The Impact of Genetic Relationship and Linkage Disequilibrium on Genomic Selection.
The Impact of Genetic Relationship and Linkage Disequilibrium on Genomic Selection.
复制标题
遗传关系和连锁不平衡对基因组选择的影响
DOI：
10.1371/journal.pone.0132379
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Pan G
中科院分区：
文献类型：
--
作者：
Liu H;Zhou H;Wu Y;Li X;Zhao J;Zuo T;Zhang X;Zhang Y;Liu S;Shen Y;Lin H;Zhang Z;Huang K;Lübberstedt T;Pan G
基因组选择在育种中的实际应用使其成为一个很有前途的研究领域。本研究考察了实现的亲缘关系和连锁不平衡（LD）对标记密度和所需训练群体大小的影响，并进一步讨论了它们对实际应用的影响。本研究基于来自同一始祖系（B73, Mo17）的两个种群的实验数据。用不同的标记组和不同的密度对两个群体进行基因分型：IBM Syn4和IBM Syn10。在低标记密度的Syn4群体中植入Syn10的高密度标记。采用随机回归最佳线性无偏预测（RR-BLUP）模型进行7种不同的预测情景。结果表明，训练种群和验证种群之间的真实遗传关系越密切，所需的标记数量越少，预测精度越高。考虑到短期成本，关系信息比LD信息更有价值。同时，结果表明，基于高LD的QTL与标记之间的准确率在代间更稳定，因此LD信息在实际应用中具有更强的预测能力。
Genomic selection is a promising research area due to its practical application in breeding. In this study, impact of realized genetic relationship and linkage disequilibrium (LD) on marker density and training population size required was investigated and their impact on practical application was further discussed. This study is based on experimental data of two populations derived from the same two founder lines (B73, Mo17). Two populations were genotyped with different marker sets at different density: IBM Syn4 and IBM Syn10. A high-density marker set in Syn10 was imputed into the Syn4 population with low marker density. Seven different prediction scenarios were carried out with a random regression best linear unbiased prediction (RR-BLUP) model. The result showed that the closer the real genetic relationship between training and validation population, the fewer markers were required to reach a good prediction accuracy. Taken the short-term cost for consideration, relationship information is more valuable than LD information. Meanwhile, the result indicated that accuracies based on high LD between QTL and markers were more stable over generations, thus LD information would provide more robust prediction capacity in practical applications.
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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.
影响因子：
5.4
作者：
HILL W G;ROBERTSON A
通讯作者：
ROBERTSON A
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：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.
影响因子：
4.2
作者：
Combs, Emily;Bernardo, Rex
通讯作者：
Bernardo, Rex