测（gBLUP）方法与两种基于谱系的BLUP方法进行了比较，一种是浅一代谱系法，另一种是深十代谱系法。研究了与1750只动物的参考数据集有不同程度关系的不同选择候选者组的估计育种值的准确性。gBLUP方法预测育种值比BLUP方法更准确。使用gBLUP对近亲动物估计出最准确的育种值。同样，基于系谱的BLUP方法对近亲动物的预测也是准确的，但是当基于系谱的BLUP方法用于预测非亲缘动物时，准确率接近于零。相比之下，对于与参考数据集中的动物没有系谱关系的动物，gBLUP育种值具有很高的准确性。动物与参考数据集的关系是基因组预测准确性的重要因素。与参考数据集有密切关系的动物在基因组预测中具有最高的准确性。然而，由参考数据集大小和总体种群有效种群大小驱动的基线准确性使gBLUP能够利用以前被基于系谱的BLUP方法所忽略的信息来估计种群（品种）中不相关动物的育种值。
The theory of genomic selection is based on the prediction of the effects of genetic markers in linkage disequilibrium with quantitative trait loci. However, genomic selection also relies on relationships between individuals to accurately predict genetic value. This study aimed to examine the importance of information on relatives versus that of unrelated or more distantly related individuals on the estimation of genomic breeding values. Simulated and real data were used to examine the effects of various degrees of relationship on the accuracy of genomic selection. Genomic Best Linear Unbiased Prediction (gBLUP) was compared to two pedigree based BLUP methods, one with a shallow one generation pedigree and the other with a deep ten generation pedigree. The accuracy of estimated breeding values for different groups of selection candidates that had varying degrees of relationships to a reference data set of 1750 animals was investigated. The gBLUP method predicted breeding values more accurately than BLUP. The most accurate breeding values were estimated using gBLUP for closely related animals. Similarly, the pedigree based BLUP methods were also accurate for closely related animals, however when the pedigree based BLUP methods were used to predict unrelated animals, the accuracy was close to zero. In contrast, gBLUP breeding values, for animals that had no pedigree relationship with animals in the reference data set, allowed substantial accuracy. An animal's relationship to the reference data set is an important factor for the accuracy of genomic predictions. Animals that share a close relationship to the reference data set had the highest accuracy from genomic predictions. However a baseline accuracy that is driven by the reference data set size and the overall population effective population size enables gBLUP to estimate a breeding value for unrelated animals within a population (breed), using information previously ignored by pedigree based BLUP methods.
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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
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.
影响因子：
1.5
作者：
Goddard, Mike
通讯作者：
Goddard, Mike
影响因子：
1.5
作者：
Hayes, B. J.;Visscher, P. M.;Goddard, M. E.
通讯作者：
Goddard, M. E.
影响因子：
3.3
作者：
Daetwyler, Hans D.;Pong-Wong, Ricardo;Woolliams, John A.
通讯作者：
Woolliams, John A.