Power of mixed-model QTL mapping from phenotypic, pedigree and marker data in self-pollinated crops
Power of mixed-model QTL mapping from phenotypic, pedigree and marker data in self-pollinated crops
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DOI：
10.1007/s00122-005-0189-7
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发表时间：
2006-03-01
影响因子：
5.4
通讯作者：
Bernardo, R
中科院分区：
文献类型：
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作者：
Arbelbide, M;Yu, J;Bernardo, R
通过混合模型方法进行QTL定位的能力已经在杂交作物中进行了研究，但在自花授粉作物中仍然未知。我们的目的是评估混合模型QTL定位在自花授粉作物育种计划中的有用性。具体而言，我们模拟了大豆（Glycine max L.）梅尔）育种计划，并应用混合模型的方法，包括三个步骤：方差分量估计，单标记分析，和多标记分析。根据显著性水平（0.01或0.0001）、QTL数量（20或80）、性状遗传力（0.40或0.70）、群体大小（600或1，200个自交系）和标记数量（300或600），检测QTL的平均功效范围为< 1至47%。相应的错误发现率范围从2%到43%。更大的群体，更高的遗传力，和更少的QTL控制的性状，导致功率大幅增加，减少错误的发现率和偏见。严格的显著性水平降低了功率和错误发现率。主效QTL的检测能力大于次效QTL。杂交作物比自花授粉作物的功效更高，错误发现率更低。因此，混合模式QTL定位在自花授粉作物的基因发现中具有重要的应用价值。
The power of QTL mapping by a mixed-model approach has been studied for hybrid crops but remains unknown in self-pollinated crops. Our objective was to evaluate the usefulness of mixed-model QTL mapping in the context of a breeding program for a self-pollinated crop. Specifically, we simulated a soybean (Glycine max L. Merr.) breeding program and applied a mixed-model approach that comprised three steps: variance component estimation, single-marker analyses, and multiple-marker analysis. Average power to detect QTL ranged from < 1 to 47% depending on the significance level (0.01 or 0.0001), number of QTL (20 or 80), heritability of the trait (0.40 or 0.70), population size (600 or 1,200 inbreds), and number of markers (300 or 600). The corresponding false discovery rate ranged from 2 to 43%. Larger populations, higher heritability, and fewer QTL controlling the trait led to a substantial increase in power and to a reduction in the false discovery rate and bias. A stringent significance level reduced both the power and false discovery rate. There was greater power to detect major QTL than minor QTL. Power was higher and the false discovery rate was lower in hybrid crops than in self-pollinated crops. We conclude that mixed-model QTL mapping is useful for gene discovery in plant breeding programs of self-pollinated crops.